6V3B

Cryo-EM structure of the Acinetobacter baumannii Ribosome: 70S in Empty state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 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

Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development.

Morgan, C.E.Huang, W.Rudin, S.D.Taylor, D.J.Kirby, J.E.Bonomo, R.A.Yu, E.W.

(2020) mBio 11

  • DOI: https://doi.org/10.1128/mBio.03117-19
  • Primary Citation of Related Structures:  
    6V39, 6V3A, 6V3B, 6V3D, 6V3E

  • PubMed Abstract: 

    Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is Acinetobacter baumannii , a Gram-negative opportunistic pathogen that exhibits the remarkable ability to resist antibiotics through multiple mechanisms. As bacterial ribosomes represent a target for multiple distinct classes of existing antimicrobial agents, we here use single-particle cryo-electron microscopy (cryo-EM) to elucidate five different structural states of the A. baumannii ribosome, including the 70S, 50S, and 30S forms. We also determined interparticle motions of the 70S ribosome in different tRNA bound states using three-dimensional (3D) variability analysis. Together, our structural data further our understanding of the ribosome from A. baumannii and other Gram-negative pathogens and will enable structure-based drug discovery to combat antibiotic-resistant bacterial infections. IMPORTANCE Acinetobacter baumannii is a severe nosocomial threat largely due to its intrinsic antibiotic resistance and remarkable ability to acquire new resistance determinants. The bacterial ribosome serves as a major target for modern antibiotics and the design of new therapeutics. Here, we present cryo-EM structures of the A. baumannii 70S ribosome, revealing several unique species-specific structural features that may facilitate future drug development to combat this recalcitrant bacterial pathogen.


