5LYB image
Deposition Date 2016-09-26
Release Date 2016-11-23
Last Version Date 2024-10-16
Entry Detail
PDB ID:
5LYB
Keywords:
RIBOSOME
Title:
Crystal structure of the S.cerevisiae 80S ribosome in complex with the A-site bound aminoacyl-tRNA analog ACCPmn
Biological Source:
Source Organism:
synthetic construct (Taxon ID: 32630)
Saccharomyces cerevisiae (Taxon ID: 4932)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.25 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1 21 1
5LYB validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:25S rRNA
Chain IDs:JA (auth: 1), KD (auth: 5)
Chain Length:3394
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:A (auth: 2), BC (auth: 6)
Chain Length:1800
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:KA (auth: 3), LD (auth: 7)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:5.8S rRNA
Chain IDs:LA (auth: 4), MD (auth: 8)
Chain Length:158
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Molecule:aminoacyl-tRNA fragment ACCPmn
Chain IDs:GF (auth: A), HF (auth: a)
Chain Length:3
Number of Molecules:2
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10-A,40S ribosomal protein S10-A,40S Ribosomal Protein S10-A
Gene (Uniprot):RPS10A
Chain IDs:L (auth: C0)
Chain Length:96
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q08745 Pfam ID:PF03501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11-A,40S ribosomal protein S11-A,40S Ribosomal Protein S11-A
Gene (Uniprot):RPS11A
Chain IDs:M (auth: C1), NC (auth: c1)
Chain Length:155
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX47 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal Protein S12
Gene (Uniprot):RPS12
Chain IDs:N (auth: C2)
Chain Length:124
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P48589 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Gene (Uniprot):RPS13
Chain IDs:O (auth: C3), PC (auth: c3)
Chain Length:150
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05756 Pfam ID:PF08069, PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal Protein S14
Gene (Uniprot):RPS14A
Chain IDs:P (auth: C4), QC (auth: c4)
Chain Length:128
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P06367 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:Q (auth: C5)
Chain Length:131
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q01855 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16-A
Gene (Uniprot):RPS16A
Chain IDs:R (auth: C6), SC (auth: c6)
Chain Length:142
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX51 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S17-A
Gene (Uniprot):RPS17A
Chain IDs:S (auth: C7), TC (auth: c7)
Chain Length:125
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02407 Pfam ID:PF00833
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18-A
Gene (Uniprot):RPS18A
Chain IDs:T (auth: C8), UC (auth: c8)
Chain Length:145
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX55 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S19-A
Gene (Uniprot):RPS19A
Chain IDs:U (auth: C9), VC (auth: c9)
Chain Length:143
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P07280 Pfam ID:PF01090
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Gene (Uniprot):RPS20
Chain IDs:V (auth: D0), WC (auth: d0)
Chain Length:110
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38701 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S21-A
Gene (Uniprot):RPS21A
Chain IDs:W (auth: D1), XC (auth: d1)
Chain Length:87
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0V8 Pfam ID:PF01249
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22-A
Gene (Uniprot):RPS22A
Chain IDs:X (auth: D2), YC (auth: d2)
Chain Length:129
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C0W1 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23-A
Gene (Uniprot):RPS23A
Chain IDs:Y (auth: D3), ZC (auth: d3)
Chain Length:144
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CY39 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S24-A
Gene (Uniprot):RPS24A
Chain IDs:Z (auth: D4), AD (auth: d4)
Chain Length:134
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX31 Pfam ID:PF01282
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S25-A
Gene (Uniprot):RPS25A
Chain IDs:AA (auth: D5), BD (auth: d5)
Chain Length:70
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E792 Pfam ID:PF03297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S26-B
Gene (Uniprot):RPS26B
Chain IDs:BA (auth: D6), CD (auth: d6)
Chain Length:97
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P39939 Pfam ID:PF01283
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S27-A
Gene (Uniprot):RPS27A
Chain IDs:CA (auth: D7), DD (auth: d7)
Chain Length:81
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P35997 Pfam ID:PF01667
