9JS6 | pdb_00009js6

cryoEM of antibody complexed with immature Zika virus

• PDB DOI: https://doi.org/10.2210/pdb9JS6/pdb
• EM Map EMD-61767: EMDB EMDataResource

• Classification: VIRUS/IMMUNE SYSTEM
• Organism(s): Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-09-30 Released: 2025-10-01 
• Deposition Author(s): Shu, B., Lok, S.
• Funding Organization(s): National Research Foundation (NRF, Singapore), Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.80 Å
• Aggregation State: CELL 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of mature zika virus complexed with antibody at 3 angstrom

Shu, B., Lok, S.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 480-mer - A180B180C60D60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 480-mer - A180B180C120 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 243.57 kDa 
• Atom Count: 2,229 
• Modeled Residue Count: 2,229 
• Deposited Residue Count: 2,229 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope protein E	A, C [auth B], E [auth C]	503	Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013	Mutation(s): 0
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	B [auth D], D [auth E], F	163	Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013	Mutation(s): 0  EC: 3.4.21.91 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.1.1.56 (PDB Primary Data), 2.1.1.57 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody heavy chain	G [auth H]	121	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody light chain	H [auth L]	110	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.80 Å
• Aggregation State: CELL 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Shu, B., Lok, S.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Singapore)	Singapore	NRF2016NRF-CRP001-063
Ministry of Education (MoE, Singapore)	Singapore	MOE T32023-0002

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release