1AFV

HIV-1 CAPSID PROTEIN (P24) COMPLEX WITH FAB25.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of dimeric HIV-1 capsid protein.

Momany, C.Kovari, L.C.Prongay, A.J.Keller, W.Gitti, R.K.Lee, B.M.Gorbalenya, A.E.Tong, L.McClure, J.Ehrlich, L.S.Summers, M.F.Carter, C.Rossmann, M.G.

(1996) Nat Struct Biol 3: 763-770

  • DOI: 10.1038/nsb0996-763
  • Primary Citation of Related Structures:  
    1AFV

  • PubMed Abstract: 
  • X-ray diffraction analysis of a human immunodeficiency virus (HIV-1) capsid (CA) protein shows that each monomer within the dimer consists of seven alpha-helices, five of which are arranged in a coiled coil-like structure. Sequence assignments were m ...

    X-ray diffraction analysis of a human immunodeficiency virus (HIV-1) capsid (CA) protein shows that each monomer within the dimer consists of seven alpha-helices, five of which are arranged in a coiled coil-like structure. Sequence assignments were made for two of the helices, and tentative connectivity of the remainder of the protein was confirmed by the recent solution structure of a monomeric N-terminal fragment. The C-terminal third of the protein is mostly disordered in the crystal. The longest helices in the coiled coil-like structure are separated by a long, highly antigenic peptide that includes the binding site of an antibody fragment complexed with CA in the crystal. The site of binding of the Fab, the position of the antigenic loop and the site of cleavage between the matrix protein and CA establish the side of the dimer that would be on the exterior of the retroviral core.


    Related Citations: 
    • The Use of Antibody Fragments for Crystallization and Structure Determinations
      Kovari, L.C., Momany, C., Rossmann, M.G.
      (1995) Structure 3: 1291
    • Preparation and Crystallization of a Human Immunodeficiency Virus P24-Fab Complex
      Prongay, A.J., Smith, T.J., Rossmann, M.G., Ehrlich, L.S., Carter, C.A., Mcclure, J.
      (1990) Proc Natl Acad Sci U S A 87: 9980
    • Expression in Escherichia Coli and Purification of Human Immunodeficiency Virus Type 1 Capsid Protein (P24)
      Ehrlich, L.S., Krausslich, H.G., Wimmer, E., Carter, C.A.
      (1990) AIDS Res Hum Retroviruses 6: 1169

    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CAPSID PROTEINAB151Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: GAG
EC: 3.4.23.16 (UniProt), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B (isolate NY5))
Explore P12497 
Go to UniProtKB:  P12497
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIBODY FAB25.3 FRAGMENT (LIGHT CHAIN)LM217Mus musculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIBODY FAB25.3 FRAGMENT (HEAVY CHAIN)HK220Mus musculusMutation(s): 0 
Gene Names: Igh
Find proteins for Q99LC4 (Mus musculus)
Explore Q99LC4 
Go to UniProtKB:  Q99LC4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PB
Query on PB

Download CCD File 
L, M
LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.217 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.9α = 90
b = 92.3β = 90
c = 149.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-08-20
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance