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- EMDB-2974: The cryoEM map of human gamma-Secretase complex -

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Entry
Database: EMDB / ID: 2974
TitleThe cryoEM map of human gamma-Secretase complex
Map dataReconstruction of T4-lysozyme fusion gamma-secretase
SampleT4-lysozyme fusion gamma-secretase:
gamma-secretaseGamma secretase
Keywordsgamma-secretase
Function / homologyPeptidase A22A, presenilin 1 / Presenilin / Activated NOTCH1 Transmits Signal to the Nucleus / NOTCH2 Activation and Transmission of Signal to the Nucleus / NRIF signals cell death from the nucleus / EPH-ephrin mediated repulsion of cells / Regulated proteolysis of p75NTR / Neutrophil degranulation / NOTCH3 Activation and Transmission of Signal to the Nucleus / NOTCH4 Activation and Transmission of Signal to the Nucleus ...Peptidase A22A, presenilin 1 / Presenilin / Activated NOTCH1 Transmits Signal to the Nucleus / NOTCH2 Activation and Transmission of Signal to the Nucleus / NRIF signals cell death from the nucleus / EPH-ephrin mediated repulsion of cells / Regulated proteolysis of p75NTR / Neutrophil degranulation / NOTCH3 Activation and Transmission of Signal to the Nucleus / NOTCH4 Activation and Transmission of Signal to the Nucleus / Degradation of the extracellular matrix / Nuclear signaling by ERBB4 / Nicastrin / Phage lysozyme / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Endolysin T4 type / Peptidase A22A, presenilin / T4-type lysozyme / Lysozyme-like domain superfamily / Nicastrin / Presenilin/signal peptide peptidase / Noncanonical activation of NOTCH3 / Amyloid fiber formation / Glycoside hydrolase, family 24 / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / positive regulation of L-glutamate import across plasma membrane / Cajal-Retzius cell differentiation / positive regulation of coagulation / amyloid precursor protein biosynthetic process / aspartic endopeptidase activity, intramembrane cleaving / positive regulation of amyloid precursor protein biosynthetic process / amyloid precursor protein catabolic process / Notch receptor processing, ligand-dependent / short-term synaptic potentiation / regulation of resting membrane potential / 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 / central nervous system myelination / epithelial cell proliferation / amyloid-beta formation / dorsal/ventral neural tube patterning / regulation of long-term synaptic potentiation / glutamate receptor signaling pathway / brain morphogenesis / amyloid precursor protein metabolic process / skin morphogenesis / negative regulation of epidermal growth factor-activated receptor activity / regulation of phosphorylation / endoplasmic reticulum calcium ion homeostasis / dopamine receptor signaling pathway / myeloid dendritic cell differentiation / nuclear outer membrane / positive regulation of receptor recycling / regulation of canonical Wnt signaling pathway / regulation of neuron projection development / negative regulation of axonogenesis / adult behavior / somitogenesis / smooth endoplasmic reticulum calcium ion homeostasis / azurophil granule membrane / astrocyte activation involved in immune response / positive regulation of amyloid fibril formation / cell fate specification / negative regulation of ubiquitin-protein transferase activity / embryonic limb morphogenesis / skeletal system morphogenesis / positive regulation of dendritic spine development / ciliary rootlet / myeloid cell homeostasis / autophagosome assembly / hematopoietic progenitor cell differentiation / aggresome / cerebral cortex cell migration / heart looping / blood vessel development / negative regulation of ubiquitin-dependent protein catabolic process / Hydrolases, Acting on peptide bonds (peptidases), Aspartic endopeptidases / T cell proliferation / negative regulation of apoptotic signaling pathway / modulation of age-related behavioral decline / smooth endoplasmic reticulum / mitochondrial transport / activation of MAPKK activity / protein glycosylation / neuron development / positive regulation of catalytic activity / cerebellum development / calcium channel activity / membrane protein ectodomain proteolysis / synapse organization / regulation of synaptic transmission, glutamatergic / post-embryonic development / protein processing / kinetochore / regulation of synaptic plasticity
Function and homology information
SourceHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 4.4 Å resolution
AuthorsSun LF / Zhao LY / Yang GH / Yan CY / Zhou R / Zhou XY / Xie T / Zhao YY / Wu SY / Li XM / Shi YG
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: Structural basis of human γ-secretase assembly.
Authors: Linfeng Sun / Lingyun Zhao / Guanghui Yang / Chuangye Yan / Rui Zhou / Xiaoyuan Zhou / Tian Xie / Yanyu Zhao / Shenjie Wu / Xueming Li / Yigong Shi
Validation ReportPDB-ID: 4uis

SummaryFull reportAbout validation report
DateDeposition: Apr 3, 2015 / Header (metadata) release: May 6, 2015 / Map release: Jun 17, 2015 / Last update: Aug 12, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-4uis
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-4uis
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_2974.map.gz (map file in CCP4 format, 31251 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
1.32 Å/pix.
= 264. Å
200 pix
1.32 Å/pix.
= 264. Å
200 pix
1.32 Å/pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:0.02 (by author), 0.028 (movie #1):
Minimum - Maximum-0.07044545 - 0.14689757
Average (Standard dev.)0.00043521 (0.00638579)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 264.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0700.1470.000

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Supplemental data

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Sample components

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Entire T4-lysozyme fusion gamma-secretase

EntireName: T4-lysozyme fusion gamma-secretase / Details: The sample was monodisperse / Number of components: 4
MassTheoretical: 170 kDa

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Component #1: protein, gamma-secretase

ProteinName: gamma-secretaseGamma secretase / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 170 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK 293S

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 4.2 mg/ml
Buffer solution: 0.1% digitonin, 25 mM HEPES, pH 7.4, and 150 mM NaCl.
pH: 7.4
Support filmQuantifoil Cu R1.2/1.3 grids
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % / Method: Blot for 3 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Dec 22, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 4.5 e/Å2 / Illumination mode: SPOT SCAN
LensCs: 1.4 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: DIRECT ELECTRON DE-12 (4k x 3k)

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Image acquisition

Image acquisitionNumber of digital images: 3312

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 177207
3D reconstructionSoftware: RELION / Resolution: 4.4 Å / Resolution method: FSC 0.143, gold-standard

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 4R12
Chain ID: A
Modeling #2Software: Chimera / Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 4HYG
Chain ID: B
Output model

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