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



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: 10.1128/mBio.03117-19
  • Structures With Same Primary Citation

  • 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 ...

    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 edward.w.yu@case.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
0
51Acinetobacter sp. CIP 51.11Mutation(s): 0 
Gene Names: rpmGF894_00620
Find proteins for N9PPR9 (Acinetobacter sp. CIP 51.11)
Go to UniProtKB:  N9PPR9

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
1
44Acinetobacter beijerinckii ANC 3835Mutation(s): 0 
Gene Names: rpmHF934_02549
Find proteins for N9DYI8 (Acinetobacter beijerinckii ANC 3835)
Go to UniProtKB:  N9DYI8

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
2
64Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpmIAB57_0700
Find proteins for B7I693 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7I693

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
3
38Acinetobacter sp. ANC 4470Mutation(s): 0 
Gene Names: rpmJB9T25_11870
Find proteins for A0A1Y3CHB1 (Acinetobacter sp. ANC 4470)
Go to UniProtKB:  A0A1Y3CHB1

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
274Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplBAB57_3527
Find proteins for B7IA36 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA36

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
212Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplCAB57_3530
Find proteins for B7IA39 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA39

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
200Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplDAB57_3529
Find proteins for B7IA38 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA38

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
178Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplEAB57_3518
Find proteins for B7IA27 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA27

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
177Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplFAB57_3515
Find proteins for B7IA24 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA24

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
148Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplIAB57_2511
Find proteins for B7IBC3 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IBC3

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
I
142Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplMAB57_3451
Find proteins for B7I9B0 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7I9B0

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
J
122Acinetobacter sp. NIPH 899Mutation(s): 0 
Gene Names: rplNF969_03557
Find proteins for N8WQT6 (Acinetobacter sp. NIPH 899)
Go to UniProtKB:  N8WQT6

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
K
146Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplOAB57_3511
Find proteins for B7IA20 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA20

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
L
137Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplPAB57_3523
Find proteins for B7IA32 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA32

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
M
125Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplQAB57_3504
Find proteins for B7IA13 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA13

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
N
116Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplRAB57_3514
Find proteins for B7IA23 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA23

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
O
122Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplSAB57_3615
Find proteins for B7IAS9 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IAS9

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
Q
103Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplUAB57_3151
Find proteins for B7I6V9 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7I6V9

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
R
109Acinetobacter sp. 809848Mutation(s): 0 
Gene Names: rplVJ536_1647
Find proteins for A0A009QSN8 (Acinetobacter sp. 809848)
Go to UniProtKB:  A0A009QSN8

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
S
106Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplWAB57_3528
Find proteins for B7IA37 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA37

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
T
105Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplXAB57_3519
Find proteins for B7IA28 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA28

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
U
98Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rplYAB57_0881
Find proteins for B7I7B6 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7I7B6

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
V
85Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpmAAB57_3150
Find proteins for B7I6V8 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7I6V8

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
X
65Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpmCAB57_3522
Find proteins for B7IA31 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA31

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Y
58Acinetobacter sp. CIP 102082Mutation(s): 0 
Gene Names: rpmDF970_01629
Find proteins for N8V730 (Acinetobacter sp. CIP 102082)
Go to UniProtKB:  N8V730

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
Z
61Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpmFAB57_0869
Find proteins for B7I7A4 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7I7A4

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
208Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsDAB57_3506
Find proteins for B7IA15 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA15

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
165Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsEAB57_3513
Find proteins for B7IA22 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA22

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
127Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsFAB57_2509
Find proteins for B7IBC1 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IBC1

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
156Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsGAB57_0912
Find proteins for B7I7S0 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7I7S0

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
131Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsHAB57_3516
Find proteins for B7IA25 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA25

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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
103Acinetobacter sp. ANC 5600Mutation(s): 0 
Gene Names: rpsJB1201_04115
Find proteins for A0A1T1GZ10 (Acinetobacter sp. ANC 5600)
Go to UniProtKB:  A0A1T1GZ10

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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
128Acinetobacter sp. 263903-1Mutation(s): 0 
Gene Names: rpsKJ577_0021
Find proteins for A0A062C259 (Acinetobacter sp. 263903-1)
Go to UniProtKB:  A0A062C259

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
124Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsLAB57_0911
Find proteins for B7I7R9 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7I7R9

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
118Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsMAB57_3508
Find proteins for B7IA17 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA17

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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
n
101Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsNAB57_3517
Find proteins for B7IA26 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA26

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
89Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsOAB57_0438
Find proteins for B7I3U0 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7I3U0

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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
101Acinetobacter baumanniiMutation(s): 0 
Gene Names: rpsPB4R90_06690B9W69_03135B9X95_19530
Find proteins for A0A1V3DIZ9 (Acinetobacter baumannii)
Go to UniProtKB:  A0A1V3DIZ9

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
75Acinetobacter venetianusMutation(s): 0 
Gene Names: rpsRAVENLUH13518_00382AVENLUH5627_01667AYL20_00180
Find proteins for A0A150HZL5 (Acinetobacter venetianus)
Go to UniProtKB:  A0A150HZL5

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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
91Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsSAB57_3526
Find proteins for B7IA35 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA35

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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
88Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsTAB57_1842
Find proteins for B7I5N9 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7I5N9

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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
u
71Acinetobacter sp. 263903-1Mutation(s): 0 
Gene Names: rpsUJ577_0524
Find proteins for A0A062C3F9 (Acinetobacter sp. 263903-1)
Go to UniProtKB:  A0A062C3F9

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
W
78Acinetobacter rudis CIP 110305Mutation(s): 0 
Gene Names: rpmBF945_00480
Find proteins for S3NQR5 (Acinetobacter rudis CIP 110305)
Go to UniProtKB:  S3NQR5

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
85Acinetobacter baumannii AB0057Mutation(s): 0 
Gene Names: rpsQAB57_3521
Find proteins for B7IA30 (Acinetobacter baumannii (strain AB0057))
Go to UniProtKB:  B7IA30

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Entity ID: 5
MoleculeChainsLengthOrganism
23s ribosomal RNAAN12918Acinetobacter baumannii AB0057

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Entity ID: 6
MoleculeChainsLengthOrganism
5s ribosomal RNAB115Acinetobacter baumannii

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Entity ID: 31
MoleculeChainsLengthOrganism
16s Ribosomal RNAsN11544Acinetobacter baumannii AB0057
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
3
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
AN1, sN1
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
AN1
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.91 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-11-25 
  • Released Date: 2020-02-05 
  • Deposition Author(s): Morgan, C.E., Yu, E.W.

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

Revision History 

  • Version 1.0: 2020-02-05
    Type: Initial release