8CXI | pdb_00008cxi

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

• PDB DOI: https://doi.org/10.2210/pdb8CXI/pdb
• EM Map EMD-27058: EMDB EMDataResource

• Classification: VIRUS/IMMUNE SYSTEM
• Organism(s): Zika virus, Homo sapiens
• 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: 3.40 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 10-mer - A3B3C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A4B3C3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content 

• Total Structure Weight: 1,401.23 kDa 
• Atom Count: 16,832 
• Modeled Residue Count: 2,196 
• Deposited Residue Count: 12,674 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ankyrin repeat family A protein 2,Envelope E protein	A, E [auth B], I [auth C]	639	Zika virus	Mutation(s): 0  Gene Names: ANKRA2, ANKRA
UniProt & NIH Common Fund Data Resources
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1
Find proteins for Q9H9E1 (Homo sapiens) Explore Q9H9E1  Go to UniProtKB:  Q9H9E1
PHAROS:  Q9H9E1 GTEx:  ENSG00000164331
UniProt Groups	A0A024B7W1Q9H9E1
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q9H9E1-1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane M protein	B [auth D], F [auth E], J [auth F]	3,423	Zika virus	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
A11 heavy chain	C [auth H], G [auth h]	133	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
A11 light chain	D [auth L], H [auth l]	111	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth G], L [auth I]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 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: 2024-11-06
  Changes: Data collection, Structure summary