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- EMDB-3239: Cryo-EM structure of gamma secretase in class 2 of the apo-state ... -

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Entry
Database: EMDB / ID: 3239
TitleCryo-EM structure of gamma secretase in class 2 of the apo-state ensemble
Map dataReconstruction of gamma secretase in class 2 of the apo-state ensemble
Samplehuman gamma secretase in class 2 of the apo-state ensemble:
gamma-secretaseGamma secretase
Function / homologyGamma-secretase subunit Aph-1 / Nicastrin / Degradation of the extracellular matrix / Regulated proteolysis of p75NTR / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Presenilin/signal peptide peptidase / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus ...Gamma-secretase subunit Aph-1 / Nicastrin / Degradation of the extracellular matrix / Regulated proteolysis of p75NTR / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Presenilin/signal peptide peptidase / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / EPH-ephrin mediated repulsion of cells / Peptidase A22A, presenilin 1 / Peptidase A22A, presenilin / Nicastrin / Presenilin / Aph-1 protein / Neutrophil degranulation / NOTCH3 Activation and Transmission of Signal to the Nucleus / NOTCH4 Activation and Transmission of Signal to the Nucleus / Noncanonical activation of NOTCH3 / Amyloid fiber formation / Nuclear signaling by ERBB4 / positive regulation of L-glutamate import across plasma membrane / Cajal-Retzius cell differentiation / positive regulation of coagulation / amyloid precursor protein biosynthetic process / amyloid precursor protein catabolic process / positive regulation of amyloid precursor protein biosynthetic process / aspartic endopeptidase activity, intramembrane cleaving / 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 / T cell activation involved in immune response / neural retina development / central nervous system myelination / epithelial cell proliferation / amyloid-beta formation / dorsal/ventral neural tube patterning / regulation of long-term synaptic potentiation / membrane protein intracellular domain proteolysis / glutamate receptor signaling pathway / brain morphogenesis / amyloid precursor protein metabolic process / skin morphogenesis / negative regulation of epidermal growth factor-activated receptor activity / metanephros development / 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 / azurophil granule membrane / smooth endoplasmic reticulum calcium ion homeostasis / 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 / Golgi cisterna membrane / 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 Å resolution
AuthorsBai XC / Rajendra E / Yang GH / Shi YG / Scheres SHW
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 ReportPDB-ID: 5fn4

SummaryFull reportAbout validation report
DateDeposition: Nov 10, 2015 / Header (metadata) release: Nov 18, 2015 / Map release: Dec 9, 2015 / Last update: Dec 16, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5fn4
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

Fileemd_3239.map.gz (map file in CCP4 format, 22783 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
180 pix
1.4 Å/pix.
= 252. Å
180 pix
1.4 Å/pix.
= 252. Å
180 pix
1.4 Å/pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour Level:0.04 (by author), 0.045 (movie #1):
Minimum - Maximum-0.06578127 - 0.15764602
Average (Standard dev.)0.00007033 (0.00761043)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions180180180
Origin000
Limit179179179
Spacing180180180
CellA=B=C: 252.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-189
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.0660.1580.000

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Supplemental data

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Sample components

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Entire human gamma secretase in class 2 of the apo-state ensemble

EntireName: human gamma secretase in class 2 of the apo-state ensemble
Number of components: 1 / Oligomeric State: Heterotetramer
MassTheoretical: 170 kDa / Experimental: 170 kDa

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Component #1: protein, gamma-secretase

ProteinName: gamma-secretaseGamma secretase / Oligomeric Details: Heterotetramer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 170 kDa / Experimental: 170 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pMLink / Cell of expression system: HEK 293F
Source (natural)Location in cell: membrane / Cell: HEK293F

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 6 mg/ml
Buffer solution: 25 mM HEPES, pH 7.4, 150 mM NaCl and amphipol A8-35
pH: 7.4
Support film300 mesh Au 1.2/1.3 Quantifoil grid, glow discharged for 1 minute
Stainingcryo-EM
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 85 K / Humidity: 100 % / Method: Blot for 4 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Oct 25, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 38 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 81000 X (nominal), 35714 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 81000 magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3200 nm / Energy filter: Gatan Quantum / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 85 K ( 80 - 90 K)
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2925 / Sampling size: 5 microns
Details: Use a newly developed statistical movie processing and particle polishing approach to compensate for beam-induced movement and reduce the effect of radiation-damage

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 79263
3D reconstructionSoftware: CTFFIND4, RELION / CTF correction: Each particle / Resolution: 4 Å / Resolution method: FSC 0.143, gold-standard

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