4V6F image
Deposition Date 2009-07-09
Release Date 2014-07-09
Last Version Date 2024-11-06
Entry Detail
PDB ID:
4V6F
Keywords:
RIBOSOME
Title:
Elongation complex of the 70S ribosome with three tRNAs and mRNA.
Biological Source:
Source Organism:
(Taxon ID: )Thermus thermophilus (Taxon ID: 300852)
Escherichia coli (Taxon ID: 562)
Thermus thermophilus (Taxon ID: 274)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.10 Å
R-Value Free:
0.25
R-Value Work:
0.21
Space Group:
P 21 21 21
4V6F validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L17
Gene (Uniprot):rplQ
Chain IDs:M (auth: A0), SC (auth: D0)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L20
Gene (Uniprot):rplT
Chain IDs:P (auth: A1), VC (auth: D1)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60491 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L21
Gene (Uniprot):rplU
Chain IDs:Q (auth: A2), WC (auth: D2)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60492 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: A3), BD (auth: D3)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60493 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L31
Gene (Uniprot):rpmE
Chain IDs:Z (auth: A4), FD (auth: D4)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SJE1 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: A5), GD (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80339 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: A6), HD (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P35871 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: A7), ID (auth: D7)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80340 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: A8), JD (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SKU1 Pfam ID:PF01632
Polymer Type:polyribonucleotide
Molecule:23S RIBOSOMAL RNA
Chain IDs:A (auth: AA)
Chain Length:2909
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:B (auth: AB), DC (auth: DB)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L2
Gene (Uniprot):rplB
Chain IDs:C (auth: AD), EC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60405 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L3
Gene (Uniprot):rplC
Chain IDs:D (auth: AE), FC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN8 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L4
Gene (Uniprot):rplD
Chain IDs:E (auth: AF), GC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN9 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L5
Gene (Uniprot):rplE
Chain IDs:F (auth: AG), HC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L6
Chain IDs:G (auth: AH), IC (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:A0A0M9ADP1 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L9
Gene (Uniprot):rplI
Chain IDs:H (auth: AK), KC (auth: DK)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L13
Gene (Uniprot):rplM
Chain IDs:I (auth: AM), OC (auth: DM)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60488 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L14
Gene (Uniprot):rplN
Chain IDs:J (auth: AN), PC (auth: DN)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP8 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L15
Gene (Uniprot):rplO
Chain IDs:K (auth: AO), QC (auth: DO)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ7 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L16
Gene (Uniprot):rplP
Chain IDs:L (auth: AP), RC (auth: DP)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60489 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L18
Gene (Uniprot):rplR
Chain IDs:N (auth: AQ), TC (auth: DQ)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ4 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L19
Gene (Uniprot):rplS
Chain IDs:O (auth: AR), UC (auth: DR)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60490 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L22
Gene (Uniprot):rplV
Chain IDs:R (auth: AS), XC (auth: DS)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP3 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L23
Gene (Uniprot):rplW
Chain IDs:S (auth: AT), YC (auth: DT)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP0 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L24
Gene (Uniprot):rplX
Chain IDs:T (auth: AU), ZC (auth: DU)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L25
Gene (Uniprot):rplY
Chain IDs:U (auth: AV), AD (auth: DV)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L29
Gene (Uniprot):rpmC
Chain IDs:X (auth: AW), DD (auth: DW)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP6 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L30
Gene (Uniprot):rpmD
Chain IDs:Y (auth: AX), ED (auth: DX)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L28
Gene (Uniprot):rpmB
Chain IDs:W (auth: AZ), CD (auth: DZ)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P60494 Pfam ID:PF00830
Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:CB (auth: B1), BC (auth: C1)
Chain Length:30
Number of Molecules:2
Biological Source:
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:EA (auth: BA)
Chain Length:1516
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:TRNA-PHE WITH UNMODIFIED NUCLEOTIDES EXCEPT FOR MIA37
Chain IDs:ZA (auth: BD), AB (auth: BB), BB (auth: BC), YB (auth: CD), ZB (auth: CB), AC (auth: CC)
Chain Length:76
Number of Molecules:6
Biological Source:Escherichia coli
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:FA (auth: BE), EB (auth: CE)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80371 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:GA (auth: BF), FB (auth: CF)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:HA (auth: BG), GB (auth: CG)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:IA (auth: BH), HB (auth: CH)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:JA (auth: BI), IB (auth: CI)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SLP8 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:KA (auth: BJ), JB (auth: CJ)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P17291 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:LA (auth: BK), KB (auth: CK)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P0DOY9 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:MA (auth: BL), LB (auth: CL)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80374 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:NA (auth: BM), MB (auth: CM)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN7 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:OA (auth: BN), NB (auth: CN)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80376 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:PA (auth: BO), OB (auth: CO)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN3 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:QA (auth: BP), PB (auth: CP)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80377 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:RA (auth: BQ), QB (auth: CQ)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P0DOY6 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:SA (auth: BR), RB (auth: CR)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SJ76 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:TA (auth: BS), SB (auth: CS)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SJH3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:UA (auth: BT), TB (auth: CT)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P0DOY7 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:VA (auth: BU), UB (auth: CU)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:WA (auth: BV), VB (auth: CV)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:XA (auth: BW), WB (auth: CW)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P80380 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:YA (auth: BX), XB (auth: CX)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:DB (auth: CA)
Chain Length:1515
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:23S RRNA
Chain IDs:CC (auth: DA)
Chain Length:2912
Number of Molecules:1
Biological Source:Thermus thermophilus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L7/L12
Gene (Uniprot):rplL
Chain IDs:JC (auth: DI), NC (auth: DJ)
Chain Length:125
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q8VVE2 Pfam ID:PF16320, PF00542
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:MC (auth: DL)
Chain Length:147
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLP6 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:LC (auth: DY)
Chain Length:173
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q8VVE3 Pfam ID:PF00466
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MIA ZA A ?
Ligand Molecules
MG
ZN
Primary Citation
Structural aspects of messenger RNA reading frame maintenance by the ribosome.
Nat.Struct.Mol.Biol. 17 555 560 (2010)
PMID: 20400952 DOI: 10.1038/nsmb.1790

Abstact

One key question in protein biosynthesis is how the ribosome couples mRNA and tRNA movements to prevent disruption of weak codon-anticodon interactions and loss of the translational reading frame during translocation. Here we report the complete path of mRNA on the 70S ribosome at the atomic level (3.1-A resolution), and we show that one of the conformational rearrangements that occurs upon transition from initiation to elongation is a narrowing of the downstream mRNA tunnel. This rearrangement triggers formation of a network of interactions between the mRNA downstream of the A-site codon and the elongating ribosome. Our data elucidate the mechanism by which hypermodified nucleoside 2-methylthio-N6 isopentenyl adenosine at position 37 (ms(2)i(6)A37) in tRNA(Phe)(GAA) stabilizes mRNA-tRNA interactions in all three tRNA binding sites. Another network of contacts is formed between this tRNA modification and ribosomal elements surrounding the mRNA E/P kink, resulting in the anchoring of P-site tRNA. These data allow rationalization of how modification deficiencies of ms(2)i(6)A37 in tRNAs may lead to shifts of the translational reading frame.

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Protein

Chemical

Disease

Primary Citation of related structures
4V6F
3I8F
3I8G
3I8H
3I8I
3I8G
3I8H
3I8I