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S28-A
Gene (Uniprot):RPS28A
Chain IDs:DA (auth: D8), ED (auth: d8)
Chain Length:63
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E7X9 Pfam ID:PF01200
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29-A
Gene (Uniprot):RPS29A
Chain IDs:EA (auth: D9), FD (auth: d9)
Chain Length:53
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41057 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S30-A
Gene (Uniprot):RPS30A
Chain IDs:FA (auth: E0), GD (auth: e0)
Chain Length:62
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX33 Pfam ID:PF04758
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-40S ribosomal protein S31
Gene (Uniprot):RPS31
Chain IDs:GA (auth: E1), HD (auth: e1)
Chain Length:76
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05759 Pfam ID:PF01599
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2-A
Gene (Uniprot):RPL2A
Chain IDs:MA (auth: L2), ND (auth: l2)
Chain Length:252
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:NA (auth: L3), OD (auth: l3)
Chain Length:386
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14126 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4-A
Gene (Uniprot):RPL4A
Chain IDs:OA (auth: L4), PD (auth: l4)
Chain Length:361
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:PA (auth: L5), QD (auth: l5)
Chain Length:296
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26321 Pfam ID:PF17144, PF14204
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6-A
Gene (Uniprot):RPL6A
Chain IDs:QA (auth: L6), RD (auth: l6)
Chain Length:175
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02326 Pfam ID:PF01159
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7-A
Gene (Uniprot):RPL7A
Chain IDs:RA (auth: L7), SD (auth: l7)
Chain Length:223
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A
Gene (Uniprot):RPL8A
Chain IDs:SA (auth: L8)
Chain Length:233
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P17076 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9-A
Gene (Uniprot):RPL9A
Chain IDs:TA (auth: L9), UD (auth: l9)
Chain Length:191
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05738 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Gene (Uniprot):RPL10
Chain IDs:UA (auth: M0), VD (auth: m0)
Chain Length:220
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41805 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11-B
Gene (Uniprot):RPL11B
Chain IDs:VA (auth: M1), WD (auth: m1)
Chain Length:169
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E757 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13-A
Gene (Uniprot):RPL13A
Chain IDs:WA (auth: M3), YD (auth: m3)
Chain Length:194
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12690 Pfam ID:PF01294
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14-A
Gene (Uniprot):RPL14A
Chain IDs:XA (auth: M4), ZD (auth: m4)
Chain Length:137
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36105 Pfam ID:PF00467, PF01929
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15-A
Gene (Uniprot):RPL15A
Chain IDs:YA (auth: M5), AE (auth: m5)
Chain Length:203
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05748 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16-A
Gene (Uniprot):RPL16A
Chain IDs:ZA (auth: M6), BE (auth: m6)
Chain Length:197
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26784 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17-A
Gene (Uniprot):RPL17A
Chain IDs:AB (auth: M7), CE (auth: m7)
Chain Length:183
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05740 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18-A
Gene (Uniprot):RPL18A
Chain IDs:BB (auth: M8), DE (auth: m8)
Chain Length:185
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX49 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19-A
Gene (Uniprot):RPL19A
Chain IDs:CB (auth: M9), EE (auth: m9)
Chain Length:188
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX82 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L20-A
Gene (Uniprot):RPL20A
Chain IDs:DB (auth: N0), FE (auth: n0)
Chain Length:172
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX23 Pfam ID:PF01775
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21-A
Gene (Uniprot):RPL21A
Chain IDs:EB (auth: N1), GE (auth: n1)
Chain Length:159
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02753 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L22-A
Gene (Uniprot):RPL22A
Chain IDs:FB (auth: N2), HE (auth: n2)
Chain Length:100
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05749 Pfam ID:PF01776
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23-A
Gene (Uniprot):RPL23A
Chain IDs:GB (auth: N3), IE (auth: n3)
Chain Length:136
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX41 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Gene (Uniprot):RPL24A
Chain IDs:HB (auth: N4)
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04449 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Gene (Uniprot):RPL25
Chain IDs:IB (auth: N5), KE (auth: n5)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26-A
Gene (Uniprot):RPL26A
Chain IDs:JB (auth: N6), LE (auth: n6)
Chain Length:126
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L27-A
Gene (Uniprot):RPL27A
Chain IDs:KB (auth: N7), ME (auth: n7)
Chain Length:135
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H6 Pfam ID:PF01777
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:LB (auth: N8), NE (auth: n8)
Chain Length:148
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P02406 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L29
Gene (Uniprot):RPL29
Chain IDs:MB (auth: N9), OE (auth: n9)
Chain Length:58
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05747 Pfam ID:PF01779
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30
Gene (Uniprot):RPL30
Chain IDs:NB (auth: O0), PE (auth: o0)
Chain Length:100
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P14120 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31-A
Gene (Uniprot):RPL31A
Chain IDs:OB (auth: O1), QE (auth: o1)
Chain Length:109
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0C2H8 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:PB (auth: O2), RE (auth: o2)
Chain Length:127
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38061 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L33-A
Gene (Uniprot):RPL33A
Chain IDs:QB (auth: O3), SE (auth: o3)
Chain Length:106
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05744 Pfam ID:PF01247
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L34-A
Gene (Uniprot):RPL34A
Chain IDs:RB (auth: O4), TE (auth: o4)
Chain Length:112
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P87262 Pfam ID:PF01199
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35-A
Gene (Uniprot):RPL35A
Chain IDs:SB (auth: O5), UE (auth: o5)
Chain Length:119
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX84 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L36-A
Gene (Uniprot):RPL36A
Chain IDs:TB (auth: O6), VE (auth: o6)
Chain Length:99
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05745 Pfam ID:PF01158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37-A
Gene (Uniprot):RPL37A
Chain IDs:UB (auth: O7), WE (auth: o7)
Chain Length:87
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49166 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L38
Gene (Uniprot):RPL38
Chain IDs:VB (auth: O8), XE (auth: o8)
Chain Length:77
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P49167 Pfam ID:PF01781
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Gene (Uniprot):RPL39
Chain IDs:WB (auth: O9), YE (auth: o9)
Chain Length:50
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04650 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ubiquitin-60S ribosomal protein L40
Gene (Uniprot):RPL40A
Chain IDs:XB (auth: Q0), ZE (auth: q0)
Chain Length:52
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CH08 Pfam ID:PF01020
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L41-A
Gene (Uniprot):RPL41A
Chain IDs:YB (auth: Q1), AF (auth: q1)
Chain Length:25
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX86 Pfam ID:PF05162
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42-A
Gene (Uniprot):RPL42A
Chain IDs:ZB (auth: Q2), BF (auth: q2)
Chain Length:105
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX27 Pfam ID:PF00935
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43-A
Gene (Uniprot):RPL43A
Chain IDs:AC (auth: Q3), CF (auth: q3)
Chain Length:91
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX25 Pfam ID:PF01780
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0-A
Gene (Uniprot):RPS0A
Chain IDs:B (auth: S0), CC (auth: s0)
Chain Length:206
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:B3LI22 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S1-A
Gene (Uniprot):RPS1A
Chain IDs:C (auth: S1), DC (auth: s1)
Chain Length:216
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:B3RHV0 Pfam ID:PF01015
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Gene (Uniprot):RPS2
Chain IDs:D (auth: S2), EC (auth: s2)
Chain Length:217
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P25443 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Gene (Uniprot):RPS3
Chain IDs:E (auth: S3), FC (auth: s3)
Chain Length:223
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05750 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S4-A
Gene (Uniprot):RPS4A
Chain IDs:F (auth: S4), GC (auth: s4)
Chain Length:260
