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 

wwPDB Validation   3D Report Full Report


This is version 1.1 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: 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 ...

    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

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.



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30S ribosomal protein S2B241Escherichia coliMutation(s): 0 
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30S ribosomal protein S3C233Escherichia coliMutation(s): 0 
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30S ribosomal protein S4D206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5E167Escherichia coliMutation(s): 0 
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30S ribosomal protein S6F135Escherichia coliMutation(s): 0 
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30S ribosomal protein S7G179Escherichia coliMutation(s): 0 
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30S ribosomal protein S8H130Escherichia coliMutation(s): 0 
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50S ribosomal protein L5AA [auth f]179Escherichia coliMutation(s): 0 
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50S ribosomal protein L6BA [auth g]177Escherichia coliMutation(s): 0 
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50S ribosomal protein L9CA [auth h]149Escherichia coliMutation(s): 0 
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50S ribosomal protein L13DA [auth i]142Escherichia coliMutation(s): 0 
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50S ribosomal protein L14EA [auth j]123Escherichia coliMutation(s): 0 
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50S ribosomal protein L15FA [auth k]144Escherichia coliMutation(s): 0 
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50S ribosomal protein L16GA [auth l]136Escherichia coliMutation(s): 0 
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50S ribosomal protein L17HA [auth m]127Escherichia coliMutation(s): 0 
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50S ribosomal protein L18IA [auth n]117Escherichia coliMutation(s): 0 
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50S ribosomal protein L19JA [auth o]115Escherichia coliMutation(s): 0 
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50S ribosomal protein L20KA [auth p]118Escherichia coliMutation(s): 0 
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50S ribosomal protein L21LA [auth q]103Escherichia coliMutation(s): 0 
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50S ribosomal protein L22MA [auth r]110Escherichia coliMutation(s): 0 
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50S ribosomal protein L23NA [auth s]100Escherichia coliMutation(s): 0 
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50S ribosomal protein L28RA [auth w]78Escherichia coliMutation(s): 0 
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50S ribosomal protein L30TA [auth y]59Escherichia coliMutation(s): 0 
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50S ribosomal protein L32UA [auth z]57Escherichia coliMutation(s): 0 
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50S ribosomal protein L33VA [auth 0]55Escherichia coliMutation(s): 0 
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50S ribosomal protein L35XA [auth 2]65Escherichia coliMutation(s): 0 
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50S ribosomal protein L31ZA [auth 4]70Escherichia coliMutation(s): 0 
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16S rRNAA1,542Escherichia coli
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A-site tRNA-valBB [auth Y]76Escherichia coli
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E-site tRNADB [auth 5]2Escherichia coli
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Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

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EB [auth A]PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
SPM
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KN [auth a]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
SPD
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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
 Ligand Interaction
ZN
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TN [auth 3],
UN [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
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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
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D 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 

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