5TSX | pdb_00005tsx

HIV-1 CA hexamer with NUP153 peptide - P1 crystal form

• PDB DOI: https://doi.org/10.2210/pdb5TSX/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE), Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-10-31 Released: 2017-11-08 
• Deposition Author(s): Skorupka, K., Ganser-Pornillos, B.K., Pornillos, O.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

HIV-1 CA hexamer with NUP153 peptide - P1 crystal form

Skorupka, K., Zadrozny, K., Ganser-Pornillos, B.K., Pornillos, O.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A6B3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B1C1D1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A6B2C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B1C1D1 

Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 320.14 kDa 
• Atom Count: 22,652 
• Modeled Residue Count: 2,633 
• Deposited Residue Count: 2,910 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 CA protein	A, B, C, D, E, F, G, H, I, J, K, L	231	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	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
Nuclear pore complex protein Nup153	M, N, O, P, Q [auth R], R [auth T]	23	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P49790 (Homo sapiens) Explore P49790  Go to UniProtKB:  P49790
PHAROS:  P49790 GTEx:  ENSG00000124789

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLU	S [auth A], T [auth B], U [auth G], V [auth H]	2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID C20 H12 O5 YKGGGCXBWXHKIZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.333	α = 89.54
b = 91.487	β = 90.49
c = 150.047	γ = 96.08

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-11-08 
Deposition Author(s): Skorupka, K., Ganser-Pornillos, B.K., Pornillos, O.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI120956
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P50-GM103297

Revision History  

• Version 1.0: 2017-11-08
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Author supporting evidence, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary