9LWJ | pdb_00009lwj

The head-arm region of HBx-Smc5/6 ubiquitination complex

PDB DOI: https://doi.org/10.2210/pdb9LWJ/pdb
EM Map EMD-63447: EMDB EMDataResource

Classification: ANTIVIRAL PROTEIN
Organism(s): Homo sapiens, Hepatitis B virus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-02-15 Released: 2026-04-29
Deposition Author(s): Tong, C., Lili, D., Hongshuai, L., Jinhong, Z., Qian, X., Lanfeng, W.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 7.19 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural and functional insights into HBx-Smc6 targeting for HBV inhibition.

Cheng, T., Zhou, J., Huang, W., Du, L., He, P., Yang, R., Gao, Y., Hao, M., Hu, K., Chen, J., Wang, H., Rao, Z., Yuan, Z., Wang, L.

(2026) Cell Res 36: 629-632

PubMed: 41991645 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-026-01251-7
Primary Citation Related Structures:
9LWI, 9LWJ, 9LWK, 9LWL

Organizational Affiliation

Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.

Macromolecule Content

Total Structure Weight: 631.24 kDa
Atom Count: 33,722
Modeled Residue Count: 4,185
Deposited Residue Count: 5,504
Unique protein chains: 10

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural maintenance of chromosomes protein 6	A	1,091	Homo sapiens	Mutation(s): 0 Gene Names: SMC6, SMC6L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SB8 (Homo sapiens) Explore Q96SB8 Go to UniProtKB: Q96SB8
PHAROS: Q96SB8 GTEx: ENSG00000163029
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96SB8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	B	1,140	Homo sapiens	Mutation(s): 0 Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531 Go to UniProtKB: Q16531
PHAROS: Q16531 GTEx: ENSG00000167986
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16531
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein X	C	154	Hepatitis B virus	Mutation(s): 0 Gene Names: X, x
UniProt
Find proteins for Q2F514 (Hepatitis B virus) Explore Q2F514 Go to UniProtKB: Q2F514
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2F514
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
EP300-interacting inhibitor of differentiation 3	D	333	Homo sapiens	Mutation(s): 0 Gene Names: EID3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N140 (Homo sapiens) Explore Q8N140 Go to UniProtKB: Q8N140
PHAROS: Q8N140 GTEx: ENSG00000255150
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N140
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural maintenance of chromosomes element 3 homolog	E	304	Homo sapiens	Mutation(s): 0 Gene Names: NSMCE3, HCA4, MAGEG1, NDNL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MG7 (Homo sapiens) Explore Q96MG7 Go to UniProtKB: Q96MG7
PHAROS: Q96MG7 GTEx: ENSG00000185115
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96MG7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-structural maintenance of chromosomes element 1 homolog	F	266	Homo sapiens	Mutation(s): 0 Gene Names: NSMCE1, HSPC333, HSPC337 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WV22 (Homo sapiens) Explore Q8WV22 Go to UniProtKB: Q8WV22
PHAROS: Q8WV22 GTEx: ENSG00000169189
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WV22
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cullin-4A	G	760	Homo sapiens	Mutation(s): 0 Gene Names: CUL4A
UniProt & NIH Common Fund Data Resources
Find proteins for Q13619 (Homo sapiens) Explore Q13619 Go to UniProtKB: Q13619
PHAROS: Q13619 GTEx: ENSG00000139842
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13619
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RBX1	H	108	Homo sapiens	Mutation(s): 0 Gene Names: RBX1, RNF75, ROC1 EC: 2.3.2.27 (PDB Primary Data), 2.3.2.32 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P62877 (Homo sapiens) Explore P62877 Go to UniProtKB: P62877
PHAROS: P62877 GTEx: ENSG00000100387
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62877
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Structural maintenance of chromosomes protein 5	I	1,101	Homo sapiens	Mutation(s): 0 Gene Names: SMC5, KIAA0594, SMC5L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IY18 (Homo sapiens) Explore Q8IY18 Go to UniProtKB: Q8IY18
PHAROS: Q8IY18 GTEx: ENSG00000198887
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IY18
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Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 SUMO-protein ligase NSE2	J	247	Homo sapiens	Mutation(s): 0 Gene Names: NSMCE2, C8orf36, MMS21 EC: 2.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MF7 (Homo sapiens) Explore Q96MF7 Go to UniProtKB: Q96MF7
PHAROS: Q96MF7 GTEx: ENSG00000156831
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96MF7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain L [auth F] SDF format, chain M [auth F] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain P [auth H] MOL2 format, chain K [auth C] MOL2 format, chain L [auth F] MOL2 format, chain M [auth F] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] mmCIF format, chain K [auth C] mmCIF format, chain L [auth F] mmCIF format, chain M [auth F] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H]	K [auth C] L [auth F] M [auth F] N [auth H] O [auth H] K [auth C], L [auth F], M [auth F], N [auth H], O [auth H], P [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain L [auth F] Focus chain M [auth F] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Interactions & Density Focus chain K [auth C] Focus chain L [auth F] Focus chain M [auth F] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H]