ISDA: 4V9N

Deposition Date 2013-04-26

Release Date 2014-07-09

Last Version Date 2024-10-16

Entry Detail

PDB ID:

4V9N

Keywords:

RIBOSOME

Title:

Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.

Biological Source:

Source Organism:

Thermus thermophilus (Taxon ID: 262724)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.40 Å

R-Value Free:

0.26

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S rRNA (1504-MER)
Chain IDs:A (auth: AA), DB (auth: CA)
Chain Length:1504
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:E (auth: AB), HB (auth: CB)
Chain Length:234
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62662 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:F (auth: AC), IB (auth: CC)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62663 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:G (auth: AD), JB (auth: CD)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62664 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:H (auth: AE), KB (auth: CE)
Chain Length:151
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62665 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:I (auth: AF), LB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62666 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:J (auth: AG), MB (auth: CG)
Chain Length:155
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62667 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:P62668 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:L (auth: AI), OB (auth: CI)
Chain Length:127
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62669 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:M (auth: AJ), PB (auth: CJ)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62653 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:N (auth: AK), QB (auth: CK)
Chain Length:114
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62654 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:O (auth: AL), RB (auth: CL)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P61941 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:P (auth: AM), SB (auth: CM)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62655 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsZ
Chain IDs:Q (auth: AN), TB (auth: CN)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62656 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:R (auth: AO), UB (auth: CO)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62657 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:S (auth: AP), VB (auth: CP)
Chain Length:83
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62238 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:T (auth: AQ), WB (auth: CQ)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62658 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:U (auth: AR), XB (auth: CR)
Chain Length:70
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62659 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:V (auth: AS), YB (auth: CS)
Chain Length:78
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62660 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:W (auth: AT), ZB (auth: CT)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62661 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:X (auth: AU), AC (auth: CU)
Chain Length:24
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62613 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')
Chain IDs:B (auth: AV), EB (auth: CV)
Chain Length:10
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:P-site tRNA-fMet
Chain IDs:C (auth: AW), FB (auth: CW)
Chain Length:77
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Bacterial peptide chain release factor 2 (RF-2)
Gene (Uniprot):prfB
Chain IDs:D (auth: AY), GB (auth: CY)
Chain Length:362
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GJ6 Pfam ID:PF03462, PF00472

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:UA (auth: B0), XC (auth: D0)
Chain Length:76
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72HR3 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:VA (auth: B1), YC (auth: D1)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72G84 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:WA (auth: B2), ZC (auth: D2)
Chain Length:62
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I12 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:XA (auth: B3), AD (auth: D3)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I22 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:YA (auth: B4), BD (auth: D4)
Chain Length:30
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72JR0 Pfam ID:PF01197

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:ZA (auth: B5), CD (auth: D5)
Chain Length:52
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62652 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:AB (auth: B6), DD (auth: D6)
Chain Length:44
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GW3 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:BB (auth: B7), ED (auth: D7)
Chain Length:48
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80340 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:CB (auth: B8), FD (auth: D8)
Chain Length:63
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72L77 Pfam ID:PF01632

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:Y (auth: BA), BC (auth: DA)
Chain Length:2879
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:Z (auth: BB), CC (auth: DB)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:AA (auth: BD), DC (auth: DD)
Chain Length:271
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I07 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:BA (auth: BE), EC (auth: DE)
Chain Length:204
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I04 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:CA (auth: BF), FC (auth: DF)
Chain Length:202
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I05 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:DA (auth: BG), GC (auth: DG)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I16 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:EA (auth: BH), HC (auth: DH)
Chain Length:159
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I19 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:FA (auth: BI), IC (auth: DI)
Chain Length:145
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GV5 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:GA (auth: BK), JC (auth: DK)
Chain Length:147
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62442 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:HA (auth: BN), KC (auth: DN)
Chain Length:137
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72IN1 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:Q72I14 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:JA (auth: BP), MC (auth: DP)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I23 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:KA (auth: BQ), NC (auth: DQ)
Chain Length:134
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I11 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:LA (auth: BR), OC (auth: DR)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I33 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:MA (auth: BS), PC (auth: DS)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I20 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:NA (auth: BT), QC (auth: DT)
Chain Length:137
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72JU9 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:OA (auth: BU), RC (auth: DU)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72L76 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

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

UniProt ID:Q72HR2 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:QA (auth: BW), TC (auth: DW)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I09 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:RA (auth: BX), UC (auth: DX)
Chain Length:92
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I06 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:SA (auth: BY), VC (auth: DY)
Chain Length:100
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I15 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:TA (auth: BZ), WC (auth: DZ)
Chain Length:187
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72IA7 Pfam ID:PF01386, PF14693

Ligand Molecules

Primary Citation

Crystal Structure of the 70S Ribosome Bound with the Q253P Mutant Form of Release Factor RF2.

Santos, N, Zhu, J, Donohue, J.P, Korostelev, A.A, Noller, H.F.Show

Structure 21 1258 1263 (2013)

PMID: 23769667 DOI: 10.1016/j.str.2013.04.028

Abstact

Bacterial translation termination is mediated by release factors RF1 and RF2, which recognize stop codons and catalyze hydrolysis of the peptidyl-tRNA ester bond. The catalytic mechanism has been debated. We proposed that the backbone amide NH group, rather than the side chain, of the glutamine of the universally conserved GGQ motif participates in catalysis by H-bonding to the tetrahedral transition-state intermediate and by product stabilization. This was supported by complete loss of RF1 catalytic activity when glutamine is replaced by proline, the only residue that lacks a backbone NH group. Here, we present the 3.4 Å crystal structure of the ribosome complex containing the RF2 Q253P mutant and find that its fold, including the GGP sequence, is virtually identical to that of wild-type RF2. This rules out proline-induced misfolding and further supports the proposal that catalytic activity requires interaction of the Gln-253 backbone amide with the 3' end of peptidyl-tRNA.

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Protein

Chemical

Disease

Primary Citation of related structures