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- PDB-9lwi: The head region of HBx-Smc5/6 ubiquitination complex -

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Basic information

Entry
Database: PDB / ID: 9lwi
TitleThe head region of HBx-Smc5/6 ubiquitination complex
Components
  • (Non-structural maintenance of chromosomes element ...) x 2
  • (Structural maintenance of chromosomes protein ...) x 2
  • Cullin-4A
  • DNA damage-binding protein 1
  • E3 ubiquitin-protein ligase RBX1
  • EP300-interacting inhibitor of differentiation 3
  • Protein X
KeywordsANTIVIRAL PROTEIN / HBx / Smc5/6 / Cul4A-RBx / HBV
Function / homology
Function and homology information


sex chromosome / cellular response to radiation / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of mitotic cytokinesis / positive regulation of chromosome segregation / Smc5-Smc6 complex / DNA secondary structure binding / symbiont-mediated activation of host NF-kappaB cascade / regulation of miRNA-mediated gene silencing / symbiont-mediated arrest of host cell cycle during G2/M transition ...sex chromosome / cellular response to radiation / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of mitotic cytokinesis / positive regulation of chromosome segregation / Smc5-Smc6 complex / DNA secondary structure binding / symbiont-mediated activation of host NF-kappaB cascade / regulation of miRNA-mediated gene silencing / symbiont-mediated arrest of host cell cycle during G2/M transition / interchromatin granule / regulation of cell cycle phase transition / regulation of stem cell population maintenance / cellular response to hydroxyurea / regulation of natural killer cell activation / host-mediated suppression of viral genome replication / negative regulation of adipose tissue development / negative regulation of beige fat cell differentiation / regulation of cellular response to stress / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / chromatin looping / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / cellular response to chemical stress / positive regulation of protein autoubiquitination / positive regulation by virus of viral protein levels in host cell / RNA polymerase II transcription initiation surveillance / telomere maintenance via recombination / protein neddylation / spindle assembly involved in female meiosis / epigenetic programming in the zygotic pronuclei / NEDD8 ligase activity / regulation of telomere maintenance / negative regulation of response to oxidative stress / UV-damage excision repair / protein K27-linked ubiquitination / regulation of DNA-templated DNA replication initiation / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / biological process involved in interaction with symbiont / mitotic spindle pole / Cul3-RING ubiquitin ligase complex / regulation of mitotic cell cycle phase transition / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / WD40-repeat domain binding / negative regulation of mitophagy / Prolactin receptor signaling / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / Cul4B-RING E3 ubiquitin ligase complex / ectopic germ cell programmed cell death / ubiquitin ligase complex scaffold activity / replication fork processing / viral release from host cell / regulation of embryonic development / protein sumoylation / chromosome, centromeric region / protein monoubiquitination / cullin family protein binding / host cell mitochondrion / positive regulation of viral genome replication / SUMOylation of DNA damage response and repair proteins / signal transduction in response to DNA damage / site of DNA damage / Nuclear events stimulated by ALK signaling in cancer / protein K48-linked ubiquitination / positive regulation of gluconeogenesis / negative regulation of insulin receptor signaling pathway / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / intrinsic apoptotic signaling pathway / post-translational protein modification / epigenetic regulation of gene expression / viral genome replication / positive regulation of protein ubiquitination / negative regulation of canonical NF-kappaB signal transduction / cellular response to amino acid stimulus / regulation of autophagy / Regulation of BACH1 activity / T cell activation / sperm end piece / sperm principal piece / G1/S transition of mitotic cell cycle / nucleotide-excision repair / proteasomal protein catabolic process / negative regulation of canonical Wnt signaling pathway / Degradation of DVL / Degradation of CRY and PER proteins / cell population proliferation / Degradation of GLI1 by the proteasome
Similarity search - Function
Transactivation protein X / Trans-activation protein X / Non-structural maintenance of chromosomes element 1 / Zinc finger, RING-like / Nse1 non-SMC component of SMC5-6 complex / RING-like domain / Non-structural maintenance of chromosome element 4, C-terminal / Nse4/EID family / Nse4/EID protein, Nse3/MAGE-binding domain / Nse4 C-terminal ...Transactivation protein X / Trans-activation protein X / Non-structural maintenance of chromosomes element 1 / Zinc finger, RING-like / Nse1 non-SMC component of SMC5-6 complex / RING-like domain / Non-structural maintenance of chromosome element 4, C-terminal / Nse4/EID family / Nse4/EID protein, Nse3/MAGE-binding domain / Nse4 C-terminal / Binding domain of Nse4/EID3 to Nse3-MAGE / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein neddylation domain / Cullin, conserved site / Cullin family signature. / Cullin, N-terminal / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin alpha solenoid domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / : / RSE1/DDB1/CPSF1 second beta-propeller / Cleavage/polyadenylation specificity factor, A subunit, C-terminal / Cleavage/polyadenylation specificity factor, A subunit, N-terminal / : / CPSF A subunit region / RSE1/DDB1/CPSF1 first beta-propeller / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / Cullin-4A / DNA damage-binding protein 1 / Protein X / Structural maintenance of chromosomes protein 5 / EP300-interacting inhibitor of differentiation 3 / Non-structural maintenance of chromosomes element 1 homolog / Non-structural maintenance of chromosomes element 3 homolog / Structural maintenance of chromosomes protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 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
B: DNA damage-binding protein 1
C: Protein X
D: EP300-interacting inhibitor of differentiation 3
E: Non-structural maintenance of chromosomes element 3 homolog
F: Non-structural maintenance of chromosomes element 1 homolog
G: Cullin-4A
H: E3 ubiquitin-protein ligase RBX1
I: Structural maintenance of chromosomes protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)603,26215
Polymers602,8699
Non-polymers3926
Water00
1


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

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Components

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Structural maintenance of chromosomes protein ... , 2 types, 2 molecules AI

#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
#9: 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

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Protein , 5 types, 5 molecules BCDGH

#2: Protein DNA damage-binding protein 1 / DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / ...DDB p127 subunit / DNA damage-binding protein a / DDBa / Damage-specific DNA-binding protein 1 / HBV X-associated protein 1 / XAP-1 / UV-damaged DNA-binding factor / UV-damaged DNA-binding protein 1 / UV-DDB 1 / XPE-binding factor / XPE-BF / Xeroderma pigmentosum group E-complementing protein / XPCe


Mass: 127097.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDB1, XAP1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16531
#3: Protein Protein X / HBx / Peptide X / pX


Mass: 16587.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis B virus / Gene: X, x / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q2F514
#4: Protein EP300-interacting inhibitor of differentiation 3 / EID-3 / E1A-like inhibitor of differentiation 3 / EID-1-like inhibitor of differentiation 3 / Non- ...EID-3 / E1A-like inhibitor of differentiation 3 / EID-1-like inhibitor of differentiation 3 / Non-structural maintenance of chromosomes element 4 homolog B / NS4EB / Non-SMC element 4 homolog B


Mass: 38213.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EID3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8N140
#7: Protein Cullin-4A / CUL-4A


Mass: 87871.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL4A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13619
#8: Protein E3 ubiquitin-protein ligase RBX1 / E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / ...E3 ubiquitin-protein transferase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / Rbx1 / Regulator of cullins 1 / ROC1


Mass: 12289.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P62877, RING-type E3 ubiquitin transferase, cullin-RING-type E3 NEDD8 transferase

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Non-structural maintenance of chromosomes element ... , 2 types, 2 molecules EF

#5: Protein Non-structural maintenance of chromosomes element 3 homolog / Non-SMC element 3 homolog / Hepatocellular carcinoma-associated protein 4 / MAGE-G1 antigen / ...Non-SMC element 3 homolog / Hepatocellular carcinoma-associated protein 4 / MAGE-G1 antigen / Melanoma-associated antigen G1 / Necdin-like protein 2


Mass: 34361.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSMCE3, HCA4, MAGEG1, NDNL2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96MG7
#6: Protein Non-structural maintenance of chromosomes element 1 homolog / Non-SMC element 1 homolog


Mass: 30903.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NSMCE1, HSPC333, HSPC337 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8WV22, RING-type E3 ubiquitin transferase

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Non-polymers , 1 types, 6 molecules

#10: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
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: The head region of HBx-Smc5/6 ubiquitination complex / Type: COMPLEX / Entity ID: #1-#9 / 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: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 401828 / Symmetry type: POINT

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