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- PDB-6v3e: Cryo-EM structure of the Acinetobacter baumannii Ribosome: 30S subunit -

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Basic information

Entry
Database: PDB / ID: 6v3e
TitleCryo-EM structure of the Acinetobacter baumannii Ribosome: 30S subunit
Components
  • (30S ribosomal protein ...) x 19
  • 16s Ribosomal RNA
KeywordsRIBOSOME / Acinetobacter baumannii
Function / homology
Function and homology information


ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / small ribosomal subunit / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / RNA binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein S14, bacterial/plastid / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type ...Ribosomal protein S14, bacterial/plastid / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S16 / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S2 signature 2. / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / K Homology domain / K homology RNA-binding domain / Ribosomal protein S10, conserved site / Ribosomal protein S10 signature. / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / Ribosomal protein S14, conserved site / Ribosomal protein S14 signature. / Ribosomal protein S2 signature 1. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19 signature. / Ribosomal protein S10 / : / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S19 / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / S5 double stranded RNA-binding domain profile. / K homology domain superfamily, prokaryotic type / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13, conserved site / Ribosomal protein S13 signature. / Ribosomal protein S13 / 30s ribosomal protein S13, C-terminal / Ribosomal protein S13/S18 / Ribosomal protein S13 family profile. / Ribosomal protein S8 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S15 signature. / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S4/S9 / K homology domain-like, alpha/beta / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain profile. / Ribosomal S11, conserved site / Ribosomal protein S11 signature. / Ribosomal protein S10p/S20e / Ribosomal protein S11 / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS15 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein bS18 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS2
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
Acinetobacter sp. ANC 5600 (bacteria)
Acinetobacter sp. 263903-1 (bacteria)
Acinetobacter venetianus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsMorgan, C.E. / Yu, E.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: mBio / Year: 2020
Title: Cryo-electron Microscopy Structure of the Acinetobacter baumannii 70S Ribosome and Implications for New Antibiotic Development.
Authors: Christopher E Morgan / Wei Huang / Susan D Rudin / Derek J Taylor / James E Kirby / Robert A Bonomo / Edward W Yu /
Abstract: Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is , a Gram-negative opportunistic pathogen that exhibits the ...Antimicrobial resistance is a major health threat as it limits treatment options for infection. At the forefront of this serious issue is , 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 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 and other Gram-negative pathogens and will enable structure-based drug discovery to combat antibiotic-resistant bacterial infections. 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 70S ribosome, revealing several unique species-specific structural features that may facilitate future drug development to combat this recalcitrant bacterial pathogen.
History
DepositionNov 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-21034
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Assembly

Deposited unit
sN1: 16s Ribosomal RNA
b: 30S ribosomal protein S2
c: 30S ribosomal protein S3
d: 30S ribosomal protein S4
e: 30S ribosomal protein S5
f: 30S ribosomal protein S6
g: 30S ribosomal protein S7
h: 30S ribosomal protein S8
i: 30S ribosomal protein S9
j: 30S ribosomal protein S10
k: 30S ribosomal protein S11
l: 30S ribosomal protein S12
m: 30S ribosomal protein S13
n: 30S ribosomal protein S14
o: 30S ribosomal protein S15
p: 30S ribosomal protein S16
q: 30S ribosomal protein S17
r: 30S ribosomal protein S18
s: 30S ribosomal protein S19
t: 30S ribosomal protein S20


Theoretical massNumber of molelcules
Total (without water)781,36320
Polymers781,36320
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 1 types, 1 molecules sN1

#1: RNA chain 16s Ribosomal RNA


Mass: 500297.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: GenBank: CP044356.1

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30S ribosomal protein ... , 19 types, 19 molecules bcdefghijklmnopqrst

#2: Protein 30S ribosomal protein S2


Mass: 27680.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: V5VBC2
#3: Protein 30S ribosomal protein S3


Mass: 27972.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: V5V9N0
#4: Protein 30S ribosomal protein S4


Mass: 23311.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA15
#5: Protein 30S ribosomal protein S5


Mass: 17181.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA22
#6: Protein 30S ribosomal protein S6


Mass: 14986.952 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IBC1
#7: Protein 30S ribosomal protein S7


Mass: 17733.699 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7S0
#8: Protein 30S ribosomal protein S8


Mass: 14250.667 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA25
#9: Protein 30S ribosomal protein S9


Mass: 14287.610 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: V5VBA5
#10: Protein 30S ribosomal protein S10


Mass: 11718.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. ANC 5600 (bacteria) / References: UniProt: A0A1T1GZ10
#11: Protein 30S ribosomal protein S11


Mass: 13558.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter sp. 263903-1 (bacteria) / References: UniProt: A0A062C259
#12: Protein 30S ribosomal protein S12


Mass: 13797.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I7R9
#13: Protein 30S ribosomal protein S13


Mass: 13295.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA17
#14: Protein 30S ribosomal protein S14


Mass: 11438.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA26
#15: Protein 30S ribosomal protein S15


Mass: 10145.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I3U0
#16: Protein 30S ribosomal protein S16


Mass: 11223.060 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter baumannii (bacteria) / References: UniProt: A0A1V3DIZ9
#17: Protein 30S ribosomal protein S17


Mass: 9543.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA30
#18: Protein 30S ribosomal protein S18


Mass: 9009.452 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Acinetobacter venetianus (bacteria) / References: UniProt: A0A150HZL5
#19: Protein 30S ribosomal protein S19


Mass: 10206.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7IA35
#20: Protein 30S ribosomal protein S20


Mass: 9723.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Acinetobacter baumannii (strain AB0057) (bacteria)
Strain: AB0057 / References: UniProt: B7I5N9

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Acinetobacter baumannii Small ribosomal subunit / Type: RIBOSOME / Entity ID: all / Source: NATURAL
Molecular weightValue: 2.3 MDa / Experimental value: NO
Source (natural)Organism: Acinetobacter baumannii AB0057 (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.15_3459refinement
PHENIX1.15_3459refinement
EM software
IDNameCategoryDetails
2Latitudeimage acquisition
4cryoSPARCCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12RELIONclassificationFocused classification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10555 / Symmetry type: POINT
Atomic model buildingPDB-ID: 5AFI

5afi


Accession code: 5AFI / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001655033
ELECTRON MICROSCOPYf_angle_d0.412881899
ELECTRON MICROSCOPYf_chiral_restr0.026710408
ELECTRON MICROSCOPYf_plane_restr0.00284723
ELECTRON MICROSCOPYf_dihedral_angle_d15.221529623

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