5JUY Apoptosis date May 10, 2016
title Active Human Apoptosome With Procaspase-9
authors T.C.Cheng, C.Hong, I.V.Akey, S.Yuan, C.W.Akey
compound source
Molecule: Apoptotic Protease-Activating Factor 1
Chain: A, B, C, D, E, F, G
Synonym: Apaf-1
Engineered: Yes
Other_details: Without N-Terminal Cards
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Apaf1, Kiaa0413
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108

Molecule: Cytochrome C
Chain: H, I, J, K, L, M, N

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Caspase-9
Chain: O, P, Q, R
Fragment: N-Terminal Caspase Recognition Domain
Synonym: Casp-9,Apoptotic Protease Mch-6,Apoptotic Protease Activating Factor 3,Apaf-3,Ice-Like Apoptotic Protease 6,Ic
Ec: 3.4.22.62
Engineered: Yes
Other_details: N-Terminal Caspase Recognition Domain (Card) Procaspase-9

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Casp9, Mch6
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768
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 4.10 Å
ligand DTP, HEC enzyme Hydrolase E.C.3.4.22.62 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, E, C, A, B, D, G


N, K, M, L, J, H, I


Q, O, P, R


Primary referenceA near atomic structure of the active human apoptosome., Cheng TC, Hong C, Akey IV, Yuan S, Akey CW, Elife. 2016 Oct 4;5. pii: e17755. doi: 10.7554/eLife.17755. PMID:27697150
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1305 Kb) [Save to disk]
  • Biological Unit Coordinates (5juy.pdb1.gz) 1294 Kb
  • LPC: Ligand-Protein Contacts for 5JUY
  • CSU: Contacts of Structural Units for 5JUY
  • Retrieve 5JUY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5JUY from S2C, [Save to disk]
  • View 5JUY 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 5JUY
  • 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
  • Fold representative 5juy from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5juy] [5juy_O] [5juy_F] [5juy_J] [5juy_C] [5juy_I] [5juy_E] [5juy_L] [5juy_M] [5juy_A] [5juy_H] [5juy_Q] [5juy_K] [5juy_D] [5juy_N] [5juy_G] [5juy_P] [5juy_B] [5juy_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5JUY: [CARD] [WD40 ] by SMART
  • Other resources with information on 5JUY
  • Community annotation for 5JUY at PDBWiki (http://pdbwiki.org)

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