5A63

Cryo-EM structure of the human gamma-secretase complex at 3.4 angstrom resolution.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: Particle
  • Reconstruction Method: Single Particle

Literature

Macromolecules
Sequence Display for 5A63

Classification: HYDROLASE

Total Structure Weight: 178134.38

Macromolecule Entities
Molecule Chains Length Organism Details
NICASTRIN A 709 Homo sapiens Gene Name(s): NCSTN Gene View KIAA0253 UNQ1874/PRO4317
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PRESENILIN-1 B 467 Homo sapiens EC#: 3.4.23 IUBMB
Gene Name(s): PSEN1 Gene View AD3 PS1 PSNL1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
GAMMA-SECRETASE SUBUNIT APH-1A C 265 Homo sapiens Gene Name(s): APH1A Gene View PSF CGI-78 UNQ579/PRO1141
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
GAMMA-SECRETASE SUBUNIT PEN-2 D 101 Homo sapiens Gene Name(s): PSENEN Gene View PEN2 MDS033
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Intramembrane Proteases

Protein Name: γ-secretase


Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PC1
Query on PC1

B, C 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE (Synonym)
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Reconstruction Method: Single Particle

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-06-24
  • Released Date: 2015-08-05
  • Deposition author(s): Bai, X., Yan, C., Yang, G., Lu, P., Ma, D., Sun, L., Zhou, R., Scheres, S.H.W., Shi, Y.
  • Previous versions: 4UPC

Revision History

  • 2015-08-19
    Type: Database references
  • 2015-08-26
    Type: Database references
  • 2015-09-16
    Type: Database references, Structure summary
  • 2016-12-28
    Type: Other
  • 2017-08-02
    Type: Data collection