6N9E

Crystal structure of the Thermus thermophilus 70S ribosome in complex with a short substrate mimic CC-Pmn and bound to mRNA and P-site tRNA at 3.7A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanistic insights into the slow peptide bond formation with D-amino acids in the ribosomal active site.

Melnikov, S.V.Khabibullina, N.F.Mairhofer, E.Vargas-Rodriguez, O.Reynolds, N.M.Micura, R.Soll, D.Polikanov, Y.S.

(2019) Nucleic Acids Res. 47: 2089-2100


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L2
1D, 2D
276N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L3
1E, 2E
206N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L4
1F, 2F
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L5
1G, 2G
182N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L6
1H, 2H
180N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L9
1I, 2I
148N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L13
1N, 2N
140N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L14
1O, 2O
122N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L15
1P, 2P
150N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L16
1Q, 2Q
141N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L17
1R, 2R
118N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L18
1S, 2S
112N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L19
1T, 2T
146N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L20
1U, 2U
118N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L21
1V, 2V
101N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L22
1W, 2W
113N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L23
1X, 2X
96N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
1Y, 2Y
110Thermus thermophilusMutation(s): 0 
Gene Names: rplX (rpl24)
Find proteins for Q56435 (Thermus thermophilus)
Go to UniProtKB:  Q56435
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
1Z, 2Z
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: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
10, 20
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: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
11, 21
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: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
12, 22
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: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
13, 23
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmD (rpl30)
Find proteins for P74909 (Thermus thermophilus)
Go to UniProtKB:  P74909
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
14, 24
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: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
15, 25
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: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
16, 26
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: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
17, 27
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: 30
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L35
18, 28
65N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L36
19, 29
37N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S2
1b, 2b
256N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S3
1c, 2c
239N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S4
1d, 2d
209N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S5
1e, 2e
162N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S6
1f, 2f
101N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S7
1g, 2g
156N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S8
1h, 2h
138N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
1i, 2i
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
1j, 2j
105Thermus thermophilusMutation(s): 0 
Gene Names: rpsJ (rps10)
Find proteins for P80375 (Thermus thermophilus)
Go to UniProtKB:  P80375
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
1k, 2k
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: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
1l, 2l
132Thermus thermophilusMutation(s): 0 
Gene Names: rpsL (rps12)
Find proteins for P17293 (Thermus thermophilus)
Go to UniProtKB:  P17293
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
1m, 2m
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: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
1n, 2n
61Thermus thermophilusMutation(s): 0 
Gene Names: rpsZ (rps14, rpsN)
Find proteins for P24320 (Thermus thermophilus)
Go to UniProtKB:  P24320
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
1o, 2o
89Thermus thermophilusMutation(s): 0 
Gene Names: rpsO (rps15)
Find proteins for P80378 (Thermus thermophilus)
Go to UniProtKB:  P80378
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
1p, 2p
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: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
1q, 2q
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: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
1r, 2r
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: 50
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S19
1s, 2s
93N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S20
1t, 2t
106N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein Thx
1u, 2u
27Thermus thermophilusMutation(s): 0 
Gene Names: rpsU
Find proteins for P62612 (Thermus thermophilus)
Go to UniProtKB:  P62612
Entity ID: 1
MoleculeChainsLengthOrganism
23S Ribosomal RNA1A,2A2915Thermus thermophilus
Entity ID: 2
MoleculeChainsLengthOrganism
5S Ribosomal RNA1B,2B121Thermus thermophilus
Entity ID: 32
MoleculeChainsLengthOrganism
16S Ribosomal RNA1a,2a1521Thermus thermophilus
Entity ID: 53
MoleculeChainsLengthOrganism
mRNA1v,2v24Escherichia virus T4
Entity ID: 54
MoleculeChainsLengthOrganism
CC-Pmn1w,2w3Escherichia coli
Entity ID: 55
MoleculeChainsLengthOrganism
P-site tRNA, Deacylated Initiator Methionyl-tRNA1x,2x77Escherichia coli
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
1d, 2d
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
14, 15, 16, 19, 1n, 1Y, 24, 25, 26, 29, 2n, 2Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
10, 13, 15, 16, 17, 18, 1a, 1A, 1B, 1d, 1D, 1E, 1F, 1l, 1Q, 1r, 1S, 1U, 1V, 1W, 1x, 20, 21, 23, 25, 27, 28, 2a, 2A, 2B, 2D, 2d, 2E, 2f, 2l, 2O, 2Q, 2r, 2R, 2T, 2Y
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  15 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1a, 1A, 1x, 2a, 2A, 2x
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
1A, 1a, 1x, 2a, 2A, 2x
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
1a, 2a
RNA LINKINGC12 H18 N5 O8 PG
MA6
Query on MA6
1a, 2a
RNA LINKINGC12 H18 N5 O7 PA
4SU
Query on 4SU
1x, 2x
RNA LINKINGC9 H13 N2 O8 P SU
2MG
Query on 2MG
1a, 2a
RNA LINKINGC11 H16 N5 O8 PG
UR3
Query on UR3
1a, 2a
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
1A, 2A
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
1a, 2a
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
1A, 1x, 2A, 2x
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
1A, 2A
RNA LINKINGC11 H16 N5 O7 PA
PPU
Query on PPU
1w, 2w
RNA LINKINGC22 H30 N7 O8 PA
2MU
Query on 2MU
1A, 2A
RNA LINKINGC11 H17 N2 O9 PU
0TD
Query on 0TD
1l, 2l
L-PEPTIDE LINKINGC5 H9 N O4 SASP
4OC
Query on 4OC
1a, 1A, 2a, 2A
RNA LINKINGC11 H18 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 212.240α = 90.00
b = 452.840β = 90.00
c = 620.300γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction
XSCALEdata scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United StatesIllinois State Startup Funds
National Institutes of Health/National Institute of General Medical SciencesUnited StatesRO1-GM122560
Austrian Science FundAustriaP27947

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-19
    Type: Data collection, Database references
  • Version 1.2: 2019-03-13
    Type: Data collection, Database references