8CXG | pdb_00008cxg

Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy

• PDB DOI: https://doi.org/10.2210/pdb8CXG/pdb
• EM Map EMD-27055: EMDB EMDataResource

• Classification: VIRUS/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Zika virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-05-21 Released: 2023-06-07 
• Deposition Author(s): Liu, W., Zhang, X.K., Gong, D.Y., Dai, X.H., Sharma, A., Zhang, T.H., Rey, F., Zhou, Z.H.
• Funding Organization(s): National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy

Liu, W., Zhang, X.K., Gong, D.Y., Dai, X.H., Sharma, A., Zhang, T.H., Rey, F., Zhou, Z.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A3B3C3D3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - C2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 1,423.18 kDa 
• Atom Count: 18,381 
• Modeled Residue Count: 2,399 
• Deposited Residue Count: 12,879 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C8 scFv heavy chain	A [auth H], E [auth h], K [auth 1]	122	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C8 scFv light chain	B [auth L], F [auth l], L [auth 2]	109	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ankyrin repeat family A protein 2,Envelope E protein	C [auth A], G [auth B], I [auth C]	639	Zika virus	Mutation(s): 0  Gene Names: ANKRA2, ANKRA
UniProt & NIH Common Fund Data Resources
Find proteins for A0A142DS37 (Zika virus) Explore A0A142DS37  Go to UniProtKB:  A0A142DS37
Find proteins for Q9H9E1 (Homo sapiens) Explore Q9H9E1  Go to UniProtKB:  Q9H9E1
PHAROS:  Q9H9E1 GTEx:  ENSG00000164331
UniProt Groups	A0A142DS37Q9H9E1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane M protein	D, H [auth E], J [auth F]	3,423	Zika virus	Mutation(s): 0
UniProt
Find proteins for A0A1S6LXE0 (Zika virus) Explore A0A1S6LXE0  Go to UniProtKB:  A0A1S6LXE0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-06-07 
Deposition Author(s): Liu, W., Zhang, X.K., Gong, D.Y., Dai, X.H., Sharma, A., Zhang, T.H., Rey, F., Zhou, Z.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)	United States	DE028583, DE025567
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1S10RR23057, 1S10OD018111, and 1U24GM116792
National Science Foundation (NSF, United States)	United States	DBI-1338135 and DMR-1548924

Revision History  

• Version 1.0: 2023-06-07
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary