2XXM

Crystal structure of the HIV-1 capsid protein C-terminal domain in complex with a camelid VHH and the CAI peptide.

• PDB DOI: https://doi.org/10.2210/pdb2XXM/pdb

• Classification: IMMUNE SYSTEM/PEPTIDE
• Organism(s): Human immunodeficiency virus, Vicugna pacos, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-11-10 Released: 2011-10-12 
• Deposition Author(s): Igonet, S., Vaney, M.C., Bartonova, V., Helma, J., Rothbauer, U., Leonhardt, H., Stura, E., Krausslich, H.-G., Rey, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Targeting HIV-1 Virion Formation with Nanobodies -Implications for the Design of Assembly Inhibitors

Igonet, S., Vaney, M.C., Bartonova, V., Helma, J., Rothbauer, U., Leonhardt, H., Stura, E., Krausslich, H.-G., Rey, F.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 23.2 kDa 
• Atom Count: 1,700 
• Modelled Residue Count: 194 
• Deposited Residue Count: 207 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAPSID PROTEIN P24	A	75	Human immunodeficiency virus	Mutation(s): 0
UniProt
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5)) Explore P12497  Go to UniProtKB:  P12497

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMELID VHH 9	B	121	Vicugna pacos	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
INHIBITOR OF CAPSID ASSEMBLY	C [auth T]	11	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	D [auth B], E [auth B], F [auth T]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.72	α = 90
b = 39.51	β = 90
c = 35.21	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Igonet, S., Vaney, M.C., Bartonova, V., Helma, J., Rothbauer, U., Leonhardt, H., Stura, E., Krausslich, H.-G., Rey, F.A.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2019-08-14
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary