2XT1

Crystal structure of the HIV-1 capsid protein C-terminal domain (146- 231) in complex with a camelid VHH.

• PDB DOI: https://doi.org/10.2210/pdb2XT1/pdb

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus 1, Vicugna pacos
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-10-03 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: 1.32 Å
• R-Value Free: 0.183 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Starting Models: 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 22.93 kDa 
• Atom Count: 1,861 
• Modelled Residue Count: 200 
• Deposited Residue Count: 207 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GAG POLYPROTEIN	A	86	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for Q71B32 (Human immunodeficiency virus type 1) Explore Q71B32  Go to UniProtKB:  Q71B32

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.183 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.06	α = 90
b = 88.17	β = 90
c = 35.66	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: 2018-06-20
  Changes: Data collection, Derived calculations
• Version 1.2: 2019-08-14
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-09
  Changes: Structure summary