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- EMDB-10898: Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-10898
TitleAcinetobacter baumannii ribosome-tigecycline complex - 50S subunit
Map data
SampleAcinetobacter baumannii ribosome-tigecycline complex - 50S subunit:
(50S ribosomal protein ...) x 28 / (nucleic-acidNucleic acid) x 3 / (ligand) x 3
Function / homology
Function and homology information


large ribosomal subunit / ribosomal large subunit assembly / 5S rRNA binding / transferase activity / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / metal ion binding
Similarity search - Function
Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site ...Ribosomal protein L31 type A / Ribosomal protein L25, short-form / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L6 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L17 signature. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28 / Ribosomal protein L33 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L35 signature. / Ribosomal protein L5, bacterial-type / Ribosomal protein L34 signature. / Ribosomal protein L19 signature. / Ribosomal protein L19, conserved site / Ribosomal protein L34, conserved site / Ribosomal protein L18, bacterial-type / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L36 / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L20 signature. / Ribosomal protein L6, bacterial-type / Ribosomal protein L14P, bacterial-type / Ribosomal L28 family / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L35 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L18 / Ribosomal protein L20 / L28p-like / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal L32p protein family / Ribosomal L27 protein / Ribosomal protein L27 / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L34 / Ribosomal protein L21 / Ribosomal protein L34 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 superfamily / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L20 / Ribosomal protein L32p / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L21-like / Ribosomal protein L17 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L13, bacterial-type / Ribosomal protein L24 / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / Ribosomal protein L5, conserved site / Ribosomal protein L5 signature. / Ribosomal protein L5, N-terminal / Ribosomal protein L5 / Ribosomal protein L15 signature. / Ribosomal protein L15, conserved site / ribosomal L5P family C-terminus / Ribosomal protein L5, C-terminal / Ribosomal protein L22 signature. / Ribosomal protein L22/L17, conserved site / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6, alpha-beta domain superfamily / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L14 signature. / Ribosomal protein L14P, conserved site / Ribosomal protein L2, domain 3 / Ribosomal L29 protein
Similarity search - Domain/homology
50S ribosomal protein L30 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L17 / 50S ribosomal protein L15 / 50S ribosomal protein L36 / 50S ribosomal protein L29 / 50S ribosomal protein L21 ...50S ribosomal protein L30 / 50S ribosomal protein L24 / 50S ribosomal protein L5 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L17 / 50S ribosomal protein L15 / 50S ribosomal protein L36 / 50S ribosomal protein L29 / 50S ribosomal protein L21 / 50S ribosomal protein L27 / 50S ribosomal protein L34 / 50S ribosomal protein L14 / 50S ribosomal protein L2 / 50S ribosomal protein L16 / 50S ribosomal protein L22 / 50S ribosomal protein L23 / 50S ribosomal protein L4 / 50S ribosomal protein L3 / 50S ribosomal protein L19 / 50S ribosomal protein L31 / 50S ribosomal protein L33 / 50S ribosomal protein L28 / 50S ribosomal protein L35 / 50S ribosomal protein L20 / 50S ribosomal protein L25 / 50S ribosomal protein L32 / 50S ribosomal protein L13
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria) / Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsNicholson D / Edwards TA / O'Neill AJ / Ranson NA
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust203743/Z/16/Z United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: Structure / Year: 2020
Title: Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics.
Authors: David Nicholson / Thomas A Edwards / Alex J O'Neill / Neil A Ranson /
Abstract: Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and ...Acinetobacter baumannii is a Gram-negative bacterium primarily associated with hospital-acquired, often multidrug-resistant (MDR) infections. The ribosome-targeting antibiotics amikacin and tigecycline are among the limited arsenal of drugs available for treatment of such infections. We present high-resolution structures of the 70S ribosome from A. baumannii in complex with these antibiotics, as determined by cryoelectron microscopy. Comparison with the ribosomes of other bacteria reveals several unique structural features at functionally important sites, including around the exit of the polypeptide tunnel and the periphery of the subunit interface. The structures also reveal the mode and site of interaction of these drugs with the ribosome. This work paves the way for the design of new inhibitors of translation to address infections caused by MDR A. baumannii.
History
DepositionApr 22, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateOct 14, 2020-
Current statusOct 14, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ysi
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_10898.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 400 pix.
= 426. Å
1.07 Å/pix.
x 400 pix.
= 426. Å
1.07 Å/pix.
x 400 pix.
= 426. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.27180347 - 0.576126
Average (Standard dev.)0.00060091226 (±0.012268005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 426.00003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z426.000426.000426.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.2720.5760.001

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Supplemental data

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Segmentation: #1

Fileemd_10898_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Acinetobacter baumannii ribosome-tigecycline complex, consensus map filtered by...

