ISDA

Deposition Date 2008-05-16

Release Date 2014-07-09

Last Version Date 2024-11-20

Entry Detail

PDB ID:

4V63

Keywords:

RIBOSOME

Title:

Structural basis for translation termination on the 70S ribosome.

Biological Source:

Source Organism:

(Taxon ID: )Thermus thermophilus (Taxon ID: 262724)
Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.21 Å

R-Value Free:

0.31

R-Value Work:

0.29

R-Value Observed:

0.29

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S RRNA
Chain IDs:A (auth: AA), EB (auth: CA)
Chain Length:1525
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:E (auth: AB), IB (auth: CB)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62662 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:F (auth: AC), JB (auth: CC)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62663 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:G (auth: AD), KB (auth: CD)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62664 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:H (auth: AE), LB (auth: CE)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62665 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:I (auth: AF), MB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62666 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:J (auth: AG), NB (auth: CG)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62667 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:K (auth: AH), OB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62668 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:L (auth: AI), PB (auth: CI)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62669 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:M (auth: AJ), QB (auth: CJ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62653 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:N (auth: AK), RB (auth: CK)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62654 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:O (auth: AL), SB (auth: CL)
Chain Length:134
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P61941 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:P (auth: AM), TB (auth: CM)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62655 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsZ
Chain IDs:Q (auth: AN), UB (auth: CN)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62656 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:R (auth: AO), VB (auth: CO)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62657 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:S (auth: AP), WB (auth: CP)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62238 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:T (auth: AQ), XB (auth: CQ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62658 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:U (auth: AR), YB (auth: CR)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62659 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:V (auth: AS), ZB (auth: CS)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62660 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:W (auth: AT), AC (auth: CT)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62661 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:X (auth: AU), BC (auth: CU)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62613 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:C (auth: AV), GB (auth: CV)
Chain Length:27
Number of Molecules:2
Biological Source:

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Peptide chain release factor 1
Gene (Uniprot):prfA
Chain IDs:Y (auth: AX), CC (auth: CX)
Chain Length:354
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72HB8 Pfam ID:PF03462, PF00472

Polymer Type:polyribonucleotide
Molecule:P and E-site tRNA(fMet)
Chain IDs:B (auth: AZ), D (auth: AY), FB (auth: CZ), HB (auth: CY)
Chain Length:77
Number of Molecules:4
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:VA (auth: B0), XC (auth: D0)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72HR3 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:WA (auth: B1), YC (auth: D1)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72G84 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:XA (auth: B2), ZC (auth: D2)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I12 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:YA (auth: B3), AD (auth: D3)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I22 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:ZA (auth: B4), BD (auth: D4)
Chain Length:97
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72JR0 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AB (auth: B5), CD (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62652 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BB (auth: B6), DD (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GW3 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CB (auth: B7), ED (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:DB (auth: B8), FD (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72L77 Pfam ID:PF01632

Polymer Type:polyribonucleotide
Molecule:23S RRNA
Chain IDs:Z (auth: BA), GD (auth: DA)
Chain Length:2894
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:5S RRNA
Chain IDs:AA (auth: BB), HD (auth: DB)
Chain Length:124
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:BA (auth: BD), DC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I07 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:CA (auth: BE), EC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I04 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:DA (auth: BF), FC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I05 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:EA (auth: BG), GC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I16 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:FA (auth: BH), HC (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I19 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:GA (auth: BI), IC (auth: DI)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GV5 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:HA (auth: BJ), JC (auth: DJ)
Chain Length:173
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GS1 Pfam ID:PF00466

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:IA (auth: BN), KC (auth: DN)
Chain Length:163
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72IN1 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:JA (auth: BO), LC (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I14 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:KA (auth: BP), MC (auth: DP)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I23 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:LA (auth: BQ), NC (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I11 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:MA (auth: BR), OC (auth: DR)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I33 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:NA (auth: BS), PC (auth: DS)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I20 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:OA (auth: BT), QC (auth: DT)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72JU9 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:PA (auth: BU), RC (auth: DU)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72L76 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:QA (auth: BV), SC (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72HR2 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:RA (auth: BW), TC (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I09 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:SA (auth: BX), UC (auth: DX)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I06 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:TA (auth: BY), VC (auth: DY)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I15 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:UA (auth: BZ), WC (auth: DZ)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72IA7 Pfam ID:PF01386, PF14693

Ligand Molecules

Primary Citation

Structural basis for translation termination on the 70S ribosome

Laurberg, M, Asahara, H, Korostelev, A, Zhu, J, Trakhanov, S, Noller, H.F.Show

Nature 454 852 857 (2008)

PMID: 18596689 DOI: 10.1038/nature07115

Abstact

At termination of protein synthesis, type I release factors promote hydrolysis of the peptidyl-transfer RNA linkage in response to recognition of a stop codon. Here we describe the crystal structure of the Thermus thermophilus 70S ribosome in complex with the release factor RF1, tRNA and a messenger RNA containing a UAA stop codon, at 3.2 A resolution. The stop codon is recognized in a pocket formed by conserved elements of RF1, including its PxT recognition motif, and 16S ribosomal RNA. The codon and the 30S subunit A site undergo an induced fit that results in stabilization of a conformation of RF1 that promotes its interaction with the peptidyl transferase centre. Unexpectedly, the main-chain amide group of Gln 230 in the universally conserved GGQ motif of the factor is positioned to contribute directly to peptidyl-tRNA hydrolysis.

Legend

Protein

Chemical

Disease

Primary Citation of related structures