9NL5 | pdb_00009nl5

E. coli pre-elongation complex without an A-site tRNA with EQ2-EttA in Hydrolytic 1 conformation

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli
  • Mutation(s): No 

  • Deposited: 2025-03-02 Released: 2025-04-02 
  • Deposition Author(s): Singh, S., Hunt, J.F.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

E. coli pre-elongation complex without an A-site tRNA with EttA-EQ2

Singh, S., Hunt, J.F.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL1A [auth 1]220Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13B [auth 13]142Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14C [auth 14]122Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15D [auth 15]143Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16E [auth 16]136Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17F [auth 17]120Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18G [auth 18]116Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19H [auth 19]114Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2I [auth 2]271Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20J [auth 20]117Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21K [auth 21]103Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22L [auth 22]110Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23M [auth 23]93Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24N [auth 24]102Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25O [auth 25]94Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL27P [auth 27]85Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Q [auth 28]77Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29R [auth 29]63Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3S [auth 3]209Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30T [auth 30]58Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31U [auth 31]66Escherichia coliMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32V [auth 32]56Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33W [auth 33]50Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34X [auth 34]46Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35Y [auth 35]64Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36Z [auth 36]38Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4AA [auth 4]201Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth 5]177Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6CA [auth 6]176Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9DA [auth 9]149Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
EttAEA [auth E]551Escherichia coliMutation(s): 0 
EC: 3.6.1
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2KA [auth sb]218Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3LA [auth sc]206Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4MA [auth sd]205Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5NA [auth se]157Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6, non-modified isoformOA [auth sf]100Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7PA [auth sg]151Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8QA [auth sh]129Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9RA [auth si]127Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10SA [auth sj]98Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11TA [auth sk]116Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12UA [auth sl]123Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13VA [auth sm]112Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14WA [auth sn]100Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15XA [auth so]88Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16YA [auth sp]82Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17ZA [auth sq]80Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18AB [auth sr]65Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19BB [auth ss]79Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20CB [auth st]85Escherichia coliMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21DB [auth su]65Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains LengthOrganismImage
mRNAFA [auth M]9Escherichia coli
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Entity ID: 33
MoleculeChains LengthOrganismImage
23S ribosomal RNAGA [auth R1]2,903Escherichia coli
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Entity ID: 34
MoleculeChains LengthOrganismImage
5S ribosomal RNAHA [auth R2]119Escherichia coli
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Entity ID: 35
MoleculeChains LengthOrganismImage
16S ribosomal RNAIA [auth R3]1,531Escherichia coli
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Entity ID: 36
MoleculeChains LengthOrganismImage
tRNAJA [auth T]76Escherichia coli
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
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HB [auth E],
IB [auth E]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN
Query on ZN
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GB [auth 36]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AC [auth R1]
AD [auth R1]
AE [auth R1]
AF [auth R3]
AG [auth R3]
AC [auth R1],
AD [auth R1],
AE [auth R1],
AF [auth R3],
AG [auth R3],
BC [auth R1],
BD [auth R1],
BE [auth R1],
BF [auth R3],
BG [auth R3],
CC [auth R1],
CD [auth R1],
CE [auth R1],
CF [auth R3],
CG [auth R3],
DC [auth R1],
DD [auth R1],
DE [auth R1],
DF [auth R3],
DG [auth sn],
EB [auth 32],
EC [auth R1],
ED [auth R1],
EE [auth R1],
EF [auth R3],
FB [auth 33],
FC [auth R1],
FD [auth R1],
FE [auth R1],
FF [auth R3],
GC [auth R1],
GD [auth R1],
GE [auth R1],
GF [auth R3],
HC [auth R1],
HD [auth R1],
HE [auth R1],
HF [auth R3],
IC [auth R1],
ID [auth R1],
IE [auth R1],
IF [auth R3],
JC [auth R1],
JD [auth R1],
JE [auth R1],
JF [auth R3],
KC [auth R1],
KD [auth R1],
KE [auth R1],
KF [auth R3],
LB [auth R1],
LC [auth R1],
LD [auth R1],
LE [auth R1],
LF [auth R3],
MB [auth R1],
MC [auth R1],
MD [auth R1],
ME [auth R1],
MF [auth R3],
NB [auth R1],
NC [auth R1],
ND [auth R1],
NE [auth R1],
NF [auth R3],
OB [auth R1],
OC [auth R1],
OD [auth R1],
OE [auth R1],
OF [auth R3],
PB [auth R1],
PC [auth R1],
PD [auth R1],
PE [auth R1],
PF [auth R3],
QB [auth R1],
QC [auth R1],
QD [auth R1],
QE [auth R2],
QF [auth R3],
RB [auth R1],
RC [auth R1],
RD [auth R1],
RE [auth R3],
RF [auth R3],
SB [auth R1],
SC [auth R1],
SD [auth R1],
SE [auth R3],
SF [auth R3],
TB [auth R1],
TC [auth R1],
TD [auth R1],
TE [auth R3],
TF [auth R3],
UB [auth R1],
UC [auth R1],
UD [auth R1],
UE [auth R3],
UF [auth R3],
VB [auth R1],
VC [auth R1],
VD [auth R1],
VE [auth R3],
VF [auth R3],
WB [auth R1],
WC [auth R1],
WD [auth R1],
WE [auth R3],
WF [auth R3],
XB [auth R1],
XC [auth R1],
XD [auth R1],
XE [auth R3],
XF [auth R3],
YB [auth R1],
YC [auth R1],
YD [auth R1],
YE [auth R3],
YF [auth R3],
ZB [auth R1],
ZC [auth R1],
ZD [auth R1],
ZE [auth R3],
ZF [auth R3]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
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JB [auth E],
KB [auth E]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release