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- EMDB-2678: Three-dimensional structure of human gamma-secretase at 5.4 angst... -

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Entry
Database: EMDB / ID: 2678
TitleThree-dimensional structure of human gamma-secretase at 5.4 angstrom resoltuion
Map dataReconstruction of human gamma-secretase. The particles were selected by two-steps of 3D classification. This map has good density for the transmembrane domain. All the 19 TM helices and some of the linkers are visible.
Samplehuman gamma-secretaseGamma secretase:
gamma-secretaseGamma secretase
Keywordshuman gamma-secretase / cryo EM
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 / 5.4 Å resolution
AuthorsLu PL / Bai XC / Ma D / Xie T / Yan CY / Sun LF / Yang GH / Zhao YY / Zhou R / Scheres SHW / Shi YG
CitationJournal: Nature / Year: 2014
Title: Three-dimensional structure of human γ-secretase.
Authors: Peilong Lu / Xiao-Chen Bai / Dan Ma / Tian Xie / Chuangye Yan / Linfeng Sun / Guanghui Yang / Yanyu Zhao / Rui Zhou / Sjors H W Scheres / Yigong Shi
Validation ReportPDB-ID: 5a63

SummaryFull reportAbout validation report
DateDeposition: Jun 14, 2014 / Header (metadata) release: Jun 25, 2014 / Map release: Jun 25, 2014 / Last update: Aug 19, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5a63
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_2678.map.gz (map file in CCP4 format, 10720 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
140 pix
1.76 Å/pix.
= 246.4 Å
140 pix
1.76 Å/pix.
= 246.4 Å
140 pix
1.76 Å/pix.
= 246.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.76 Å
Density
Contour Level:0.12 (by author), 0.12 (movie #1):
Minimum - Maximum-0.35781333 - 0.64387774
Average (Standard dev.)0.00054414 (0.02294301)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions140140140
Origin000
Limit139139139
Spacing140140140
CellA=B=C: 246.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.761.761.76
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z246.400246.400246.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.3580.6440.001

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Supplemental data

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Sample components

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Entire human gamma-secretase

EntireName: human gamma-secretase / Number of components: 1 / Oligomeric State: Homotetramer
MassTheoretical: 170 kDa / Experimental: 170 kDa

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Component #1: protein, gamma-secretase

ProteinName: gamma-secretaseGamma secretase / Oligomeric Details: Homotetramer / Recombinant expression: Yes / Number of Copies: 4
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)Cell: HEK 293F

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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
Stainingcryo-EM
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 90 K / Humidity: 100 % / Method: Blot for 4S before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Feb 26, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 38 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 64000 X (nominal), 28409 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1400 - 4400 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 85 K ( 80 - 90 K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1471 / Sampling size: 5 microns / Details: 15 frames were recorded during the imaging.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 37310
3D reconstructionSoftware: CTFFIND3, RELION / CTF correction: Each particle
Details: Use a newly developed statistical movie processing approach to compensate for beam-induced movement.
Resolution: 5.4 Å / Resolution method: FSC 0.143, gold-standard

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