4V9N

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.

(2013) Structure 21: 1258-1263

  • DOI: 10.1016/j.str.2013.04.028
  • Primary Citation of Related Structures:  4KFH, 4KFI, 4KFK, 4KFL

  • PubMed Abstract: 
  • 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, ...

    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.


    Organizational Affiliation

    Center for Molecular Biology of RNA and Department of Molecular, Cell and Developmental Biology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Bacterial peptide chain release factor 2 (RF-2)
AY, CY
362Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)N/A
Find proteins for Q72GJ6 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GJ6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, CB
234Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsB (rps2)
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, CC
206Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsC (rps3)
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, CD
208Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsD (rps4)
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, CE
151Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsE (rps5)
Find proteins for P62665 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62665
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, CF
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsF (rps6)
Find proteins for P62666 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62666
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, CG
155Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsG (rps7)
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, CH
138Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsH (rps8)
Find proteins for P62668 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62668
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, CI
127Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsI (rps9)
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62669
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, CJ
98Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsJ (rps10)
Find proteins for P62653 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62653
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, CK
114Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsK (rps11)
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, CL
122Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsL (rps12)
Find proteins for P61941 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P61941
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, CM
117Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsM (rps13)
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN, CN
60Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsZ (rps14, rpsN)
Find proteins for P62656 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62656
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, CO
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsO (rps15)
Find proteins for P62657 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62657
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, CP
83Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsP (rps16)
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, CQ
99Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsQ (rps17)
Find proteins for P62658 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62658
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, CR
70Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsR (rps18)
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, CS
78Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsS (rps19)
Find proteins for P62660 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62660
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, CT
99Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsT (rps20)
Find proteins for P62661 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62661
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
AU, CU
24Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpsU
Find proteins for P62613 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62613
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD, DD
271Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplB
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I07
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE, DE
204Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplC
Find proteins for Q72I04 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I04
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF, DF
202Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplD
Find proteins for Q72I05 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I05
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG, DG
181Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplE
Find proteins for Q72I16 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I16
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH, DH
159Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplF
Find proteins for Q72I19 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I19
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BI, DI
145Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplI
Find proteins for Q72GV5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GV5
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BK, DK
147Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplK
Find proteins for P62442 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62442
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BN, DN
137Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplM
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IN1
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BO, DO
122Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplN
Find proteins for Q72I14 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I14
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BP, DP
146Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplO
Find proteins for Q72I23 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I23
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BQ, DQ
134Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplP
Find proteins for Q72I11 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I11
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BR, DR
117Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplQ
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I33
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BS, DS
98Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplR
Find proteins for Q72I20 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I20
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BT, DT
137Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplS
Find proteins for Q72JU9 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JU9
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BU, DU
117Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplT
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L76
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BV, DV
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplU
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR2
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BW, DW
112Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplV
Find proteins for Q72I09 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I09
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BX, DX
92Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplW
Find proteins for Q72I06 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I06
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BY, DY
100Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplX
Find proteins for Q72I15 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I15
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BZ, DZ
187Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rplY (ctc)
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
B0, D0
76Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmA
Find proteins for Q72HR3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
B1, D1
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmB
Find proteins for Q72G84 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72G84
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B2, D2
62Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmC
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B3, D3
59Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmD
Find proteins for Q72I22 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I22
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B4, D4
30Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmE
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JR0
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B5, D5
52Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmF (rpl32)
Find proteins for P62652 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62652
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B6, D6
44Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmG
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GW3
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B7, D7
48Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B8, D8
63Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpmI
Find proteins for Q72L77 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L77
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNA (1504-MER)AA,CA1504Thermus thermophilus HB27
Entity ID: 2
MoleculeChainsLengthOrganism
messenger RNA (5'-R(*AP*AP*UP*GP*UP*AP*G)-3')AV,CV10Thermus thermophilus HB27
Entity ID: 3
MoleculeChainsLengthOrganism
P-site tRNA-fMetAW,CW77Thermus thermophilus HB27
Entity ID: 25
MoleculeChainsLengthOrganism
23S ribosomal RNABA,DA2879Thermus thermophilus HB27
Entity ID: 26
MoleculeChainsLengthOrganism
5S ribosomal RNABB,DB119Thermus thermophilus HB27
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
AD, AN, CD, CN
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
AA, AC, AG, AO, AQ, AT, AV, AW, AY, B0, B1, B3, B5, B8, BA, BB, BD, BE, BF, BP, BT, BX, BY, CA, CD, CM, CR, CV, CW, CY, D0, D1, D5, D7, DA, DB, DD, DE, DF, DH, DI, DN, DP, DQ, DV, DW, DX
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 212.070α = 90.00
b = 454.400β = 90.00
c = 618.450γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
XDSdata scaling
CNSrefinement
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other