9T2Q | pdb_00009t2q

E. coli 70S ribosome from delta-9 strain, PTC class 7

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

Ribosomal RNA modifications around the peptidyl transfer center stimulate catalytic activity and prevent the formation of alternative structures

Larsson, D.S.D., Liiv, A., Ero, R., Remme, J., Selmer, M.

(2026) bioRxiv 

Macromolecule Content 

  • Total Structure Weight: 1,194.72 kDa 
  • Atom Count: 15,318 
  • Modeled Residue Count: 844 
  • Deposited Residue Count: 4,637 
  • Unique protein chains: 10
  • Unique nucleic acid chains: 4

Macromolecules


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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2D [auth c]273Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60422 (Escherichia coli (strain K12))
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UniProt GroupP60422
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3E [auth d]209Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4F [auth e]201Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
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UniProt GroupP60723
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13G [auth i]142Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12))
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UniProt GroupP0AA10
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15H [auth k]144Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02413 (Escherichia coli (strain K12))
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UniProt GroupP02413
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16I [auth l]136Escherichia coliMutation(s): 0 
UniProt
Find proteins for A7ZSK2 (Escherichia coli O139:H28 (strain E24377A / ETEC))
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21J [auth q]103Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22K [auth r]110Escherichia coliMutation(s): 0 
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27L [auth v]85Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL32M [auth z]57Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Reference Sequence
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Entity ID: 1
MoleculeChains LengthOrganismImage
tRNA(fMet)A [auth Z]77Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S rRNAB [auth a]2,904Escherichia coli
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth b]120Escherichia coli
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Entity ID: 14
MoleculeChains LengthOrganismImage
tRNA(Phe)N [auth Y]76Escherichia coli
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SR0

Query on SR0


Download:Ideal Coordinates CCD File
O [auth a],
P [auth a]		N~1~-(3-azaniumylpropyl)butane-1,4-diaminium
C7 H22 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-Q
PUT

Query on PUT


Download:Ideal Coordinates CCD File
Q [auth a]1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
K

Query on K


Download:Ideal Coordinates CCD File
AF [auth e]
CB [auth a]
DB [auth a]
EB [auth a]
FB [auth a]
AF [auth e],
CB [auth a],
DB [auth a],
EB [auth a],
FB [auth a],
FC [auth a],
GB [auth a],
GC [auth a],
HB [auth a],
HC [auth a],
IB [auth a],
IC [auth a],
JB [auth a],
JC [auth a],
KB [auth a],
KC [auth a],
LB [auth a],
LC [auth a],
MB [auth a],
MC [auth a],
NB [auth a],
NC [auth a],
OB [auth a],
OC [auth a],
PB [auth a],
PC [auth a],
QB [auth a],
QC [auth a],
QD [auth a],
QE [auth a],
RC [auth a],
RD [auth a],
RE [auth a],
SC [auth a],
SD [auth a],
TC [auth a],
TD [auth a],
UC [auth a],
UD [auth a],
YE [auth a]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
AA [auth a]
AB [auth a]
AC [auth a]
AD [auth a]
AE [auth a]
AA [auth a],
AB [auth a],
AC [auth a],
AD [auth a],
AE [auth a],
BA [auth a],
BB [auth a],
BC [auth a],
BD [auth a],
BE [auth a],
BF [auth z],
CA [auth a],
CC [auth a],
CD [auth a],
CE [auth a],
DA [auth a],
DC [auth a],
DD [auth a],
DE [auth a],
EA [auth a],
EC [auth a],
ED [auth a],
EE [auth a],
FA [auth a],
FD [auth a],
FE [auth a],
GA [auth a],
GD [auth a],
GE [auth a],
HA [auth a],
HD [auth a],
HE [auth a],
IA [auth a],
ID [auth a],
IE [auth a],
JA [auth a],
JD [auth a],
JE [auth a],
KA [auth a],
KD [auth a],
KE [auth a],
LA [auth a],
LD [auth a],
LE [auth a],
MA [auth a],
MD [auth a],
ME [auth a],
NA [auth a],
ND [auth a],
NE [auth a],
OA [auth a],
OD [auth a],
OE [auth a],
PA [auth a],
PD [auth a],
PE [auth a],
QA [auth a],
R [auth a],
RA [auth a],
RB [auth a],
S [auth a],
SA [auth a],
SB [auth a],
SE [auth a],
T [auth a],
TA [auth a],
TB [auth a],
TE [auth a],
U [auth a],
UA [auth a],
UB [auth a],
UE [auth a],
V [auth a],
VA [auth a],
VB [auth a],
VC [auth a],
VD [auth a],
VE [auth a],
W [auth a],
WA [auth a],
WB [auth a],
WC [auth a],
WD [auth a],
WE [auth a],
X [auth a],
XA [auth a],
XB [auth a],
XC [auth a],
XD [auth a],
XE [auth a],
Y [auth a],
YA [auth a],
YB [auth a],
YC [auth a],
YD [auth a],
Z [auth a],
ZA [auth a],
ZB [auth a],
ZC [auth a],
ZD [auth a],
ZE [auth d]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
MEQ
Query on MEQ		E [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4		I [auth l]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
MS6
Query on MS6		I [auth l]L-PEPTIDE LINKINGC5 H11 N O S2MET

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4
MODEL REFINEMENTServalcat0.4.77

Structure Validation

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Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-06264
Swedish Research CouncilSweden2017-03827
Swedish Research CouncilSweden2022-04511

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-18
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Data collection