3JCA Viral Protein date Nov 24, 2015
title Core Model Of The Mouse Mammary Tumor Virus Intasome
authors D.L.Lyumkis, A.Ballandras-Colas, M.Brown, N.J.Cook, T.G.Dewdney, B.Demeler, P.Cherepanov, A.N.Engelman
compound source
Molecule: Integrase
Chain: A, B, E, F
Fragment: Unp Residues 1437-1701
Engineered: Yes
Organism_scientific: Mouse Mammary Tumor Virus
Organism_common: Mmtv
Organism_taxid: 11757
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Pc2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Integrase
Chain: C, D, G, H
Fragment: C-Terminal Domain (Unp Residues 1653-1701)
Engineered: Yes

Organism_scientific: Mouse Mammary Tumor Virus
Organism_common: Mmtv
Organism_taxid: 11757
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Pc2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: 5'-D(Apaptpgpcpcpgpcpapgptpcpgpgpc Cpcptpg)-3';
Chain: I, K
Engineered: Yes
Other_details: Pre-Cleaved Viral Dna 3' Strand

Synthetic: Yes
Organism_scientific: Mouse Mammary Tumor Virus
Organism_taxid: 11757

Molecule: 5'-D(Cpapgpgptpcpgpgpcpcpgpapcptpg Cpa)-3';
Chain: J, L
Engineered: Yes
Other_details: Pre-Cleaved Viral Dna 5' Strand

Synthetic: Yes
Organism_scientific: Mouse Mammary Tumor Virus
Organism_taxid: 11757
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 4.80 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B


H, C, D, G


Primary referenceCryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function., Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B, Cherepanov P, Lyumkis D, Engelman AN, Nature. 2016 Feb 18;530(7590):358-61. doi: 10.1038/nature16955. PMID:26887496
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (232 Kb) [Save to disk]
  • Biological Unit Coordinates (3jca.pdb1.gz) 227 Kb
  • LPC: Ligand-Protein Contacts for 3JCA
  • CSU: Contacts of Structural Units for 3JCA
  • Retrieve 3JCA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JCA from S2C, [Save to disk]
  • View 3JCA 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 3JCA
  • 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: [3jca_J] [3jca_I] [3jca_C] [3jca_H] [3jca_G] [3jca_A] [3jca] [3jca_E] [3jca_D] [3jca_L] [3jca_K] [3jca_F] [3jca_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3JCA
  • Community annotation for 3JCA at PDBWiki (http://pdbwiki.org)

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