5A63 Hydrolase date Jun 24, 2015
title Cryo-Em Structure Of The Human Gamma-Secretase Complex At 3. Resolution.
authors X.Bai, C.Yan, G.Yang, P.Lu, D.Ma, L.Sun, R.Zhou, S.H.W.Scheres, Y.Sh
compound source
Molecule: Nicastrin
Chain: A
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek 293f
Gene: Ncstn, Kiaa0253, Unq1874pro4317
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek 293f
Expression_system_vector_type: Plasmid
Expression_system_vector: Pmlink

Molecule: Presenilin-1
Chain: B
Synonym: Ps-1,Protein S182
Ec: 3.4.23.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek 293f
Gene: Psen1, Ad3, Ps1, Psnl1
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek 293f
Expression_system_vector_type: Plasmid
Expression_system_vector: Pmlink

Molecule: Gamma-Secretase Subunit Aph-1a
Chain: C
Synonym: Aph-1a,Aph-1alpha,Presenilin-Stabilization Factor
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek 293f
Gene: Aph1a, Psf, Cgi-78, Unq579pro1141
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek 293f
Expression_system_vector_type: Plasmid
Expression_system_vector: Pmlink

Molecule: Gamma-Secretase Subunit Pen-2
Chain: D
Synonym: Presenilin Enhancer Protein 2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hek 293f
Gene: Psenen, Pen2, Mds033
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: Hek 293f
Expression_system_vector_type: Plasmid
Expression_system_vector: Pmlink
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 3.40 Å
ligand BMA, NAG, PC1 enzyme Hydrolase E.C.3.4.23 BRENDA
note 5A63 supersedes 4UPC
Gene
Ontology
ChainFunctionProcessComponent
A


B
  • calcium channel activity


  • C


    D


    Primary referenceAn atomic structure of human gamma-secretase., Bai XC, Yan C, Yang G, Lu P, Ma D, Sun L, Zhou R, Scheres SH, Shi Y, Nature. 2015 Aug 17. doi: 10.1038/nature14892. PMID:26280335
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (211 Kb) [Save to disk]
  • Biological Unit Coordinates (5a63.pdb1.gz) 202 Kb
  • LPC: Ligand-Protein Contacts for 5A63
  • CSU: Contacts of Structural Units for 5A63
  • Retrieve 5A63 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5A63 from S2C, [Save to disk]
  • View 5A63 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 5A63
  • Cartoon representation from PDB Cartoon
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  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5a63 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5a63_D] [5a63] [5a63_B] [5a63_C] [5a63_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5A63: [PSN ] by SMART
  • Other resources with information on 5A63
  • Community annotation for 5A63 at PDBWiki (http://pdbwiki.org)

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