3J5M Viral Protein Immune System date Oct 26, 2013
title Cryo-Em Structure Of The Bg505 Sosip.664 Hiv-1 Env Trimer Wi Fabs
authors D.Lyumkis, J.P.Julien, I.A.Wilson, A.B.Ward
compound source
Molecule: Bg505 Sosip Gp120
Chain: A, E, I
Fragment: Unp Residues 30-504
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Env
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek

Molecule: Bg505 Sosip Gp41
Chain: B, F, J
Fragment: See Remark 999
Engineered: Yes

Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Env
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek

Molecule: Pgv04 Light Chain
Chain: C, G, K
Fragment: Fab
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek

Molecule: Pgv04 Heavy Chain
Chain: D, H, L
Fragment: Fab
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek
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 5.80 Å
note 3J5M (Molecule of the Month:pdb169)
Gene
Ontology
ChainFunctionProcessComponent
A, I, E


Primary referenceCryo-EM Structure of a Fully Glycosylated Soluble Cleaved HIV-1 Envelope Trimer., Lyumkis D, Julien JP, de Val N, Cupo A, Potter CS, Klasse PJ, Burton DR, Sanders RW, Moore JP, Carragher B, Wilson IA, Ward AB, Science. 2013 Oct 31. PMID:24179160
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (359 Kb) [Save to disk]
  • Biological Unit Coordinates (3j5m.pdb1.gz) 352 Kb
  • CSU: Contacts of Structural Units for 3J5M
  • Retrieve 3J5M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J5M from S2C, [Save to disk]
  • View 3J5M 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 3J5M
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3J5M, from MSDmotif at EBI
  • Fold representative 3j5m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j5m_H] [3j5m_B] [3j5m_E] [3j5m_L] [3j5m_A] [3j5m_D] [3j5m_G] [3j5m_C] [3j5m_K] [3j5m_J] [3j5m_F] [3j5m_I] [3j5m]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3J5M: [IG_like] [IGv ] by SMART
  • Other resources with information on 3J5M
  • Community annotation for 3J5M at PDBWiki (http://pdbwiki.org)

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