7K00

Structure of the Bacterial Ribosome at 2 Angstrom Resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Structure of the bacterial ribosome at 2 angstrom resolution.

Watson, Z.L.Ward, F.R.Meheust, R.Ad, O.Schepartz, A.Banfield, J.F.Cate, J.H.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.60482
  • Primary Citation of Related Structures:  
    7K00

  • PubMed Abstract: 

    Using cryo-electron microscopy (cryo-EM), we determined the structure of the Escherichia coli 70S ribosome with a global resolution of 2.0 Å. The maps reveal unambiguous positioning of protein and RNA residues, their detailed chemical interactions, and chemical modifications. Notable features include the first examples of isopeptide and thioamide backbone substitutions in ribosomal proteins, the former likely conserved in all domains of life. The maps also reveal extensive solvation of the small (30S) ribosomal subunit, and interactions with A-site and P-site tRNAs, mRNA, and the antibiotic paromomycin. The maps and models of the bacterial ribosome presented here now allow a deeper phylogenetic analysis of ribosomal components including structural conservation to the level of solvation. The high quality of the maps should enable future structural analyses of the chemical basis for translation and aid the development of robust tools for cryo-EM structure modeling and refinement.


  • Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, Berkeley, United States.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2241Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3233Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4206Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5167Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6135Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7179Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8130Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9130Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10103Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11129Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12124Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13118Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14101Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1589Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1682Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1784Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1875Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1992Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2087Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2171Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2X [auth c]273Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3Y [auth d]209Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4Z [auth e]201Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5AA [auth f]179Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6BA [auth g]177Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9CA [auth h]149Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13DA [auth i]142Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14EA [auth j]123Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15FA [auth k]144Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16GA [auth l]136Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17HA [auth m]127Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18IA [auth n]117Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19JA [auth o]115Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20KA [auth p]118Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21LA [auth q]103Escherichia coliMutation(s): 0 
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Entity ID: 39
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50S ribosomal protein L22MA [auth r]110Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23NA [auth s]100Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24OA [auth t]104Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25PA [auth u]94Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27QA [auth v]85Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28RA [auth w]78Escherichia coliMutation(s): 0 
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50S ribosomal protein L29SA [auth x]63Escherichia coliMutation(s): 0 
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50S ribosomal protein L30TA [auth y]59Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32UA [auth z]57Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33VA [auth 0]55Escherichia coliMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34WA [auth 1]46Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35XA [auth 2]65Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36YA [auth 3]38Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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UniProt GroupP0A7Q6
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31ZA [auth 4]70Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12))
Explore P0A7M9 
Go to UniProtKB:  P0A7M9
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UniProt GroupP0A7M9
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,542Escherichia coli
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Entity ID: 22
MoleculeChains LengthOrganismImage
23S rRNAV [auth a]2,904Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
5S rRNAW [auth b]120Escherichia coli
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Entity ID: 53
MoleculeChains LengthOrganismImage
mRNAAB [auth X]28Escherichia coli
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Entity ID: 54
MoleculeChains LengthOrganismImage
A-site tRNA-valBB [auth Y]76Escherichia coli
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Entity ID: 55
MoleculeChains LengthOrganismImage
P-site tRNA-fMetCB [auth Z]76Escherichia coli
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Entity ID: 56
MoleculeChains LengthOrganismImage
E-site tRNADB [auth 5]2Escherichia coli
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
EB [auth A]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
SPM
Query on SPM

Download Ideal Coordinates CCD File 
KN [auth a]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD
Query on SPD

