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- EMDB-3237: Cryo-EM structure of gamma secretase in complex with a drug DAPT -

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Basic information

Entry
Database: EMDB / ID: EMD-3237
TitleCryo-EM structure of gamma secretase in complex with a drug DAPT
Map dataReconstruction of gamma secretase in complex with a drug DAPT
Sample
  • Sample: human gamma secretase in complex with a drug DAPT
  • Protein or peptide: gamma-secretase
Function / homology
Function and homology information


positive regulation of endopeptidase activity / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / Noncanonical activation of NOTCH3 / protein catabolic process at postsynapse / TGFBR3 PTM regulation / Notch receptor processing / skin morphogenesis / membrane protein intracellular domain proteolysis / NOTCH4 Activation and Transmission of Signal to the Nucleus ...positive regulation of endopeptidase activity / gamma-secretase complex / aspartic endopeptidase activity, intramembrane cleaving / Noncanonical activation of NOTCH3 / protein catabolic process at postsynapse / TGFBR3 PTM regulation / Notch receptor processing / skin morphogenesis / membrane protein intracellular domain proteolysis / NOTCH4 Activation and Transmission of Signal to the Nucleus / ciliary rootlet / neural retina development / Regulated proteolysis of p75NTR / mitochondria-associated endoplasmic reticulum membrane contact site / aggresome / amyloid precursor protein metabolic process / endoplasmic reticulum calcium ion homeostasis / regulation of synaptic vesicle cycle / regulation of postsynapse organization / astrocyte activation involved in immune response / regulation of neuron projection development / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / regulation of canonical Wnt signaling pathway / Golgi cisterna membrane / growth factor receptor binding / azurophil granule membrane / positive regulation of amyloid fibril formation / positive regulation of dendritic spine development / amyloid-beta formation / amyloid precursor protein catabolic process / membrane protein ectodomain proteolysis / smooth endoplasmic reticulum / positive regulation of receptor recycling / nuclear outer membrane / EPH-ephrin mediated repulsion of cells / cerebellum development / Notch signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / Nuclear signaling by ERBB4 / endopeptidase activator activity / calcium ion homeostasis / Degradation of the extracellular matrix / rough endoplasmic reticulum / neuron projection maintenance / astrocyte activation / positive regulation of glycolytic process / NOTCH2 Activation and Transmission of Signal to the Nucleus / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / dendritic shaft / protein processing / PDZ domain binding / neuromuscular junction / NOTCH3 Activation and Transmission of Signal to the Nucleus / cell-cell adhesion / memory / synapse organization / sarcolemma / beta-catenin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / cellular response to amyloid-beta / calcium channel activity / kinetochore / positive regulation of tumor necrosis factor production / melanosome / regulation of gene expression / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / synaptic vesicle / nuclear membrane / ATPase binding / growth cone / presynaptic membrane / early endosome membrane / endopeptidase activity / cell cortex / aspartic-type endopeptidase activity / molecular adaptor activity / early endosome / learning or memory / protein-macromolecule adaptor activity / postsynapse / endosome membrane / neuron projection / mitochondrial inner membrane / intracellular signal transduction / cadherin binding / membrane raft / Amyloid fiber formation / negative regulation of gene expression / Golgi membrane / lysosomal membrane / focal adhesion / apoptotic process / neuronal cell body / centrosome / positive regulation of gene expression / negative regulation of apoptotic process / Neutrophil degranulation
Similarity search - Function
Peptidase A22A, presenilin 1 / Gamma-secretase subunit Aph-1 / Gamma-secretase aspartyl protease complex, presenilin enhancer-2 subunit / Aph-1 protein / Presenilin enhancer-2 subunit of gamma secretase / Peptidase A22A, presenilin / Presenilin, C-terminal / Presenilin / Nicastrin / Nicastrin, small lobe ...Peptidase A22A, presenilin 1 / Gamma-secretase subunit Aph-1 / Gamma-secretase aspartyl protease complex, presenilin enhancer-2 subunit / Aph-1 protein / Presenilin enhancer-2 subunit of gamma secretase / Peptidase A22A, presenilin / Presenilin, C-terminal / Presenilin / Nicastrin / Nicastrin, small lobe / Nicastrin large lobe / Nicastrin small lobe / Presenilin/signal peptide peptidase / Presenilin, signal peptide peptidase, family
Similarity search - Domain/homology
Presenilin-1 / Nicastrin / Gamma-secretase subunit APH-1A / Gamma-secretase subunit PEN-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 4.2 Å
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 /
Abstract: Human γ-secretase is an intra-membrane protease that cleaves many different substrates. Aberrant cleavage of Notch is implicated in cancer, while abnormalities in cutting amyloid precursor protein ...Human γ-secretase is an intra-membrane protease that cleaves many different substrates. Aberrant cleavage of Notch is implicated in cancer, while abnormalities in cutting amyloid precursor protein lead to Alzheimer's disease. Our previous cryo-EM structure of γ-secretase revealed considerable disorder in its catalytic subunit presenilin. Here, we describe an image classification procedure that characterizes molecular plasticity at the secondary structure level, and apply this method to identify three distinct conformations in our previous sample. In one of these conformations, an additional transmembrane helix is visible that cannot be attributed to the known components of γ-secretase. In addition, we present a γ-secretase structure in complex with the dipeptidic inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT). Our results reveal how conformational mobility in the second and sixth transmembrane helices of presenilin is greatly reduced upon binding of DAPT or the additional helix, and form the basis for a new model of how substrate enters the transmembrane domain.
History
DepositionNov 10, 2015-
Header (metadata) releaseNov 18, 2015-
Map releaseDec 9, 2015-
UpdateDec 16, 2015-
Current statusDec 16, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fn2
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
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Supplemental images

EMD-3237.jpg

Downloads & links

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Map

FileDownload / File: emd_3237.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of gamma secretase in complex with a drug DAPT
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.05
Minimum - Maximum-0.12731156 - 0.21583737
Average (Standard dev.)0.00013833 (±0.01161833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 252.0 Å
α=β=γ: 90.0 °

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-0.1270.2160.000

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Supplemental data

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Sample components

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Entire : human gamma secretase in complex with a drug DAPT

EntireName: human gamma secretase in complex with a drug DAPT
Components
  • Sample: human gamma secretase in complex with a drug DAPT
  • Protein or peptide: gamma-secretase

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Supramolecule #1000: human gamma secretase in complex with a drug DAPT

SupramoleculeName: human gamma secretase in complex with a drug DAPT / type: sample / ID: 1000 / Oligomeric state: Heterotetramer / Number unique components: 1
Molecular weightExperimental: 170 KDa / Theoretical: 170 KDa

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Macromolecule #1: gamma-secretase

MacromoleculeName: gamma-secretase / type: protein_or_peptide / ID: 1 / Details: a drug DAPT was bound to gamma scretase complex / Number of copies: 1 / Oligomeric state: Heterotetramer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Location in cell: membrane
Molecular weightExperimental: 170 KDa / Theoretical: 170 KDa
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293F / Recombinant plasmid: pMLink

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration6 mg/mL
BufferpH: 7.4
Details: 25 mM HEPES, pH 7.4, 150 mM NaCl and amphipol A8-35
StainingType: NEGATIVE / Details: cryo-EM
GridDetails: 300 mesh Au 1.2/1.3 Quantifoil grid, glow discharged for 1 minute
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 85 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80 K / Max: 90 K / Average: 85 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 81000 magnification
Specialist opticsEnergy filter - Name: Gatan Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateDec 31, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 2206 / Average electron dose: 38 e/Å2
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: OTHER / Software - Name: CTFFIND4, RELION
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
Number images used: 51366

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