2XXC | pdb_00002xxc

Crystal structure of a camelid VHH raised against the HIV-1 capsid protein C-terminal domain.

• PDB DOI: https://doi.org/10.2210/pdb2XXC/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Vicugna pacos
• 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: 1.67 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.181 (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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 13.21 kDa 
• Atom Count: 1,064 
• Modelled Residue Count: 114 
• Deposited Residue Count: 121 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMELID VHH 9	A [auth B]	121	Vicugna pacos	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.208	α = 90
b = 80.208	β = 90
c = 52.686	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, Other, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary