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- PDB-9uxl: type II Lamassu, LmuACB from Vibrio cholerae O1 El -

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Basic information

Entry
Database: PDB / ID: 9uxl
Titletype II Lamassu, LmuACB from Vibrio cholerae O1 El
Components
  • ABC-three component systems C-terminal domain-containing protein
  • DUF3732 domain-containing protein
  • Lamassu C
KeywordsDNA BINDING PROTEIN / endonuclease / Structural maintenance of chromosomes (SMC) proteins
Function / homologyProtein of unknown function DUF3732 / ABC-three component system, Middle Component 3 / Protein of unknown function (DUF3732) / ABC-three component (ABC-3C) system Middle Component 3 / ABC-three component systems, C-terminal domain 7 / C-terminal domain 7 of the ABC-three component (ABC-3C) systems / DUF3732 domain-containing protein / ABC-three component systems C-terminal domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsZhao, X. / Li, M. / Li, S. / Feng, Y. / Zhang, K.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Nat.Chem.Biol. / Year: 2026
Title: Structural insights into type-I and type-II Lamassu antiphage systems.
Authors: Li, M. / Zhao, X. / Zhao, X. / Li, D. / Xiong, W. / Gao, Z. / Huang, L. / An, L. / Gao, Y. / Li, S. / Feng, Y. / Zhang, K. / Zhang, Y.
History
DepositionMay 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF3732 domain-containing protein
D: Lamassu C
F: DUF3732 domain-containing protein
C: ABC-three component systems C-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)213,8094
Polymers213,8094
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein DUF3732 domain-containing protein / Lamassu B / Plasmid-related protein / Protein of uncharacterized function (DUF3732)


Mass: 74870.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: D6U24_12495, ERS013200_03521, ERS013201_03641, KIN13_15860, VC_0490
Production host: Escherichia coli (E. coli) / References: UniProt: A0A060KSR0
#2: Protein Lamassu C


Mass: 19483.674 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ERS013200_03522, KIN13_15855 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A655W4S5
#3: Protein ABC-three component systems C-terminal domain-containing protein / Lamassu A


Mass: 44584.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: D6U24_12485, ERS013200_03523, ERS013201_03639, KIN13_15850, VC_0492
Production host: Escherichia coli (E. coli) / References: UniProt: A0A060KT36
Has protein modificationN

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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: Cryo-EM structure of VcLmuACB complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.21 MDa / Experimental value: YES
Source (natural)Organism: Vibrio cholerae (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 1.5 mg/ml / Embedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 52.83 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
8PHENIXmodel refinement
12cryoSPARC2.2classification
13cryoSPARC4.73D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 10027902
3D reconstructionResolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78853 / Symmetry type: POINT
RefinementHighest resolution: 4.07 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415332
ELECTRON MICROSCOPYf_angle_d0.7120716
ELECTRON MICROSCOPYf_dihedral_angle_d5.0432021
ELECTRON MICROSCOPYf_chiral_restr0.0452339
ELECTRON MICROSCOPYf_plane_restr0.0052653

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