[English] 日本語
Yorodumi
- PDB-5fn5: Cryo-EM structure of gamma secretase in class 3 of the apo- state... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5fn5
TitleCryo-EM structure of gamma secretase in class 3 of the apo- state ensemble
Components
  • GAMMA-SECRETASE SUBUNIT APH-1AGamma secretase
  • GAMMA-SECRETASE SUBUNIT PEN-2Gamma secretase
  • NICASTRIN
  • PRESENILIN-1PSEN1
KeywordsHYDROLASE
Function / homologyNicastrin small lobe / Presenilin enhancer-2 subunit of gamma secretase / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / NRIF signals cell death from the nucleus / Regulated proteolysis of p75NTR / Degradation of the extracellular matrix / Nuclear signaling by ERBB4 / Aph-1 protein / NOTCH2 Activation and Transmission of Signal to the Nucleus ...Nicastrin small lobe / Presenilin enhancer-2 subunit of gamma secretase / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / NRIF signals cell death from the nucleus / Regulated proteolysis of p75NTR / Degradation of the extracellular matrix / Nuclear signaling by ERBB4 / Aph-1 protein / NOTCH2 Activation and Transmission of Signal to the Nucleus / Nicastrin / Presenilin / Gamma-secretase aspartyl protease complex, presenilin enhancer-2 subunit / Gamma-secretase subunit Aph-1 / Nicastrin / Presenilin/signal peptide peptidase / Peptidase A22A, presenilin 1 / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Peptidase A22A, presenilin / NOTCH4 Activation and Transmission of Signal to the Nucleus / EPH-ephrin mediated repulsion of cells / Noncanonical activation of NOTCH3 / Neutrophil degranulation / NOTCH3 Activation and Transmission of Signal to the Nucleus / Cajal-Retzius cell differentiation / positive regulation of L-glutamate import across plasma membrane / regulation of resting membrane potential / positive regulation of coagulation / amyloid precursor protein catabolic process / aspartic endopeptidase activity, intramembrane cleaving / Notch receptor processing, ligand-dependent / gamma-secretase complex / negative regulation of core promoter binding / choline transport / synaptic vesicle targeting / Notch receptor processing / neural retina development / T cell activation involved in immune response / epithelial cell proliferation / amyloid-beta formation / dorsal/ventral neural tube patterning / brain morphogenesis / membrane protein intracellular domain proteolysis / skin morphogenesis / amyloid precursor protein metabolic process / metanephros development / negative regulation of epidermal growth factor-activated receptor activity / endoplasmic reticulum calcium ion homeostasis / regulation of phosphorylation / myeloid dendritic cell differentiation / regulation of canonical Wnt signaling pathway / positive regulation of receptor recycling / nuclear outer membrane / somitogenesis / azurophil granule membrane / astrocyte activation involved in immune response / smooth endoplasmic reticulum calcium ion homeostasis / embryonic limb morphogenesis / negative regulation of axonogenesis / positive regulation of amyloid fibril formation / negative regulation of ubiquitin-protein transferase activity / hematopoietic progenitor cell differentiation / cell fate specification / skeletal system morphogenesis / ciliary rootlet / positive regulation of dendritic spine development / autophagosome assembly / blood vessel development / myeloid cell homeostasis / aggresome / canonical Wnt signaling pathway / cerebral cortex cell migration / heart looping / T cell proliferation / Aspartic endopeptidases / modulation of age-related behavioral decline / negative regulation of apoptotic signaling pathway / smooth endoplasmic reticulum / Golgi cisterna membrane / negative regulation of ubiquitin-dependent protein catabolic process / mitochondrial transport / activation of MAPKK activity / neuron development / protein glycosylation / positive regulation of catalytic activity / positive regulation of protein import into nucleus, translocation / calcium channel activity / synapse organization / membrane protein ectodomain proteolysis / regulation of synaptic transmission, glutamatergic / post-embryonic development / kinetochore / protein processing / astrocyte activation / regulation of synaptic plasticity / neuron projection maintenance / dendritic shaft / rough endoplasmic reticulum / integral component of presynaptic membrane / cell-cell adhesion
Function and homology information
Specimen sourceHOMO SAPIENS (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.3 Å resolution
AuthorsBai, X.C. / Rajendra, E. / Yang, G.H. / Shi, Y.G. / Scheres, S.H.W.
CitationJournal: Elife / Year: 2015
Title: Sampling the conformational space of the catalytic subunit of human γ-secretase.
Authors: Xiao-chen Bai / Eeson Rajendra / Guanghui Yang / Yigong Shi / Sjors H W Scheres
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 10, 2015 / Release: Dec 16, 2015
RevisionDateData content typeGroupProviderType
1.0Dec 16, 2015Structure modelrepositoryInitial release
1.1Dec 21, 2016Structure modelDatabase references

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-3240
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NICASTRIN
B: PRESENILIN-1
C: GAMMA-SECRETASE SUBUNIT APH-1A
D: GAMMA-SECRETASE SUBUNIT PEN-2


Theoretical massNumber of molelcules
Total (without water)172,2534
Polyers172,2534
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

#1: Protein/peptide NICASTRIN / / GAMMA-SECRETASE


Mass: 78483.570 Da / Num. of mol.: 1 / Details: A DRUG DAPT WAS BOUND TO GAMMA SECRETASE COMPLEX / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HEK293F / Plasmid name: PMLINK / Production host: HOMO SAPIENS (human) / References: UniProt: Q92542
#2: Protein/peptide PRESENILIN-1 / PSEN1 / PS-1 / PROTEIN S182 / GAMMA-SECRETASE


Mass: 52713.535 Da / Num. of mol.: 1 / Details: A DRUG DAPT WAS BOUND TO GAMMA SECRETASE COMPLEX / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HEK293F / Plasmid name: PMLINK / Production host: HOMO SAPIENS (human) / References: UniProt: P49768, Aspartic endopeptidases
#3: Protein/peptide GAMMA-SECRETASE SUBUNIT APH-1A / Gamma secretase / APH-1A / APH-1ALPHA / PRESENILIN-STABILIZATION FACTOR / GAMMA-SECRETASE


Mass: 29017.943 Da / Num. of mol.: 1 / Details: A DRUG DAPT WAS BOUND TO GAMMA SECRETASE COMPLEX / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HEK293F / Plasmid name: PMLINK / Production host: HOMO SAPIENS (human) / References: UniProt: Q96BI3
#4: Protein/peptide GAMMA-SECRETASE SUBUNIT PEN-2 / Gamma secretase / PRESENILIN ENHANCER PROTEIN 2 / GAMMA-SECRETASE


Mass: 12038.029 Da / Num. of mol.: 1 / Details: A DRUG DAPT WAS BOUND TO GAMMA SECRETASE COMPLEX / Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: HEK293F / Plasmid name: PMLINK / Production host: HOMO SAPIENS (human) / References: UniProt: Q9NZ42

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: GAMMA SECRETASE / Type: COMPLEX
Buffer solutionName: 25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35
Details: 25 MM HEPES, PH 7.4, 150 MM NACL AND AMPHIPOL A8-35
pH: 7.4
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Oct 25, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 / Calibrated magnification: 35714 / Nominal defocus max: 3200 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderTemperature: 85 kelvins
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
Image scansNumber digital images: 2000

-
Processing

SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 66720 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT
Least-squares processHighest resolution: 4.3 Å
Refine hist #LASTHighest resolution: 4.3 Å
Number of atoms included #LASTProtein: 9645 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 9645

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more