6C5L

Conformation of methylated GGQ in the Peptidyl Transferase Center during translation termination (T. thermophilus)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination.

Zeng, F.Jin, H.

(2018) Sci Rep 8: 2349-2349

  • DOI: 10.1038/s41598-018-20107-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The glutamine of the GGQ is methylated post-translationally ...

    The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The glutamine of the GGQ is methylated post-translationally at the N 5 position in vivo; this covalent modification is essential for optimal cell growth and efficient translation termination. However, the precise conformation of the methylated-GGQ tripeptide in the ribosome remains unknown. Using cryoEM and X-ray crystallography, we report the conformation of methylated-GGQ in the peptidyl transferase center of the ribosome during canonical translational termination and co-translation quality control. It has been suggested that the GGQ motif arose independently through convergent evolution among otherwise unrelated proteins that catalyze peptide release. The requirement for this tripeptide in the highly conserved peptidyl transferase center suggests that the conformation reported here is likely shared during termination of protein synthesis in all domains of life.


    Organizational Affiliation

    Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, CB
256Thermus thermophilusMutation(s): 0 
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, CC
239Thermus thermophilusMutation(s): 0 
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, CD
209Thermus thermophilusMutation(s): 0 
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, CE
162Thermus thermophilusMutation(s): 0 
Gene Names: rpsErps5
Find proteins for P27152 (Thermus thermophilus)
Go to UniProtKB:  P27152

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, CF
101Thermus thermophilusMutation(s): 0 
Gene Names: rpsFrps6
Find proteins for P23370 (Thermus thermophilus)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, CG
156Thermus thermophilusMutation(s): 0 
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, CH
138Thermus thermophilusMutation(s): 0 
Gene Names: rpsHrps8
Find proteins for P24319 (Thermus thermophilus)
Go to UniProtKB:  P24319

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, CI
128Thermus thermophilusMutation(s): 0 
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62669

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, CJ
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsJrps10
Find proteins for P80375 (Thermus thermophilus)
Go to UniProtKB:  P80375

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, CK
129Thermus thermophilusMutation(s): 0 
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, CL
132Thermus thermophilusMutation(s): 0 
Gene Names: rpsLrps12
Find proteins for P17293 (Thermus thermophilus)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, CM
126Thermus thermophilusMutation(s): 0 
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
AN, CN
61Thermus thermophilusMutation(s): 0 
Gene Names: rpsZrps14rpsN
Find proteins for P24320 (Thermus thermophilus)
Go to UniProtKB:  P24320

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, CO
89Thermus thermophilusMutation(s): 0 
Gene Names: rpsOrps15
Find proteins for P80378 (Thermus thermophilus)
Go to UniProtKB:  P80378

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, CP
88Thermus thermophilusMutation(s): 0 
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, CQ
105Thermus thermophilusMutation(s): 0 
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, CR
88Thermus thermophilusMutation(s): 0 
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, CS
93Thermus thermophilusMutation(s): 0 
Gene Names: rpsSrps19
Find proteins for P80381 (Thermus thermophilus)
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, CT
106Thermus thermophilusMutation(s): 0 
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
AU, CU
27Thermus thermophilusMutation(s): 0 
Gene Names: rpsU
Find proteins for P62612 (Thermus thermophilus)
Go to UniProtKB:  P62612

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 2
AY, CY
357Thermus thermophilusMutation(s): 0 
Gene Names: prfBThthe16_0244
Find proteins for F6DD48 (Thermus thermophilus (strain SG0.5JP17-16))
Go to UniProtKB:  F6DD48

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
B0, D0
85Thermus thermophilusMutation(s): 0 
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
B1, D1
98Thermus thermophilusMutation(s): 0 
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60494

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B2, D2
72Thermus thermophilusMutation(s): 0 
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B3, D3
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmDrpl30
Find proteins for P74909 (Thermus thermophilus)
Go to UniProtKB:  P74909

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B4, D4
71Thermus thermophilusMutation(s): 0 
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JR0

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B5, D5
60Thermus thermophilusMutation(s): 0 
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B6, D6
54Thermus thermophilusMutation(s): 0 
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GW3