Fileemd_10898_additional.map
AnnotationAcinetobacter baumannii ribosome-tigecycline complex, consensus map filtered by local resolution
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit, half...

Fileemd_10898_half_map_1.map
AnnotationAcinetobacter baumannii ribosome-tigecycline complex - 50S subunit, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit, half...

Fileemd_10898_half_map_2.map
AnnotationAcinetobacter baumannii ribosome-tigecycline complex - 50S subunit, half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit

EntireName: Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit
Number of components: 35

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Component #1: protein, Acinetobacter baumannii ribosome-tigecycline complex - 5...

ProteinName: Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit
Recombinant expression: No
SourceSpecies: Acinetobacter baumannii (bacteria)

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Component #2: protein, 50S ribosomal protein L2

ProteinName: 50S ribosomal protein L2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.319092 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #3: protein, 50S ribosomal protein L3

ProteinName: 50S ribosomal protein L3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.512639 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #4: protein, 50S ribosomal protein L4

ProteinName: 50S ribosomal protein L4 / Details: residues 2-12 modelled without side chains / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.583904 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #5: protein, 50S ribosomal protein L5

ProteinName: 50S ribosomal protein L5 / Details: modelled without side chains / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.051471 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #6: protein, 50S ribosomal protein L6

ProteinName: 50S ribosomal protein L6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.126047 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #7: protein, 50S ribosomal protein L13

ProteinName: 50S ribosomal protein L13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.95144 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #8: protein, 50S ribosomal protein L14

ProteinName: 50S ribosomal protein L14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.523863 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #9: protein, 50S ribosomal protein L15

ProteinName: 50S ribosomal protein L15 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.509915 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #10: protein, 50S ribosomal protein L16

ProteinName: 50S ribosomal protein L16 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.498312 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #11: protein, 50S ribosomal protein L17

ProteinName: 50S ribosomal protein L17 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.02123 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #12: protein, 50S ribosomal protein L18

ProteinName: 50S ribosomal protein L18 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.443341 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #13: protein, 50S ribosomal protein L19

ProteinName: 50S ribosomal protein L19 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.619865 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #14: protein, 50S ribosomal protein L20

ProteinName: 50S ribosomal protein L20 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.468946 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #15: protein, 50S ribosomal protein L21

ProteinName: 50S ribosomal protein L21 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.496364 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #16: protein, 50S ribosomal protein L22

ProteinName: 50S ribosomal protein L22 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.960126 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #17: protein, 50S ribosomal protein L23

ProteinName: 50S ribosomal protein L23 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.607392 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #18: protein, 50S ribosomal protein L24

ProteinName: 50S ribosomal protein L24 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.187929 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #19: protein, 50S ribosomal protein L25

ProteinName: 50S ribosomal protein L25 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.914539 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #20: protein, 50S ribosomal protein L27

ProteinName: 50S ribosomal protein L27 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.072387 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #21: protein, 50S ribosomal protein L28

ProteinName: 50S ribosomal protein L28 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 9.125756 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #22: protein, 50S ribosomal protein L29

ProteinName: 50S ribosomal protein L29 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.449678 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #23: protein, 50S ribosomal protein L30

ProteinName: 50S ribosomal protein L30 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.654788 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #24: protein, 50S ribosomal protein L31

ProteinName: 50S ribosomal protein L31 / Details: modelled without side chains / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.343693 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #25: protein, 50S ribosomal protein L32

ProteinName: 50S ribosomal protein L32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.096888 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #26: protein, 50S ribosomal protein L33

ProteinName: 50S ribosomal protein L33 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.10531 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #27: protein, 50S ribosomal protein L34