  • Organizational Affiliation

    Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33A [auth 0]51Acinetobacter sp. CIP 51.11Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34B [auth 1]44Acinetobacter beijerinckii ANC 3835Mutation(s): 0 
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Find proteins for N9DYI8 (Acinetobacter beijerinckii ANC 3835)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35C [auth 2]64Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36D [auth 3]38Acinetobacter sp. ANC 4470Mutation(s): 0 
UniProt
Find proteins for A0A1Y3CHB1 (Acinetobacter sp. ANC 4470)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2G [auth C]274Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3H [auth D]212Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4I [auth E]200Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5J [auth F]178Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6K [auth G]177Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9L [auth H]148Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13M [auth I]142Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14N [auth J]122Acinetobacter variabilisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15O [auth K]146Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16P [auth L]137Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17Q [auth M]125Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18R [auth N]116Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19S [auth O]122Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20T [auth P]119Acinetobacter baumanniiMutation(s): 0 
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Find proteins for V5VGC9 (Acinetobacter baumannii)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21U [auth Q]103Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22V [auth R]109Acinetobacter sp. 809848Mutation(s): 0 
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Find proteins for A0A009QSN8 (Acinetobacter sp. 809848)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23W [auth S]106Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24X [auth T]105Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25Y [auth U]98Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27Z [auth V]85Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28AA [auth W]78Acinetobacter rudis CIP 110305Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29BA [auth X]65Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30CA [auth Y]58Acinetobacter sp. CIP 102082Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32DA [auth Z]61Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2FA [auth b]250Acinetobacter baumanniiMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3GA [auth c]250Acinetobacter baumanniiMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4HA [auth d]208Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5IA [auth e]165Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6JA [auth f]127Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7KA [auth g]156Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8LA [auth h]131Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9MA [auth i]128Acinetobacter baumanniiMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10NA [auth j]103Acinetobacter sp. ANC 5600Mutation(s): 0 
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Find proteins for A0A1T1GZ10 (Acinetobacter sp. ANC 5600)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11OA [auth k]128Acinetobacter sp. 263903-1Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12PA [auth l]124Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13QA [auth m]118Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14RA [auth n]101Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15SA [auth o]89Acinetobacter baumannii AB0057Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16TA [auth p]101Acinetobacter baumanniiMutation(s): 0 
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Find proteins for A0A1V3DIZ9 (Acinetobacter baumannii)
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UniProt GroupA0A1V3DIZ9
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17UA [auth q]85Acinetobacter baumannii AB0057Mutation(s): 0 
UniProt
Find proteins for B7IA30 (Acinetobacter baumannii (strain AB0057))
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UniProt GroupB7IA30
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18VA [auth r]75Acinetobacter venetianusMutation(s): 0 
UniProt
Find proteins for A0A150HZL5 (Acinetobacter venetianus)
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UniProt GroupA0A150HZL5
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19WA [auth s]91Acinetobacter baumannii AB0057Mutation(s): 0 
UniProt
Find proteins for B7IA35 (Acinetobacter baumannii (strain AB0057))
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UniProt GroupB7IA35
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20XA [auth t]88Acinetobacter baumannii AB0057Mutation(s): 0 
UniProt
Find proteins for B7I5N9 (Acinetobacter baumannii (strain AB0057))
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UniProt GroupB7I5N9
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S21YA [auth u]71Acinetobacter sp. 263903-1Mutation(s): 0 
UniProt
Find proteins for A0A062C3F9 (Acinetobacter sp. 263903-1)
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UniProt GroupA0A062C3F9
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Entity ID: 5
MoleculeChains LengthOrganismImage
23s ribosomal RNAE [auth AN1]2,918Acinetobacter baumannii AB0057
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Entity ID: 6
MoleculeChains LengthOrganismImage
5s ribosomal RNAF [auth B]115Acinetobacter baumannii
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Entity ID: 31
MoleculeChains LengthOrganismImage
16s Ribosomal RNAEA [auth sN1]1,544Acinetobacter baumannii AB0057
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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ZA [auth 3]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth AN1]
AC [auth AN1]
AE [auth sN1]
BB [auth AN1]
BC [auth AN1]
AB [auth AN1],
AC [auth AN1],
AE [auth sN1],
BB [auth AN1],
BC [auth AN1],
BD [auth sN1],
BE [auth sN1],
CB [auth AN1],
CC [auth AN1],
CD [auth sN1],
CE [auth sN1],
DB [auth AN1],
DC [auth AN1],
DD [auth sN1],
DE [auth sN1],
EB [auth AN1],
EC [auth AN1],
ED [auth sN1],
EE [auth sN1],
FB [auth AN1],
FC [auth AN1],
FD [auth sN1],
FE [auth sN1],
GB [auth AN1],
GC [auth AN1],
GD [auth sN1],
GE [auth sN1],
HB [auth AN1],
HC [auth AN1],
HD [auth sN1],
HE [auth sN1],
IB [auth AN1],
IC [auth AN1],
ID [auth sN1],
IE [auth sN1],
JB [auth AN1],
JC [auth AN1],
JD [auth sN1],
JE [auth sN1],
KB [auth AN1],
KC [auth AN1],
KD [auth sN1],
KE [auth sN1],
LB [auth AN1],
LC [auth AN1],
LD [auth sN1],
LE [auth sN1],
MB [auth AN1],
MC [auth AN1],
MD [auth sN1],
ME [auth sN1],
NB [auth AN1],
NC [auth AN1],
ND [auth sN1],
NE [auth sN1],
OB [auth AN1],
OC [auth AN1],
OD [auth sN1],
OE [auth sN1],
PB [auth AN1],
PC [auth AN1],
PD [auth sN1],
PE [auth sN1],
QB [auth AN1],
QC [auth AN1],
QD [auth sN1],
RB [auth AN1],
RC [auth AN1],
RD [auth sN1],
SB [auth AN1],
SC [auth AN1],
SD [auth sN1],
TB [auth AN1],
TC [auth AN1],
TD [auth sN1],
UB [auth AN1],
UC [auth AN1],
UD [auth sN1],
VB [auth AN1],
VC [auth AN1],
VD [auth sN1],
WB [auth AN1],
WC [auth AN1],
WD [auth sN1],
XB [auth AN1],
XC [auth AN1],
XD [auth sN1],
YB [auth AN1],
YC [auth AN1],
YD [auth sN1],
ZB [auth AN1],
ZC [auth AN1],
ZD [auth sN1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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AD [auth AN1]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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: 2020-02-05
    Type: Initial release