Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Hetero 720-mer - A180B180C180D180 Pseudo Symmetry: Icosahedral - I  (3D View)
Pseudo Stoichiometry: Hetero 720-mer - A360B180C180 

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

Macromolecule Content

• Total Structure Weight: 266.40 kDa 
• Atom Count: 18517 
• Modelled Residue Count: 2425 
• Deposited Residue Count: 2445 
• Unique protein chains: 4

5H37

Cryo-EM structure of zika virus complexed with Fab C10 at pH 8.0

• PDB DOI: 10.2210/pdb5H37/pdb
• EM Map EMD-9575: EMDB EMDataResource

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


• Deposited: 2016-10-20 Released: 2016-11-30 
• Deposition Author(s): Zhang, S., Kostyuchenko, V., Ng, T.-S., Lim, X.-N., Ooi, J.S.G., Lambert, S., Tan, T.Y., Widman, D., Shi, J., Baric, R.S., Lok, S.-M.
• Funding Organization(s): Ministry of Education Tier 3 grant, National Research Foundation Investigatorship award, National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Neutralization mechanism of a highly potent antibody against Zika virus

Zhang, S., Kostyuchenko, V.A., Ng, T.-S., Lim, X.-N., Ooi, J.S.G., Lambert, S., Tan, T.Y., Widman, D.G., Shi, J., Baric, R.S., Lok, S.-M.

(2016) Nat Commun 7: 13679-13679

• PubMed: 27882950 
• DOI: 10.1038/ncomms13679
• Primary Citation of Related Structures:  
  5H30, 5H32, 5H37


• PubMed Abstract: 
  

The rapid spread of Zika virus (ZIKV), which causes microcephaly and Guillain-Barré syndrome, signals an urgency to identify therapeutics. Recent efforts to rescreen dengue virus human antibodies for ZIKV cross-neutralization activity showed antibody C10 as one of the most potent. To investigate the ability of the antibody to block fusion, we determined the cryoEM structures of the C10-ZIKV complex at pH levels mimicking the extracellular (pH8.0), early (pH6.5) and late endosomal (pH5.0) environments. The 4.0 Å resolution pH8.0 complex structure shows that the antibody binds to E proteins residues at the intra-dimer interface, and the virus quaternary structure-dependent inter-dimer and inter-raft interfaces. At pH6.5, antibody C10 locks all virus surface E proteins, and at pH5.0, it locks the E protein raft structure, suggesting that it prevents the structural rearrangement of the E proteins during the fusion event-a vital step for infection. This suggests antibody C10 could be a good therapeutic candidate.

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Organizational Affiliation: 

Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
structural protein E	A, D [auth B], B [auth C]	504	Zika virus	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt) Membrane Entity: Yes
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
strutural protein M	C [auth D], E, F	75	Zika virus	Mutation(s): 0  EC: 3.4.21.91 (UniProt), 3.6.1.15 (UniProt), 3.6.4.13 (UniProt), 2.1.1.56 (UniProt), 2.1.1.57 (UniProt), 2.7.7.48 (UniProt) Membrane Entity: Yes
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
C10 IgG heavy chain variable region	G, K [auth I], I [auth K]	127	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
C10 IgG light chain variable region	H, J [auth L], L [auth M]	109	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-10-20 
• Released Date: 2016-11-30 
Deposition Author(s): Zhang, S., Kostyuchenko, V., Ng, T.-S., Lim, X.-N., Ooi, J.S.G., Lambert, S., Tan, T.Y., Widman, D., Shi, J., Baric, R.S., Lok, S.-M.

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Funding Organization	Location	Grant Number
Ministry of Education Tier 3 grant	Singapore	MOE2012-T3-1-008
National Research Foundation Investigatorship award	Singapore	NRF-NRFI2016-01
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI100625 and AI 107731

Revision History  

• Version 1.0: 2016-11-30
  Type: Initial release
  
• Version 1.1: 2017-01-25
  Changes: Database references
• Version 1.2: 2019-11-06
  Changes: Data collection, Other
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2022-03-23
  Changes: Author supporting evidence, Database references, Derived calculations, Structure summary