ProteinName: 50S ribosomal protein L34 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 5.192247 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #28: nucleic-acid, 23S ribosomal RNA

nucleic acidName: 23S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence: AGUCAAGUAA UUAAGUGCAU GUGGUGGAUG CCUUGGCAGU CAGAGGCGAU GAAAGACGUG AUAGCCUGCG AAAAGCUCCG GGGAGGCGGC AAAUAUCCUU UGAUCCGGAG AUGUCUGAAU GGGGGAACCC ACCUACUUUA AGGUAGGUAU UGCAACAUGA AUACAUAGUG ...Sequence:
AGUCAAGUAA UUAAGUGCAU GUGGUGGAUG CCUUGGCAGU CAGAGGCGAU GAAAGACGUG AUAGCCUGCG AAAAGCUCCG GGGAGGCGGC AAAUAUCCUU UGAUCCGGAG AUGUCUGAAU GGGGGAACCC ACCUACUUUA AGGUAGGUAU UGCAACAUGA AUACAUAGUG UUGCAAGGCG AACGAGGGGA AGUGAAACAU CUCAGUACCC UUAGGAAAAG AAAUCAAUUG AGAUUCCCUC AGUAGCGGCG AGCGAACGGG GAUCAGCCCA UUAAGUUAUG UGUGUUUUAG UGGAACGCUC UGGGAAGUGC GAACGUAGAG GGUGAUAUUC CCGUACACGA AAGGGCACAC AUAAUGAUGA CGAGUAGGGC GAGGCACGUG AAACCUUGUC UGAAUAUGGG GGGACCAUCC UCCAAGGCUA AAUACUCCUG ACUGACCGAU AGUGAACCAG UACCGUGAGG GAAAGGCGAA AAGAACCCCU GUGAGGGGAG UGAAAUAGAU CCUGAAACCG CAUGCAUACA AGCAGUGGGA GCACCUUUGU GGUGUGACUG CGUACCUUUU GUAUAAUGGG UCAGCGACUU AUAUUCAGUA GCGAGGUUAA CCGUAUAGGG GAGCCGUAGA GAAAUCGAGU CUUAAUAGGG CGUUUAGUUG CUGGGUAUAG ACCCGAAACC AGGCGAUCUA UCCAUGAGCA GGUUGAAGGU UGGGUAACAC UAACUGGAGG ACCGAACCCA CUGUCGUUGA AAAGCCAGGG GAUGACUUGU GGAUAGGGGU GAAAGGCUAA UCAAGCCUGG UGAUAGCUGG UUCUCCCCGA AAGCUAUUUA GGUAGCGCCU CGGACGAAUA CCAUAGGGGG UAGAGCACUG UUUCGGCUAG GGGGUCAUCC CGACUUACCA AACCGAUGCA AACUCCGAAU ACCUAUGAGU ACUAUCCGGG AGACAGACUG CGGGUGCUAA CGUCCGUAGU CAAGAGGAAA ACAAUCCAGA CCGCCAGCUA AGGCCCCAAA AUCAUAGUUA AGUGGGAAAC GAUGUGGGAA GGCAUAGACA GCUAGGAGGU UGGCUUAGAA GCAGCCACCC UUUAAAGAAA GCGUAAUAGC UCACUAGUCG AGUCGGCCUG CGCGGAAGAU GUAACGGGGC UAAAACUAUG UGCCGAAGCU GCGGAUGUAU ACUUUGUAUA CGUGGUAGGG GAGCGUUCUG UAAGCCGAUG AAGGUGUGUU GAGAAGCAUG CUGGAGGUAU CAGAAGUGCG AAUGCUGACG UGAGUAACGA CAAAACGGGU GAAAAACCCG UUCGCCGAAA GACCAAGGGU UCCAGUCCAA CGUUAAUCGG GGCUGGGUGA GUCGACCCCU AAGGCGAGGC CGAAAGGCGU AGUCGAUGGG AAAAUGGUUA AUAUUCCAUU ACUUCUGUGU AAUGCGAUGA GAGGACGGAG AAGGCUAAAU CAGCCUGGCG UUGGUUGUCC AGGUGAAAGG AUGUAGGCAU GUAUCUUAGG CAAAUCCGGG GUACUCUAUG CUGAGAUCUG AUAGCAAGCU GUACUUGUAC AGCGAAGUGG UUGAUGCCAU GCUUCCAGGA AAAGUCUCUA AGCUUCAGUU ACACAGGAAU CGUACCCGAA ACCGACACAG GUGGUCAGGU CGAGUAGACC AAGGCGCUUG AGAGAACUCU GCUGAAGGAA CUAGGCAAAA UGGUACCGUA ACUUCGGGAG AAGGUACGCU GUUGUUGGUG AUGGAACUCG CUUCCUGAGC UGACGACAGC CGCAGAAACC AGGCCGCUGC AACUGUUUAU UAAAAACAUA GCACUCUGCA AACACGAAAG UGGACGUAUA GGGUGUGAUG CCUGCCCGGU GCUGGAAGGU UAAUUGAUGG GGUUAGCGUA AGCGAAGCUC UUGAUCGAAG CCCCAGUAAA CGGCGGCCGU AACUAUAACG GUCCUAAGGU AGCGAAAUUC CUUGUCGGGU AAGUUCCGAC CUGCACGAAU GGCAUAAUGA UGGCGGCGCU GUCUCCAGCA GAGGCUCAGU GAAAUCGAAA UCGCUGUGAA GAUGCAGUGU ACCCGCGGCU AGACGGAAAG ACCCCGUGAA CCUUUACUGC AGCUUGACAC UGAACUUUGA CCUUACUUGU GUAGGAUAGG UGGGAGGCUU UGAAGCUGGA ACGCUAGUUC CAGUGGAGCC GUCCUUGAAA UACCACCCUG GUAAUGUUGA GGUUCUAACU CUGUCCCGUG AUCCGGGACG AGGACCGUGU CUGGUGGGUA GUUUGACUGG GGCGGUCUCC UCCUAAAGAG UAACGGAGGA GUACGAAGGU GCGCUCAGCG UGGUCGGAAA UCACGCGUAG AGUAUAAAGG CAAAAGCGCG CUUAACUGCG AGACCCACAA GUCGAGCAGG UACGAAAGUA GGUCUUAGUG AUCCGGUGGU UCUGUAUGGA AGGGCCAUCG CUCAACGGAU AAAAGGUACU CUGGGGAUAA CAGGCUGAUA CCGCCCAAGA GUUCAUAUCG ACGGCGGUGU UUGGCACCUC GAUGUCGGCU CAUCUCAUCC UGGGGCUGAA GCAGGUCCCA AGGGUAUGGC UGUUCGCCAU UUAAAGAGGU ACGCGAGCUG GGUUUAGAAC GUCGUGAGAC AGUUCGGUCC CUAUCUACCG UGGGCGCUGG AAAUUUGAGA GGAUCUGCUC CUAGUACGAG AGGACCAGAG UGGACGAACC UCUGGUGUAC CGGUUGUGAC GCCAGUCGCA UCGCCGGGUA GCUAUGUUCG GAAGGGAUAA CCGCUGAAAG CAUCUAAGCG GGAAGCCUAC CUCAAGAUAA GAUUUCCCUA GGACUUUAUG UCCUCUAAAG AGCCGUUCGA GACUAGGACG UUGAUAGGUU GGAUGUGGAA GCAUAGUGAU AUGUGAAGCU GACCAAUACU AAUUGCUCGU GAGGCUUGAC UAUACAACAC CCA
MassTheoretical: 940.330125 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #29: nucleic-acid, 5S ribosomal RNA

