4YBB image
Deposition Date 2015-02-18
Release Date 2015-03-18
Last Version Date 2025-03-19
Entry Detail
PDB ID:
4YBB
Keywords:
RIBOSOME
Title:
High-resolution structure of the Escherichia coli ribosome
Biological Source:
Source Organism:
Escherichia coli K-12 (Taxon ID: 83333)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.10 Å
R-Value Free:
0.23
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 21
4YBB validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: AA), V (auth: BA)
Chain Length:1534
Number of Molecules:2
Biological Source:Escherichia coli K-12
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB), W (auth: BB)
Chain Length:224
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7V0 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC), X (auth: BC)
Chain Length:206
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AD), Y (auth: BD)
Chain Length:205
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: AE), Z (auth: BE)
Chain Length:155
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: AF), AA (auth: BF)
Chain Length:106
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P02358 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AG), BA (auth: BG)
Chain Length:151
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P02359 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H (auth: AH), CA (auth: BH)
Chain Length:129
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7W7 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI), DA (auth: BI)
Chain Length:127
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7X3 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AJ), EA (auth: BJ)
Chain Length:99
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7R5 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK), FA (auth: BK)
Chain Length:117
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7R9 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AL), GA (auth: BL)
Chain Length:123
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7S3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM), HA (auth: BM)
Chain Length:114
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7S9 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:N (auth: AN), IA (auth: BN)
Chain Length:100
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0AG59 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AO), JA (auth: BO)
Chain Length:88
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0ADZ4 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AP), KA (auth: BP)
Chain Length:82
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7T3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: AQ), LA (auth: BQ)
Chain Length:80
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0AG63 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR), MA (auth: BR)
Chain Length:55
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7T7 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AS), NA (auth: BS)
Chain Length:79
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7U3 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT), OA (auth: BT)
Chain Length:86
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7U7 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Gene (Uniprot):rpsU
Chain IDs:U (auth: AU), PA (auth: BU)
Chain Length:56
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P68679 Pfam ID:PF01165
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:PB (auth: C0), VC (auth: D0)
Chain Length:58
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0AG51 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:QB (auth: C1), WC (auth: D1)
Chain Length:56
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7N4 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:RB (auth: C2), XC (auth: D2)
Chain Length:51
Number of Molecules:2
Biological Source:Escherichia coli
UniProt ID:P0A7N9 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:SB (auth: C3), YC (auth: D3)
Chain Length:46
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7P5 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:TB (auth: C4), ZC (auth: D4)
Chain Length:64
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7Q1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:UB (auth: C5), AD (auth: D5)
Chain Length:38
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7Q6 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:QA (auth: CA)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli K-12
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:RA (auth: CB), WB (auth: DB)
Chain Length:120
Number of Molecules:2
Biological Source:Escherichia coli K-12
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:SA (auth: CC), XB (auth: DC)
Chain Length:271
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P60422 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:TA (auth: CD)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
UniProt ID:P60438 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:UA (auth: CE), ZB (auth: DE)
Chain Length:201
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P60723 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:VA (auth: CF), AC (auth: DF)
Chain Length:177
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P62399 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:WA (auth: CG), BC (auth: DG)
Chain Length:176
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0AG55 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:XA (auth: CH), CC (auth: DH)
Chain Length:149
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:YA (auth: CJ), EC (auth: DJ)
Chain Length:134
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:ZA (auth: CK), FC (auth: DK)
Chain Length:142
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0AA10 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:AB (auth: CL), GC (auth: DL)
Chain Length:123
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0ADY3 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:BB (auth: CM), HC (auth: DM)
Chain Length:144
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P02413 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:CB (auth: CN), IC (auth: DN)
Chain Length:136
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0ADY7 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:DB (auth: CO), JC (auth: DO)
Chain Length:125
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0AG44 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:EB (auth: CP), KC (auth: DP)
Chain Length:117
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0C018 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:FB (auth: CQ), LC (auth: DQ)
Chain Length:114
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7K6 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:GB (auth: CR), MC (auth: DR)
Chain Length:117
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7L3 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:HB (auth: CS), NC (auth: DS)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0AG48 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:IB (auth: CT), OC (auth: DT)
Chain Length:110
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P61175 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:JB (auth: CU), PC (auth: DU)
Chain Length:93
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0ADZ0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:KB (auth: CV), QC (auth: DV)
Chain Length:102
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P60624 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:LB (auth: CW), RC (auth: DW)
Chain Length:94
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P68919 Pfam ID:PF01386
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:MB (auth: CX), SC (auth: DX)
Chain Length:76
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7L8 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:NB (auth: CY), TC (auth: DY)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7M2 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:OB (auth: CZ), UC (auth: DZ)
Chain Length:62
Number of Molecules:2
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7M6 Pfam ID:PF00831
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:VB (auth: DA)
Chain Length:2903
Number of Molecules:1
Biological Source:Escherichia coli K-12
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:YB (auth: DD)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
UniProt ID:P60438 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:DC (auth: DI)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli (strain K12)
UniProt ID:P0A7J3 Pfam ID:PF00466
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MG QA G modified residue
2MA QA A modified residue
2MG A G modified residue
3TD QA U modified residue
4D4 CB ARG modified residue
4OC A C modified residue
5MC A C modified residue
5MU QA U modified residue
6MZ QA A modified residue
D2T L ASP modified residue
G7M A G modified residue
H2U VB U modified residue
MA6 A A modified residue
MEQ YB GLN modified residue
OMC QA C modified residue
OMG QA G modified residue
OMU QA U modified residue
PSU A U modified residue
UR3 A U modified residue
Ligand Molecules
1PE
ACY
EDO
GUN
MG
MPD
PEG
PG4
PGE
PUT
SPD
TRS
ZN
Primary Citation
High-resolution structure of the Escherichia coli ribosome.
Nat.Struct.Mol.Biol. 22 336 341 (2015)
PMID: 25775265 DOI: 10.1038/nsmb.2994

Abstact

Protein synthesis by the ribosome is highly dependent on the ionic conditions in the cellular environment, but the roles of ribosome solvation have remained poorly understood. Moreover, the functions of modifications to ribosomal RNA and ribosomal proteins have also been unclear. Here we present the structure of the Escherichia coli 70S ribosome at 2.4-Å resolution. The structure reveals details of the ribosomal subunit interface that are conserved in all domains of life, and it suggests how solvation contributes to ribosome integrity and function as well as how the conformation of ribosomal protein uS12 aids in mRNA decoding. This structure helps to explain the phylogenetic conservation of key elements of the ribosome, including post-transcriptional and post-translational modifications, and should serve as a basis for future antibiotic development.

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Protein

Chemical

Disease

Primary Citation of related structures
4YBB
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