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 1.1 of the entry. See complete history. 


Literature

Cryo-EM studies of the four E. coli paralogs establish ABCF proteins as master plumbers of the peptidyl-transferase center of the ribosome

Singh, S., Gentry, R.C., Fu, Z., Bailey, N.A., Altomare, C.G., Wong, K.H., Neky, M.J., Wang, C., Ray, K.K., Chi, Y.C., Zhang, Z., Grassucci, R.A., Frank, J., Boel, G., Gonzalez, R.L., Hunt, J.F.

(2023) bioRxiv 


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL1A [auth 1]220Escherichia coliMutation(s): 0 
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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 
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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 
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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 
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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 
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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 
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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 
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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
Find proteins for P0AG63 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18AB [auth sr]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7T7 (Escherichia coli (strain K12))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19BB [auth ss]79Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20CB [auth st]85Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7U7 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21DB [auth su]65Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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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
Download Ideal Coordinates CCD File 
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
  • Version 1.1: 2026-04-15
    Changes: Database references