6PU1 | pdb_00006pu1

Cysteine stabilized hexameric HIV-1 CA in complex with SEC24C peptide

• PDB DOI: https://doi.org/10.2210/pdb6PU1/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-07-16 Released: 2021-01-06 
• Deposition Author(s): Lindenberger, J.J., Kvaratskhelia, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Cysteine stabilized hexameric HIV-1 CA in complex with SEC24C peptide

Lindenberger, J.J., Kvaratskhelia, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B1C1D1E1F1G1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.35 kDa 
• Atom Count: 1,739 
• Modeled Residue Count: 222 
• Deposited Residue Count: 246 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag polyprotein	A	231	Human immunodeficiency virus 1	Mutation(s): 4  Gene Names: gag
UniProt
Find proteins for P12493 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12493  Go to UniProtKB:  P12493

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein transport protein Sec24C	B	15	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P53992 (Homo sapiens) Explore P53992  Go to UniProtKB:  P53992
PHAROS:  P53992 GTEx:  ENSG00000176986

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	C [auth A], D [auth A], G [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL	E [auth A], F [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.58	α = 90
b = 92.58	β = 90
c = 58.019	γ = 120

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-06 
Deposition Author(s): Lindenberger, J.J., Kvaratskhelia, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI062520

Revision History  

• Version 1.0: 2021-01-06
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description