8PX3 | pdb_00008px3

Hepatitis B core protein with bound P1dC

PDB DOI: https://doi.org/10.2210/pdb8PX3/pdb
EM Map EMD-18000: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Hepatitis B virus, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-22 Released: 2024-07-31
Deposition Author(s): Makbul, C., Khayenko, V., Maric, M.H., Bottcher, B.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8PX3

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

Literature

Induction of hepatitis B core protein aggregation targeting an unconventional binding site

Khayenko, V., Makbul, C., Schulte, C., Hemmelmann, N., Kachler, S., Bottcher, B., Maric, H.M., Comas-Garcia, M., Dotsch, V.

(2025) Elife 13

DOI: https://doi.org/10.7554/eLife.98827

Macromolecule Content

Total Structure Weight: 86.66 kDa
Atom Count: 4,727
Modeled Residue Count: 593
Deposited Residue Count: 756
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
External core antigen	A [auth B], B [auth A], C, D	183	Hepatitis B virus	Mutation(s): 0
UniProt
Find proteins for P0C573 (Hepatitis B virus genotype D subtype ayw (isolate France/Tiollais/1979)) Explore P0C573 Go to UniProtKB: P0C573
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C573
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P1dC	E [auth F], F [auth E]	12	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	BO1150/17-1
German Research Foundation (DFG)	Germany	MA6957/1-1
German Research Foundation (DFG)	Germany	INST 93/903-1
German Research Foundation (DFG)	Germany	INST 93/1042-1
German Research Foundation (DFG)	Germany	INST 93/1143-1

Revision History (Full details and data files)

Version 1.0: 2024-07-31
Type: Initial release
Version 1.1: 2025-08-13
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.