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- PDB-9lwk: The hinge-arm region of HBx-Smc5/6 ubiquitination complex -

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Basic information

Entry
Database: PDB / ID: 9lwk
TitleThe hinge-arm region of HBx-Smc5/6 ubiquitination complex
Components
  • Structural maintenance of chromosomes protein 5
  • Structural maintenance of chromosomes protein 6
KeywordsDNA BINDING PROTEIN / Smc5/6
Function / homology
Function and homology information


sex chromosome / positive regulation of maintenance of mitotic sister chromatid cohesion / mitotic cell cycle phase transition / positive regulation of chromosome segregation / Smc5-Smc6 complex / DNA secondary structure binding / interchromatin granule / host-mediated suppression of viral genome replication / protein localization to chromosome, centromeric region / chromatin looping ...sex chromosome / positive regulation of maintenance of mitotic sister chromatid cohesion / mitotic cell cycle phase transition / positive regulation of chromosome segregation / Smc5-Smc6 complex / DNA secondary structure binding / interchromatin granule / host-mediated suppression of viral genome replication / protein localization to chromosome, centromeric region / chromatin looping / telomere maintenance via recombination / chromosome condensation / regulation of telomere maintenance / mitotic spindle pole / stem cell population maintenance / protein sumoylation / chromosome, centromeric region / SUMOylation of DNA damage response and repair proteins / chromosome segregation / PML body / double-strand break repair via homologous recombination / cellular senescence / cell junction / single-stranded DNA binding / site of double-strand break / damaged DNA binding / chromosome, telomeric region / nuclear speck / cell division / DNA damage response / ubiquitin protein ligase binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Structural maintenance of chromosomes protein 5 / Structural maintenance of chromosomes protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.32 Å
AuthorsTong, C. / Lili, D. / Hongshuai, L. / Jinhong, Z. / Qian, X. / Lanfeng, W.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFA1303600 China
CitationJournal: Cell Res / Year: 2026
Title: Structural and functional insights into HBx-Smc6 targeting for HBV inhibition.
Authors: Tong Cheng / Jinhong Zhou / Wenjun Huang / Lili Du / Pengyu He / Renzheng Yang / Yan Gao / Menghan Hao / Kongying Hu / Jieliang Chen / Hongxia Wang / Zihe Rao / Zhenghong Yuan / Lanfeng Wang /
History
DepositionFeb 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 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

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Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 6
I: Structural maintenance of chromosomes protein 5


Theoretical massNumber of molelcules
Total (without water)255,5452
Polymers255,5452
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 Structural maintenance of chromosomes protein 6 / SMC protein 6 / SMC-6 / hSMC6


Mass: 126530.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC6, SMC6L1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SB8
#2: Protein Structural maintenance of chromosomes protein 5 / SMC protein 5 / SMC-5 / hSMC5


Mass: 129014.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC5, KIAA0594, SMC5L1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IY18
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: The hinge-arm region of HBx-Smc5/6 ubiquitination complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 48.5 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 7.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29615 / Symmetry type: POINT

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