4V67

Crystal structure of a translation termination complex formed with release factor RF2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a translation termination complex formed with release factor RF2.

Korostelev, A.Asahara, H.Lancaster, L.Laurberg, M.Hirschi, A.Zhu, J.Trakhanov, S.Scott, W.G.Noller, H.F.

(2008) Proc.Natl.Acad.Sci.USA 105: 19684-19689

  • DOI: 10.1073/pnas.0810953105
  • Primary Citation of Related Structures:  3F1E, 3F1G, 3F1F, 3F1H

  • PubMed Abstract: 
  • We report the crystal structure of a translation termination complex formed by the Thermus thermophilus 70S ribosome bound with release factor RF2, in response to a UAA stop codon, solved at 3 A resolution. The backbone of helix alpha5 and the side c ...

    We report the crystal structure of a translation termination complex formed by the Thermus thermophilus 70S ribosome bound with release factor RF2, in response to a UAA stop codon, solved at 3 A resolution. The backbone of helix alpha5 and the side chain of serine of the conserved SPF motif of RF2 recognize U1 and A2 of the stop codon, respectively. A3 is unstacked from the first 2 bases, contacting Thr-216 and Val-203 of RF2 and stacking on G530 of 16S rRNA. The structure of the RF2 complex supports our previous proposal that conformational changes in the ribosome in response to recognition of the stop codon stabilize rearrangement of the switch loop of the release factor, resulting in docking of the universally conserved GGQ motif in the PTC of the 50S subunit. As seen for the RF1 complex, the main-chain amide nitrogen of glutamine in the GGQ motif is positioned to contribute directly to catalysis of peptidyl-tRNA hydrolysis, consistent with mutational studies, which show that most side-chain substitutions of the conserved glutamine have little effect. We show that when the H-bonding capability of the main-chain N-H of the conserved glutamine is eliminated by substitution with proline, peptidyl-tRNA esterase activity is abolished, consistent with its proposed role in catalysis.


    Organizational Affiliation

    Center for Molecular Biology of RNA and Departments of Molecular, Cell and Developmental Biology and Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, CB
256Thermus 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: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, CC
239Thermus 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: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, CD
209Thermus 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: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, CE
162Thermus 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: 8
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: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, CG
156Thermus 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: 10
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: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, CI
128Thermus 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: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, CJ
105Thermus 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: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, CK
129Thermus 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: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, CL
134Thermus 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: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, CM
126Thermus 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: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN, CN
61Thermus 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: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, CO
89Thermus 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: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, CP
88Thermus 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: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, CQ
105Thermus 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: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, CR
88Thermus 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: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, CS
93Thermus 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: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, CT
106Thermus 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: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
AU, CU
27Thermus 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: 24
MoleculeChainsSequence LengthOrganismDetails
Bacterial peptide chain release factor 2 (RF-2)
AX, CX
378Thermus 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: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD, DD
276Thermus 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
206Thermus 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
210Thermus 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
182Thermus 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
180Thermus 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
148Thermus 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 thermophilusGene Names: rplK (rpl11)
Find proteins for P36238 (Thermus thermophilus)
Go to UniProtKB:  P36238
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BN, DN
163Thermus 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
150Thermus 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
141Thermus 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
118Thermus 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
112Thermus 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
146Thermus 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
118Thermus 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
113Thermus 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
96Thermus 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
110Thermus 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
206Thermus 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
85Thermus 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
98Thermus 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
72Thermus 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
60Thermus 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
97Thermus 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
60Thermus 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
54Thermus 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
49Thermus 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
65Thermus 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 RRNAAA,CA1525Thermus thermophilus
Entity ID: 2
MoleculeChainsLengthOrganism
P AND E-SITE TRNA(FMET)AZ,AY,CZ,CY77Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
MRNAAV,CV27N/A
Entity ID: 25
MoleculeChainsLengthOrganism
23S RRNABA,DA2894Thermus thermophilus
Entity ID: 26
MoleculeChainsLengthOrganism
5S RRNABB,DB124Thermus thermophilus
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, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AQ, AR, AT, AV, AX, AY, AZ, B0, B1, B2, B4, B5, B6, B8, BA, BB, BD, BE, BF, BG, BH, BI, BK, BN, BO, BP, BQ, BR, BS, BT, BU, BV, BW, BX, BY, BZ, CA, CB, CC, CF, CG, CH, CK, CL, CO, CQ, CS, CT, CY, CZ, D1, D6, D8, DA, DB, DD, DE, DF, DG, DI, DN, DO, DP, DQ, DR, DT, DU, DY
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.316 
  • R-Value Work: 0.280 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 211.240α = 90.00
b = 456.780β = 90.00
c = 618.710γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
CNSrefinement
CNSphasing

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