[English] 日本語
Yorodumi
- EMDB-9648: Cryo-EM structure of gamma secretase in complex with a Notch fragment -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 9648
TitleCryo-EM structure of gamma secretase in complex with a Notch fragment
Map data
Samplegamma-secretaseGamma secretase
  • Nicastrin
  • Presenilin-1PSEN1
  • (Gamma-secretase subunit ...Gamma secretase) x 2
  • Notch1
  • (ligand) x 4
Function / homologyPresenilin / Activated NOTCH1 Transmits Signal to the Nucleus / Neutrophil degranulation / Peptidase A22A, presenilin 1 / EPH-ephrin mediated repulsion of cells / NOTCH2 Activation and Transmission of Signal to the Nucleus / Nicastrin / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Constitutive Signaling by NOTCH1 PEST Domain Mutants / NRIF signals cell death from the nucleus ...Presenilin / Activated NOTCH1 Transmits Signal to the Nucleus / Neutrophil degranulation / Peptidase A22A, presenilin 1 / EPH-ephrin mediated repulsion of cells / NOTCH2 Activation and Transmission of Signal to the Nucleus / Nicastrin / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Constitutive Signaling by NOTCH1 PEST Domain Mutants / NRIF signals cell death from the nucleus / Peptidase A22A, presenilin / Regulated proteolysis of p75NTR / Gamma-secretase subunit Aph-1 / Degradation of the extracellular matrix / Nuclear signaling by ERBB4 / Gamma-secretase aspartyl protease complex, presenilin enhancer-2 subunit / Presenilin enhancer-2 subunit of gamma secretase / Aph-1 protein / Nicastrin / NOTCH3 Activation and Transmission of Signal to the Nucleus / Presenilin/signal peptide peptidase / NOTCH4 Activation and Transmission of Signal to the Nucleus / Amyloid fiber formation / Noncanonical activation of NOTCH3 / Cajal-Retzius cell differentiation / positive regulation of L-glutamate import across plasma membrane / regulation of resting membrane potential / positive regulation of coagulation / aspartic endopeptidase activity, intramembrane cleaving / amyloid precursor protein catabolic process / Notch receptor processing, ligand-dependent / negative regulation of core promoter binding / gamma-secretase complex / 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 / membrane protein intracellular domain proteolysis / brain morphogenesis / amyloid precursor protein metabolic process / skin morphogenesis / 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 / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / negative regulation of axonogenesis / positive regulation of amyloid fibril formation / negative regulation of ubiquitin-protein transferase activity / embryonic limb morphogenesis / hematopoietic progenitor cell differentiation / cell fate specification / skeletal system morphogenesis / positive regulation of dendritic spine development / ciliary rootlet / autophagosome assembly / myeloid cell homeostasis / blood vessel development / aggresome / cerebral cortex cell migration / heart looping / Hydrolases, Acting on peptide bonds (peptidases), Aspartic endopeptidases / T cell proliferation / modulation of age-related behavioral decline / negative regulation of apoptotic signaling pathway / Golgi cisterna membrane / smooth endoplasmic reticulum / protein glycosylation / mitochondrial transport / neuron development / activation of MAPKK activity / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of catalytic activity / go:0033160: / synapse organization / calcium channel activity / membrane protein ectodomain proteolysis / regulation of synaptic transmission, glutamatergic / post-embryonic development / protein processing / astrocyte activation / kinetochore / regulation of synaptic plasticity / neuron projection maintenance / dendritic shaft / rough endoplasmic reticulum / memory / Notch signaling pathway / cell-cell adhesion
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 2.7 Å resolution
AuthorsYang G / Zhou R / Zhou Q / Guo X / Yan C / Ke M / Lei J / Shi Y
CitationJournal: Nature / Year: 2019
Title: Structural basis of Notch recognition by human γ-secretase.
Authors: Guanghui Yang / Rui Zhou / Qiang Zhou / Xuefei Guo / Chuangye Yan / Meng Ke / Jianlin Lei / Yigong Shi
Validation ReportPDB-ID: 6idf

SummaryFull reportAbout validation report
DateDeposition: Sep 9, 2018 / Header (metadata) release: Dec 26, 2018 / Map release: Dec 26, 2018 / Last update: Jan 16, 2019

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6idf
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_9648.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.09 Å/pix.
= 349.12 Å
320 pix
1.09 Å/pix.
= 349.12 Å
320 pix
1.09 Å/pix.
= 349.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.19102116 - 0.37563604
Average (Standard dev.)0.00021344786 (0.0066517177)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin0.00.00.0
Limit319.0319.0319.0
Spacing320320320
CellA=B=C: 349.12 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z349.120349.120349.120
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1910.3760.000

-
Supplemental data

-
Sample components

+
Entire gamma-secretase

EntireName: gamma-secretase / Number of components: 10

+
Component #1: protein, gamma-secretase

ProteinName: gamma-secretaseGamma secretase / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #2: protein, Nicastrin

ProteinName: Nicastrin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 78.48357 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #3: protein, Presenilin-1

ProteinName: Presenilin-1PSEN1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.644543 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #4: protein, Gamma-secretase subunit APH-1A

ProteinName: Gamma-secretase subunit APH-1AGamma secretase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.017943 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #5: protein, Gamma-secretase subunit PEN-2

ProteinName: Gamma-secretase subunit PEN-2Gamma secretase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.038029 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #6: protein, Notch1

ProteinName: Notch1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.7585 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #7: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

+
Component #8: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

+
Component #9: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.790145 kDa

+
Component #10: ligand, CHOLESTEROL

LigandName: CHOLESTEROL / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.386654 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5625 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 476853
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
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