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX35 Pfam ID:PF08071, PF01479, PF00900, PF00467, PF16121
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Gene (Uniprot):RPS5
Chain IDs:G (auth: S5), HC (auth: s5)
Chain Length:206
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26783 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S6-A
Gene (Uniprot):RPS6A
Chain IDs:H (auth: S6), IC (auth: s6)
Chain Length:226
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX37 Pfam ID:PF01092
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S7-A
Gene (Uniprot):RPS7A
Chain IDs:I (auth: S7), JC (auth: s7)
Chain Length:186
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P26786 Pfam ID:PF01251
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S8-A
Gene (Uniprot):RPS8A
Chain IDs:J (auth: S8), KC (auth: s8)
Chain Length:199
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:P0CX39 Pfam ID:PF01201
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9-A
Gene (Uniprot):RPS9A
Chain IDs:K (auth: S9), LC (auth: s9)
Chain Length:185
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
UniProt ID:O13516 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Suppressor protein STM1,Suppressor protein STM1,Suppressor protein STM1
Gene (Uniprot):STM1
Chain IDs:IA (auth: SM)
Chain Length:104
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P39015 Pfam ID:PF09598
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit beta-like protein
Gene (Uniprot):ASC1
Chain IDs:HA (auth: SR)
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38011 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S10-A,40S ribosomal protein S10-A,40S Ribosomal Protein S10
Gene (Uniprot):RPS10A
Chain IDs:MC (auth: c0)
Chain Length:96
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q08745 Pfam ID:PF03501
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Gene (Uniprot):RPS15
Chain IDs:RC (auth: c5)
Chain Length:131
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q01855 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8-A,60S ribosomal protein L8-A,60S Ribosomal Protein L8
Gene (Uniprot):RPL8A
Chain IDs:TD (auth: l8)
Chain Length:233
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P17076 Pfam ID:PF01248
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal Protein L12
Chain IDs:XD (auth: m2)
Chain Length:150
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24-A
Gene (Uniprot):RPL24A
Chain IDs:JE (auth: n4)
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04449 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0,60S acidic ribosomal protein P0,60S Ribosomal Protein P0
Gene (Uniprot):RPP0
Chain IDs:DF (auth: p0)
Chain Length:219
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P05317 Pfam ID:PF00466, PF17777
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal Protein P1/2
Chain IDs:EF (auth: p1), FF (auth: p2)
Chain Length:47
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Suppressor protein STM1,Suppressor protein STM1,Ribosome-bound protein Stm1
Gene (Uniprot):STM1
Chain IDs:JD (auth: sM)
Chain Length:104
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P39015 Pfam ID:PF09598
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein subunit beta-like protein
Gene (Uniprot):ASC1
Chain IDs:ID (auth: sR)
Chain Length:318
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38011 Pfam ID:PF00400
Ligand Molecules
MG
OHX
ZN
Primary Citation
Molecular insights into protein synthesis with proline residues.
EMBO Rep. 17 1776 1784 (2016)
PMID: 27827794 DOI: 10.15252/embr.201642943

Abstact

Proline is an amino acid with a unique cyclic structure that facilitates the folding of many proteins, but also impedes the rate of peptide bond formation by the ribosome. As a ribosome substrate, proline reacts markedly slower when compared with other amino acids both as a donor and as an acceptor of the nascent peptide. Furthermore, synthesis of peptides with consecutive proline residues triggers ribosome stalling. Here, we report crystal structures of the eukaryotic ribosome bound to analogs of mono- and diprolyl-tRNAs. These structures provide a high-resolution insight into unique properties of proline as a ribosome substrate. They show that the cyclic structure of proline residue prevents proline positioning in the amino acid binding pocket and affects the nascent peptide chain position in the ribosomal peptide exit tunnel. These observations extend current knowledge of the protein synthesis mechanism. They also revise an old dogma that amino acids bind the ribosomal active site in a uniform way by showing that proline has a binding mode distinct from other amino acids.

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Disease

Primary Citation of related structures
5LYB