5MD3 Viral Protein date Nov 10, 2016
title The Structure Of The Mature Hiv-1 Ca Hexameric Lattice With Parameters: Tilt=11, Twist=12
authors S.Mattei, B.Glass, W.J.H.Hagen, H.G.Kraeusslich, J.A.G.Briggs
compound source
Molecule: Capsid Protein P24
Chain: A, B, F, W, C, D, E, G
Fragment: C-Terminal Domain, Unp Residues 141-214
 Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Strain: Nl43
Cell_line: Mt-4

Molecule: Capsid Protein P24
Chain: a, b, f, H, I, J
Fragment: N-Terminal Domain, Unp Residues 123-269
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Strain: Nl43
Cell_line: Mt-4
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 8.50 Å
Gene
Ontology
ChainFunctionProcessComponent
F, A, W, E, B, C, D, G


J, a, H, b, I, f


Primary referenceThe structure and flexibility of conical HIV-1 capsids determined within intact virions., Mattei S, Glass B, Hagen WJ, Krausslich HG, Briggs JA, Science. 2016 Dec 16;354(6318):1434-1437. PMID:27980210
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (112 Kb) [Save to disk]
  • Biological Unit Coordinates (5md3.pdb1.gz) 101 Kb
  • CSU: Contacts of Structural Units for 5MD3
  • Retrieve 5MD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5MD3 from S2C, [Save to disk]
    • View 5MD3 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5MD3
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5md3_W] [5md3_a] [5md3_H] [5md3_I] [5md3_f] [5md3_C] [5md3_F] [5md3_J] [5md3_G] [5md3_A] [5md3_b] [5md3_B] [5md3_D] [5md3_E] [5md3]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5MD3
  • Community annotation for 5MD3 at PDBWiki (http://pdbwiki.org)

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