ISDA

Deposition Date 2005-10-12

Release Date 2014-07-09

Last Version Date 2024-12-25

Entry Detail

PDB ID:

4V4S

Keywords:

RIBOSOME

Title:

Crystal structure of the whole ribosomal complex.

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)
Thermus thermophilus (Taxon ID: 300852)
(Taxon ID: )Thermus thermophilus (Taxon ID: 274)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

6.76 Å

R-Value Free:

0.35

R-Value Work:

0.34

R-Value Observed:

0.34

Space Group:

P 43 21 2

Download 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*AP*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:Peptide chain release factor 2
Gene (Uniprot):prfB
Chain IDs:Y (auth: AY)
Chain Length:365
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SM01 Pfam ID:PF03462, PF00472

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:WA (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:UA (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:VA (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:XA (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:YA (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:ZA (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:AB (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:BB (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:CB (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:AA (auth: BA)
Chain Length:2916
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:Z (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:BA (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:CA (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:DA (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:EA (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:FA (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:GA (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:DB (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:HA (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:IA (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:JA (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:KA (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:RA (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:LA (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:MA (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:SA (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:TA (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:NA (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:OA (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:PA (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:QA (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

Primary Citation

Crystal Structures of the Ribosome in Complex with Release Factors RF1 and RF2 Bound to a Cognate Stop Codon.

Petry, S, Brodersen, D.E, Murphy IV, F.V, Dunham, C.M, Selmer, M, Tarry, M.J, Kelley, A.C, Ramakrishnan, V.Show

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