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)

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Experimental Data Snapshot

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

Starting Model: experimental

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

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 360-mer - A240B120 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 360-mer - AA240AB1AC1AD1AE1AF1AG1AH1AI1AJ1AK1AL1AM1AN1AO1AP1AQ1AR1AS1AT1AU1AV1AW1AX1AY1AZ1Aa1Ab1Ac1Ad1Ae1Af1Ag1Ah1Ai1Aj1Ak1Al1Am1An1Ao1Ap1Aq1Ar1As1At1Au1Av1Aw1Ax1Ay1Az1BA1BB1BC1BD1BE1BF1BG1BH1BI1BJ1BK1BL1BM1BN1BO1BP1BQ1BR1BS1BT1BU1BV1BW1BX1BY1BZ1Ba1Bb1Bc1Bd1Be1Bf1Bg1Bh1Bi1Bj1Bk1Bl1Bm1Bn1Bo1Bp1Bq1Br1Bs1Bt1Bu1Bv1Bw1Bx1By1Bz1CA1CB1CC1CD1CE1CF1CG1CH1CI1CJ1CK1CL1CM1CN1CO1CP1CQ1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

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

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 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

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Makbul, C., Khayenko, V., Maric, M.H., Bottcher, B.

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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  

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