nucleic acidName: 5S ribosomal RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UGCUGGCGAC CAUAGCAAGA GUGAACCACC UGAUCCCUUC CCGAACUCAG AAGUGAAACC UCUUAGCGCU GAUGGUAGUG UGGGAUUACC CAUGUGAGAG UAAGUCAUCG CCAGCUC
MassTheoretical: 37.608344 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #30: nucleic-acid, E-site tRNA

nucleic acidName: E-site tRNA / Class: RNA
Details: E. coli fMet-tRNA from PDB 5AFI fitted into EM density - represents a mixture of tRNAs
Structure: OTHER / Synthetic: No
Sequence:
CGCGGGG(N)GG AGCAGCCUGG (N)AGCUCGUCG GGCUCAUAAC CCGAAGAUCG UCGG(N)(N)CAAA UCCGGCCCCC GCAACCA
MassTheoretical: 24.346498 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #31: protein, 50S ribosomal protein L35

ProteinName: 50S ribosomal protein L35 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.424098 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #32: protein, 50S ribosomal protein L36

ProteinName: 50S ribosomal protein L36 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.276201 kDa
SourceSpecies: Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)

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Component #33: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 162 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #34: ligand, TIGECYCLINE

LigandName: TIGECYCLINE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.587665 kDa

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Component #35: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 62 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 2600.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 231159
3D reconstructionSoftware: RELION / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Multi-body refinement was carried out in RELION 3.0 to obtain the final '50S subunit' reconstruction. The mask used for this procedure is deposited with this entry.
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: correlation coefficient / Refinement space: REAL
Input PDB model: 5MDZ, 5AFI
Chain ID: w
Output model

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