6C5L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.1 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


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, CB
256Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, CC
239Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, CD
209Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, CE
162Thermus thermophilusMutation(s): 0 
Gene Names: rpsE (rps5)
Find proteins for P27152 (Thermus thermophilus)
Go to UniProtKB:  P27152
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, CF
101Thermus thermophilusMutation(s): 0 
Gene Names: rpsF (rps6)
Find proteins for P23370 (Thermus thermophilus)
Go to UniProtKB:  P23370
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, CG
156Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, CH
138Thermus thermophilusMutation(s): 0 
Gene Names: rpsH (rps8)
Find proteins for P24319 (Thermus thermophilus)
Go to UniProtKB:  P24319
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, CI
128Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P62669 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62669
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, CJ
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsJ (rps10)
Find proteins for P80375 (Thermus thermophilus)
Go to UniProtKB:  P80375
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, CK
129Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, CL
132Thermus thermophilusMutation(s): 0 
Gene Names: rpsL (rps12)
Find proteins for P17293 (Thermus thermophilus)
Go to UniProtKB:  P17293
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, CM
126Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
AN, CN
61Thermus thermophilusMutation(s): 0 
Gene Names: rpsZ (rps14, rpsN)
Find proteins for P24320 (Thermus thermophilus)
Go to UniProtKB:  P24320
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, CO
89Thermus thermophilusMutation(s): 0 
Gene Names: rpsO (rps15)
Find proteins for P80378 (Thermus thermophilus)
Go to UniProtKB:  P80378
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, CP
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsP (rps16)
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, CQ
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, CR
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsR (rps18)
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, CS
93Thermus thermophilusMutation(s): 0 
Gene Names: rpsS (rps19)
Find proteins for P80381 (Thermus thermophilus)
Go to UniProtKB:  P80381
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, CT
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
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
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Peptide chain release factor 2
AY, CY
357Thermus thermophilus (strain SG0.5JP17-16)Mutation(s): 0 
Gene Names: prfB
Find proteins for F6DD48 (Thermus thermophilus (strain SG0.5JP17-16))
Go to UniProtKB:  F6DD48
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
B0, D0
85Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
B1, D1
98Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60494
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B2, D2
72Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B3, D3
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmD (rpl30)
Find proteins for P74909 (Thermus thermophilus)
Go to UniProtKB:  P74909
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B4, D4
71Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JR0
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B5, D5
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B6, D6
54Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmG
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GW3
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B7, D7
49Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B8, D8
65Thermus thermophilusMutation(s): 0 
Gene Names: rpmI (rpl35)
Find proteins for P80341 (Thermus thermophilus)
Go to UniProtKB:  P80341
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B9, D9
37Thermus thermophilusMutation(s): 0 
Gene Names: rpmJ (rpl36)
Find proteins for P80256 (Thermus thermophilus)
Go to UniProtKB:  P80256
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1
BC, DC
229Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplA
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP7
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD, DD
276Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplB
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I07
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE, DE
206Thermus thermophilusMutation(s): 0 
Gene Names: rplC (rpl3)
Find proteins for P52860 (Thermus thermophilus)
Go to UniProtKB:  P52860
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF, DF
210Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG, DG
182Thermus thermophilusMutation(s): 0 
Gene Names: rplE (rpl5)
Find proteins for P41201 (Thermus thermophilus)
Go to UniProtKB:  P41201
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH, DH
180Thermus thermophilusMutation(s): 0 
Gene Names: rplF (rpl6)
Find proteins for P24316 (Thermus thermophilus)
Go to UniProtKB:  P24316
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BI, DI
148Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10
BJ, DJ
130N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BK, DK
147Thermus thermophilusMutation(s): 0 
Gene Names: rplK (rpl11)
Find proteins for P36238 (Thermus thermophilus)
Go to UniProtKB:  P36238
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BN, DN
140Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IN1
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BO, DO
122Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP8
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BP, DP
150Thermus thermophilusMutation(s): 0 
Gene Names: rplO (rpl15)
Find proteins for P74910 (Thermus thermophilus)
Go to UniProtKB:  P74910
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BQ, DQ
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BR, DR
118Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I33
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BS, DS
112Thermus thermophilusMutation(s): 0 
Gene Names: rplR (rpl18)
Find proteins for P80320 (Thermus thermophilus)
Go to UniProtKB:  P80320
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BT, DT
146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BU, DU
118Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L76
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BV, DV
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR2
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BW, DW
113Thermus thermophilusMutation(s): 0 
Gene Names: rplV (rpl22)
Find proteins for P48286 (Thermus thermophilus)
Go to UniProtKB:  P48286
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
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BY, DY
110Thermus thermophilusMutation(s): 0 
Gene Names: rplX (rpl24)
Find proteins for Q56435 (Thermus thermophilus)
Go to UniProtKB:  Q56435
Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
BZ, DZ
206Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7
Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAAA,CA1522Thermus thermophilus
Entity ID: 22
MoleculeChainsLengthOrganism
E-site tRNA PHE OR P-site tRNA PHE (unmodified bases)AV,AW,CV,CW76Escherichia coli
Entity ID: 23
MoleculeChainsLengthOrganism
mRNAAX,CX25Escherichia coli
Entity ID: 35
MoleculeChainsLengthOrganism
23S rRNABA,DA2915Thermus thermophilus
Entity ID: 36
MoleculeChainsLengthOrganism
5S rRNABB,DB122Thermus thermophilus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
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  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
BJ, DJ
L-PEPTIDE LINKINGC4 H9 N O2

--

MEQ
Query on MEQ
AY, CY
L-PEPTIDE LINKINGC6 H12 N2 O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 211.023α = 90.00
b = 452.527β = 90.00
c = 623.443γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



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 SciencesUnited StatesR01-GM120552

Revision History 

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