2XV6 | pdb_00002xv6

Crystal structure of the HIV-1 capsid protein C-terminal domain (146- 220) in complex with a camelid VHH.

PDB DOI: https://doi.org/10.2210/pdb2XV6/pdb

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

Deposited: 2010-10-22 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.195 (Depositor), 0.196 (DCC)
R-Value Work:
0.175 (Depositor), 0.177 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2XV6

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 43.34 kDa
Atom Count: 3,192
Modeled Residue Count: 370
Deposited Residue Count: 392
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAPSID PROTEIN P24	A, C	75	Human immunodeficiency virus 1	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12497
Sequence Annotations Expand
Reference Sequence

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.195 (Depositor), 0.196 (DCC)
R-Value Work: 0.175 (Depositor), 0.177 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.451	α = 90
b = 60.118	β = 99.7
c = 96.662	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

Krausslich, H.-G.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.