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B7, D7
49Thermus thermophilusMutation(s): 0 
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B8, D8
65Thermus thermophilusMutation(s): 0 
Gene Names: rpmIrpl35
Find proteins for P80341 (Thermus thermophilus)
Go to UniProtKB:  P80341

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B9, D9
37Thermus thermophilusMutation(s): 0 
Gene Names: rpmJrpl36
Find proteins for P80256 (Thermus thermophilus)
Go to UniProtKB:  P80256

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
BC, DC
229Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP7

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD, DD
276Thermus thermophilusMutation(s): 0 
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I07

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE, DE
206Thermus thermophilusMutation(s): 0 
Gene Names: rplCrpl3
Find proteins for P52860 (Thermus thermophilus)
Go to UniProtKB:  P52860

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF, DF
210Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG, DG
182Thermus thermophilusMutation(s): 0 
Gene Names: rplErpl5
Find proteins for P41201 (Thermus thermophilus)
Go to UniProtKB:  P41201

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH, DH
180Thermus thermophilusMutation(s): 0 
Gene Names: rplFrpl6
Find proteins for P24316 (Thermus thermophilus)
Go to UniProtKB:  P24316

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BI, DI
148Thermus thermophilusMutation(s): 0 
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
BJ, DJ
130Thermus thermophilusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BK, DK
147Thermus thermophilusMutation(s): 0 
Gene Names: rplKrpl11
Find proteins for P36238 (Thermus thermophilus)
Go to UniProtKB:  P36238

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BN, DN
140Thermus thermophilusMutation(s): 0 
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IN1

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BO, DO
122Thermus thermophilusMutation(s): 0 
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP8

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BP, DP
150Thermus thermophilusMutation(s): 0 
Gene Names: rplOrpl15
Find proteins for P74910 (Thermus thermophilus)
Go to UniProtKB:  P74910

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BQ, DQ
141Thermus thermophilusMutation(s): 0 
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BR, DR
118Thermus thermophilusMutation(s): 0 
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I33

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BS, DS
112Thermus thermophilusMutation(s): 0 
Gene Names: rplRrpl18
Find proteins for P80320 (Thermus thermophilus)
Go to UniProtKB:  P80320

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BT, DT
146Thermus thermophilusMutation(s): 0 
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490

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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BU, DU
118Thermus thermophilusMutation(s): 0 
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L76

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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BV, DV
101Thermus thermophilusMutation(s): 0 
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR2

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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BW, DW
113Thermus thermophilusMutation(s): 0 
Gene Names: rplVrpl22
Find proteins for P48286 (Thermus thermophilus)
Go to UniProtKB:  P48286

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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BX, DX
96Thermus thermophilusMutation(s): 0 
Gene Names: rplW
Find proteins for Q9RA57 (Thermus thermophilus)
Go to UniProtKB:  Q9RA57

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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BY, DY
110Thermus thermophilusMutation(s): 0 
Gene Names: rplXrpl24
Find proteins for Q56435 (Thermus thermophilus)
Go to UniProtKB:  Q56435

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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BZ, DZ
206Thermus thermophilusMutation(s): 0 
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7

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Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAAA, CA1522Thermus thermophilus

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Entity ID: 22
MoleculeChainsLengthOrganism
E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)AV, AW,CV,CW76Escherichia coli

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Entity ID: 23
MoleculeChainsLengthOrganism
mRNAAX, CX25Escherichia coli

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Entity ID: 35
MoleculeChainsLengthOrganism
23S rRNABA, DA2915Thermus thermophilus

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Entity ID: 36
MoleculeChainsLengthOrganism
5S rRNABB, DB122Thermus thermophilus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
AD, AN, B9, CD, CN, D9
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
AA, B5, BA, BB, BD, BE, BF, BQ, BT, CA, D5, DA, DB, DD, DP, DU, DW
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEQ
Query on MEQ
AY,CY
L-PEPTIDE LINKINGC6 H12 N2 O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.023α = 90
b = 452.527β = 90
c = 623.443γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-01-16 
  • Released Date: 2018-02-21 
  • Deposition Author(s): Zeng, F., Jin, H.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM120552

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-02-28
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence