4V4T image
Deposition Date 2005-10-12
Release Date 2014-07-09
Last Version Date 2024-12-25
Entry Detail
PDB ID:
4V4T
Keywords:
RIBOSOME
Title:
Crystal structure of the whole ribosomal complex with a stop codon in the A-site.
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
(Taxon ID: )Thermus thermophilus (Taxon ID: 300852)
Thermus thermophilus (Taxon ID: 274)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
6.46 Å
R-Value Free:
0.36
R-Value Work:
0.35
R-Value Observed:
0.35
Space Group:
P 43 21 2
4V4T validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:A (auth: AA)
Chain Length:1522
Number of Molecules:1
Biological Source:Thermus thermophilus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:E (auth: AB)
Chain Length:256
Number of Molecules:1
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:F (auth: AC)
Chain Length:239
Number of Molecules:1
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:G (auth: AD)
Chain Length:209
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:H (auth: AE)
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:I (auth: AF)
Chain Length:101
Number of Molecules:1
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:J (auth: AG)
Chain Length:156
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P17291 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:K (auth: AH)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY9 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:L (auth: AI)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80374 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:M (auth: AJ)
Chain Length:105
Number of Molecules:1
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:N (auth: AK)
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80376 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:O (auth: AL)
Chain Length:135
Number of Molecules:1
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:P (auth: AM)
Chain Length:126
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80377 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:Q (auth: AN)
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY6 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:R (auth: AO)
Chain Length:89
Number of Molecules:1
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:S (auth: AP)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJH3 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:T (auth: AQ)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY7 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:U (auth: AR)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:V (auth: AS)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP2 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:W (auth: AT)
Chain Length:106
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80380 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Chain IDs:X (auth: AU)
Chain Length:27
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:P-site tRNA (Phe)
Chain IDs:B (auth: AV)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:E-site tRNA (Phe)
Chain IDs:C (auth: AW)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:5'-D(*AP*UP*GP*UP*UP*CP*UP*AP*GP*UP*AP*CP*AP*AP*UP*AP*AP*U)-3'
Chain IDs:D (auth: AX)
Chain Length:18
Number of Molecules:1
Biological Source:
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:VA (auth: B0)
Chain Length:91
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9RY65 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:TA (auth: B2)
Chain Length:70
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P10971 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:UA (auth: B3)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:WA (auth: B4)
Chain Length:73
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9RW44 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:XA (auth: B5)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P49228 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:YA (auth: B6)
Chain Length:82
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9RSS4 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:ZA (auth: B7)
Chain Length:47
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9RSH2 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:AB (auth: B8)
Chain Length:64
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9RSW6 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:BB (auth: B9)
Chain Length:36
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9RSK0 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:Z (auth: BA)
Chain Length:2916
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:Y (auth: BB)
Chain Length:123
Number of Molecules:1
Biological Source:Thermus thermophilus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:AA (auth: BD)
Chain Length:173
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5L3Z4 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:BA (auth: BE)
Chain Length:338
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P20279 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:CA (auth: BF)
Chain Length:246
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P12735 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:DA (auth: BG)
Chain Length:176
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P14124 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:EA (auth: BH)
Chain Length:177
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5L408 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:FA (auth: BI)
Chain Length:149
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P02417 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Chain IDs:CB (auth: BK)
Chain Length:141
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P29395 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:GA (auth: BN)
Chain Length:145
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P29198 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:HA (auth: BO)
Chain Length:122
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5L413 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:IA (auth: BP)
Chain Length:164
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P12737 Pfam ID:PF00828
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:JA (auth: BQ)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:QA (auth: BR)
Chain Length:118
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:KA (auth: BS)
Chain Length:186
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P14123 Pfam ID:PF17144
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:LA (auth: BT)
Chain Length:66
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P14116 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:RA (auth: BU)
Chain Length:118
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9RSW7 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:SA (auth: BV)
Chain Length:100
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9RY64 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:MA (auth: BW)
Chain Length:113
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP3 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:NA (auth: BX)
Chain Length:84
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P12732 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein 24
Chain IDs:OA (auth: BY)
Chain Length:119
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P10972 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein CTC
Chain IDs:PA (auth: BZ)
Chain Length:253
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9RX88 Pfam ID:PF01386, PF14693
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
PSU C U PSEUDOURIDINE-5'-MONOPHOSPHATE
YYG C G ?
Ligand Molecules
NA
Primary Citation
Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon.
Cell(Cambridge,Mass.) 123 1255 1266 (2005)
PMID: 16377566 DOI: 10.1016/j.cell.2005.09.039

Abstact

During protein synthesis, translational release factors catalyze the release of the polypeptide chain when a stop codon on the mRNA reaches the A site of the ribosome. The detailed mechanism of this process is currently unknown. We present here the crystal structures of the ribosome from Thermus thermophilus with RF1 and RF2 bound to their cognate stop codons, at resolutions of 5.9 Angstrom and 6.7 Angstrom, respectively. The structures reveal details of interactions of the factors with the ribosome and mRNA, including elements previously implicated in decoding and peptide release. They also shed light on conformational changes both in the factors and in the ribosome during termination. Differences seen in the interaction of RF1 and RF2 with the L11 region of the ribosome allow us to rationalize previous biochemical data. Finally, this work demonstrates the feasibility of crystallizing ribosomes with bound factors at a defined state along the translational pathway.

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Protein

Chemical

Disease

Primary Citation of related structures
4V4T
2B9O
2B9P
2B64
2B66
2B9M
2B9N
2B9P