Download Ideal Coordinates CCD File 
AN [auth a]
BN [auth a]
CN [auth a]
DN [auth a]
EN [auth a]
AN [auth a],
BN [auth a],
CN [auth a],
DN [auth a],
EN [auth a],
FN [auth a],
GN [auth a],
HN [auth a],
IN [auth a],
JN [auth a],
UE [auth A],
VE [auth A],
WM [auth a],
XM [auth a],
YM [auth a],
ZM [auth a]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
TN [auth 3],
UN [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth a]
AG [auth a]
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth a],
AG [auth a],
AH [auth a],
AI [auth a],
AJ [auth a],
AK [auth a],
AL [auth a],
AM [auth a],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth a],
BG [auth a],
BH [auth a],
BI [auth a],
BJ [auth a],
BK [auth a],
BL [auth a],
BM [auth a],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth a],
CG [auth a],
CH [auth a],
CI [auth a],
CJ [auth a],
CK [auth a],
CL [auth a],
CM [auth a],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth a],
DG [auth a],
DH [auth a],
DI [auth a],
DJ [auth a],
DK [auth a],
DL [auth a],
DM [auth a],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth a],
EG [auth a],
EH [auth a],
EI [auth a],
EJ [auth a],
EK [auth a],
EL [auth a],
EM [auth a],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth a],
FG [auth a],
FH [auth a],
FI [auth a],
FJ [auth a],
FK [auth a],
FL [auth a],
FM [auth a],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth a],
GG [auth a],
GH [auth a],
GI [auth a],
GJ [auth a],
GK [auth a],
GL [auth a],
GM [auth a],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth a],
HG [auth a],
HH [auth a],
HI [auth a],
HJ [auth a],
HK [auth a],
HL [auth a],
HM [auth a],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth a],
IG [auth a],
IH [auth a],
II [auth a],
IJ [auth a],
IK [auth a],
IL [auth a],
IM [auth a],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth a],
JG [auth a],
JH [auth a],
JI [auth a],
JJ [auth a],
JK [auth a],
JL [auth a],
JM [auth a],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth a],
KG [auth a],
KH [auth a],
KI [auth a],
KJ [auth a],
KK [auth a],
KL [auth a],
KM [auth a],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth a],
LG [auth a],
LH [auth a],
LI [auth a],
LJ [auth a],
LK [auth a],
LL [auth a],
LM [auth a],
LN [auth b],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth a],
MG [auth a],
MH [auth a],
MI [auth a],
MJ [auth a],
MK [auth a],
ML [auth a],
MM [auth a],
MN [auth b],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth a],
NG [auth a],
NH [auth a],
NI [auth a],
NJ [auth a],
NK [auth a],
NL [auth a],
NM [auth a],
NN [auth b],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth a],
OG [auth a],
OH [auth a],
OI [auth a],
OJ [auth a],
OK [auth a],
OL [auth a],
OM [auth a],
ON [auth b],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth a],
PG [auth a],
PH [auth a],
PI [auth a],
PJ [auth a],
PK [auth a],
PL [auth a],
PM [auth a],
PN [auth b],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth a],
QG [auth a],
QH [auth a],
QI [auth a],
QJ [auth a],
QK [auth a],
QL [auth a],
QM [auth a],
QN [auth c],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth a],
RG [auth a],
RH [auth a],
RI [auth a],
RJ [auth a],
RK [auth a],
RL [auth a],
RM [auth a],
RN [auth d],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth a],
SG [auth a],
SH [auth a],
SI [auth a],
SJ [auth a],
SK [auth a],
SL [auth a],
SM [auth a],
SN [auth z],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth a],
TG [auth a],
TH [auth a],
TI [auth a],
TJ [auth a],
TK [auth a],
TL [auth a],
TM [auth a],
UB [auth A],
UC [auth A],
UD [auth A],
UF [auth a],
UG [auth a],
UH [auth a],
UI [auth a],
UJ [auth a],
UK [auth a],
UL [auth a],
UM [auth a],
VB [auth A],
VC [auth A],
VD [auth A],
VF [auth a],
VG [auth a],
VH [auth a],
VI [auth a],
VJ [auth a],
VK [auth a],
VL [auth a],
VM [auth a],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth a],
WF [auth a],
WG [auth a],
WH [auth a],
WI [auth a],
WJ [auth a],
WK [auth a],
WL [auth a],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth a],
XF [auth a],
XG [auth a],
XH [auth a],
XI [auth a],
XJ [auth a],
XK [auth a],
XL [auth a],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth a],
YF [auth a],
YG [auth a],
YH [auth a],
YI [auth a],
YJ [auth a],
YK [auth a],
YL [auth a],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth a],
ZF [auth a],
ZG [auth a],
ZH [auth a],
ZI [auth a],
ZJ [auth a],
ZK [auth a],
ZL [auth a]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ
Y [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4
GA [auth l]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-2021739
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-114454

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description