4V7P image
Deposition Date 2010-04-29
Release Date 2014-07-09
Last Version Date 2024-11-27
Entry Detail
PDB ID:
4V7P
Keywords:
RIBOSOME
Title:
Recognition of the amber stop codon by release factor RF1.
Biological Source:
Source Organism:
Thermus thermophilus (Taxon ID: 262724)
Escherichia coli (Taxon ID: 469008)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.62 Å
R-Value Free:
0.29
R-Value Work:
0.26
R-Value Observed:
0.26
Space Group:
P 21 21 21
4V7P validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:16S rRNA (1504-MER)
Chain IDs:A (auth: AA), IC (auth: DA)
Chain Length:1504
Number of Molecules:2
Biological Source:Thermus thermophilus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB), JC (auth: DB)
Chain Length:234
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:C (auth: AC), KC (auth: DC)
Chain Length:206
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:D (auth: AD), LC (auth: DD)
Chain Length:208
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:E (auth: AE), MC (auth: DE)
Chain Length:151
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:F (auth: AF), NC (auth: DF)
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:G (auth: AG), OC (auth: DG)
Chain Length:155
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:H (auth: AH), PC (auth: DH)
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:I (auth: AI), QC (auth: DI)
Chain Length:127
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:J (auth: AJ), RC (auth: DJ)
Chain Length:98
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:K (auth: AK), SC (auth: DK)
Chain Length:119
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:L (auth: AL), TC (auth: DL)
Chain Length:124
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:M (auth: AM), UC (auth: DM)
Chain Length:117
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:N (auth: AN), VC (auth: DN)
Chain Length:60
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:O (auth: AO), WC (auth: DO)
Chain Length:88
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:P (auth: AP), XC (auth: DP)
Chain Length:83
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:Q (auth: AQ), YC (auth: DQ)
Chain Length:99
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:R (auth: AR), ZC (auth: DR)
Chain Length:70
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:S (auth: AS), AD (auth: DS)
Chain Length:78
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:T (auth: AT), BD (auth: DT)
Chain Length:99
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:U (auth: AU), CD (auth: DU)
Chain Length:24
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:P62613 Pfam ID:PF17070
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Peptide chain release factor 1
Gene (Uniprot):prfA
Chain IDs:V (auth: AV), DD (auth: DV)
Chain Length:354
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q72HB8 Pfam ID:PF03462, PF00472
Polymer Type:polyribonucleotide
Molecule:P-site tRNA-fMet
Chain IDs:W (auth: AW), ED (auth: DW)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')
Chain IDs:X (auth: AX)
Chain Length:7
Number of Molecules:1
Biological Source:Thermus thermophilus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:YA (auth: B1), DC (auth: C1)
Chain Length:71
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:ZA (auth: B2), EC (auth: C2)
Chain Length:59
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:AB (auth: B3), FC (auth: C3)
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:BB (auth: B4), GC (auth: C4)
Chain Length:48
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:CB (auth: B5), HC (auth: C5)
Chain Length:64
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), DB (auth: CA)
Chain Length:2879
Number of Molecules:2
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:Z (auth: BB), EB (auth: CB)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:AA (auth: BC), FB (auth: CC)
Chain Length:275
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:BA (auth: BD), GB (auth: CD)
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:CA (auth: BE), HB (auth: CE)
Chain Length:205
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:DA (auth: BF), IB (auth: CF)
Chain Length:181
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:EA (auth: BG), JB (auth: CG)
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:FA (auth: BH), KB (auth: CH)
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:GA (auth: BI), LB (auth: CI)
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:HA (auth: BJ), MB (auth: CJ)
Chain Length:139
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:IA (auth: BK), NB (auth: CK)
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:JA (auth: BL), OB (auth: CL)
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:KA (auth: BM), PB (auth: CM)
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:LA (auth: BN), QB (auth: CN)
Chain Length:117
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:MA (auth: BO), RB (auth: CO)
Chain Length:111
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:NA (auth: BP), SB (auth: CP)
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:OA (auth: BQ), TB (auth: CQ)
Chain Length:116
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:PA (auth: BR), UB (auth: CR)
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:QA (auth: BS), VB (auth: CS)
Chain Length:112
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:RA (auth: BT), WB (auth: CT)
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:SA (auth: BU), XB (auth: CU)
Chain Length:109
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:TA (auth: BV), YB (auth: CV)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q72IA7 Pfam ID:PF01386, PF14693
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:UA (auth: BW), ZB (auth: CW)
Chain Length:84
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:VA (auth: BX), AC (auth: CX)
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:WA (auth: BY), BC (auth: CY)
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:XA (auth: BZ), CC (auth: CZ)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus
UniProt ID:Q72I22 Pfam ID:PF00327
Polymer Type:polyribonucleotide
Molecule:messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')
Chain IDs:FD (auth: DX)
Chain Length:9
Number of Molecules:1
Biological Source:Thermus thermophilus
Ligand Molecules
MG
ZN
Primary Citation
Recognition of the amber UAG stop codon by release factor RF1.
Embo J. 29 2577 2585 (2010)
PMID: 20588254 DOI: 10.1038/emboj.2010.139

Abstact

We report the crystal structure of a termination complex containing release factor RF1 bound to the 70S ribosome in response to an amber (UAG) codon at 3.6-A resolution. The amber codon is recognized in the 30S subunit-decoding centre directly by conserved elements of domain 2 of RF1, including T186 of the PVT motif. Together with earlier structures, the mechanisms of recognition of all three stop codons by release factors RF1 and RF2 can now be described. Our structure confirms that the backbone amide of Q230 of the universally conserved GGQ motif is positioned to contribute directly to the catalysis of the peptidyl-tRNA hydrolysis reaction through stabilization of the leaving group and/or transition state. We also observe synthetic-negative interactions between mutations in the switch loop of RF1 and in helix 69 of 23S rRNA, revealing that these structural features interact functionally in the termination process. These findings are consistent with our proposal that structural rearrangements of RF1 and RF2 are critical to accurate translation termination.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4V7P
3MR8
3MRZ
3MS0
3MS1
3F1E
3D5A
1ZBT
3MS1
3MS0
3MRZ