3VRL | pdb_00003vrl

Crystal structure of BMJ4 p24 capsid protein in complex with A10F9 Fab

PDB DOI: https://doi.org/10.2210/pdb3VRL/pdb

Classification: IMMUNE SYSTEM/VIRAL PROTEIN
Organism(s): Mus musculus, Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-12 Released: 2013-04-17
Deposition Author(s): Gu, Y., Cao, F., Li, S., Yuan, Y.A., Xia, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.292 (Depositor), 0.285 (DCC)
R-Value Work:
0.211 (Depositor), 0.207 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structure of the HIV-1 capsid protein p24 in complex with the broad-spectrum antibody A10F9

Gu, Y., Cao, F., Li, S., Yuan, Y.A., Xia, N.

To be published.

Macromolecule Content

Total Structure Weight: 146.52 kDa
Atom Count: 7,806
Modeled Residue Count: 1,018
Deposited Residue Count: 1,338
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A10F9 Fab heavy chain	A [auth H], D [auth E]	224	Mus musculus	Mutation(s): 0
UniProt
Find proteins for A0N7J2 (Mus sp) Explore A0N7J2 Go to UniProtKB: A0N7J2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0N7J2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
A10F9 Fab light chain	B [auth L], E [auth F]	214	Mus musculus	Mutation(s): 0
UniProt
Find proteins for I6L978 (Mus musculus) Explore I6L978 Go to UniProtKB: I6L978
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I6L978
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag protein	C, F [auth D]	231	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: gag
UniProt
Find proteins for Q9DGV7 (Human immunodeficiency virus type 1) Explore Q9DGV7 Go to UniProtKB: Q9DGV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9DGV7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.292 (Depositor), 0.285 (DCC)
R-Value Work: 0.211 (Depositor), 0.207 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.109	α = 90
b = 124.058	β = 90
c = 150.83	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MLPHARE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-04-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-17
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-30
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.