5IZ7

Cryo-EM structure of thermally stable Zika virus strain H/PF/2013

• PDB DOI: https://doi.org/10.2210/pdb5IZ7/pdb
• EM Map EMD-8139: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Zika virus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2016-03-25 Released: 2016-05-25 
• Deposition Author(s): Kostyuchenko, V.A., Zhang, S., Fibriansah, G., Lok, S.M.
• Funding Organization(s): Ministry of Education, National Research Foundation, Ministry of Health

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 360-mer - A180B180 

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

Macromolecule Content

• Total Structure Weight: 189.49 kDa 
• Atom Count: 13,268 
• Modelled Residue Count: 1,737 
• Deposited Residue Count: 1,737 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
structural protein E	A, B [auth C], D [auth B]	504	Zika virus	Mutation(s): 0  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
structural protein M	C [auth D], E, F	75	Zika virus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)) Explore A0A024B7W1  Go to UniProtKB:  A0A024B7W1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN	1.9
MODEL REFINEMENT	CNS	1.3

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Kostyuchenko, V.A., Zhang, S., Fibriansah, G., Lok, S.M.

---

Funding Organization	Location	Grant Number
Ministry of Education	Singapore	MOE2012-T3-1-008
National Research Foundation	Singapore	NRF-NRFI2016-01
Ministry of Health	Singapore	Duke-NUS Signature Research Program

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2016-06-01
  Changes: Database references
• Version 1.2: 2019-10-09
  Changes: Data collection, Database references, Other
• Version 1.3: 2019-10-23
  Changes: Data collection, Other
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary