1AFV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.324 
  • R-Value Work: 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.Mol.Biol. 3: 763-770


  • 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: 
    • 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.USA 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
    • The Use of Antibody Fragments for Crystallization and Structure Determinations
      Kovari, L.C.,Momany, C.,Rossmann, M.G.
      (1995) Structure 3: 1291


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CAPSID PROTEIN
A, B
151Human immunodeficiency virus type 1 group M subtype BGene Names: gag-pol
EC: 3.4.23.16, 3.1.-.-, 2.7.7.49, 2.7.7.7, 3.1.26.13, 2.7.7.-, 3.1.13.2
Find proteins for P12497 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P12497
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY FAB25.3 FRAGMENT (LIGHT CHAIN)
L, M
217N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY FAB25.3 FRAGMENT (HEAVY CHAIN)
H, K
220N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PB
Query on PB

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.217 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 119.900α = 90.00
b = 92.300β = 90.00
c = 149.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
SCALEPACKdata scaling
X-PLORrefinement
X-PLORphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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