6NK5

Electron Cryo-Microscopy Of Chikungunya VLP

• PDB DOI: https://doi.org/10.2210/pdb6NK5/pdb
• EM Map EMD-9393: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Chikungunya virus strain Senegal 37997
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2019-01-04 Released: 2019-05-22 
• Deposition Author(s): Basore, K., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 720-mer - A240B240C240 

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

Macromolecule Content

• Total Structure Weight: 444.42 kDa 
• Atom Count: 31,130 
• Modelled Residue Count: 4,036 
• Deposited Residue Count: 4,036 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E1 glycoprotein	A, D [auth B], G [auth C], J [auth D]	439	Chikungunya virus strain Senegal 37997	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997)) Explore Q5XXP3  Go to UniProtKB:  Q5XXP3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E2 glycoprotein	B [auth E], E [auth F], H [auth G], K [auth H]	419	Chikungunya virus strain Senegal 37997	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997)) Explore Q5XXP3  Go to UniProtKB:  Q5XXP3

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	C [auth I], F [auth J], I [auth K], L	151	Chikungunya virus strain Senegal 37997	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for Q5XXP3 (Chikungunya virus (strain 37997)) Explore Q5XXP3  Go to UniProtKB:  Q5XXP3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	M [auth A], N [auth E], O [auth B], P [auth F], Q [auth C], R [auth G], S [auth D], T [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.16 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cisTEM	1.0.0-beta
MODEL REFINEMENT	PHENIX	1.14

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-22 
Deposition Author(s): Basore, K., Fremont, D.H., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2019-05-22
  Type: Initial release
  
• Version 1.1: 2019-05-29
  Changes: Data collection, Database references
• Version 1.2: 2019-06-26
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary