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- PDB-6idf: Cryo-EM structure of gamma secretase in complex with a Notch fragment -

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Basic information

Entry
Database: PDB / ID: 6idf
TitleCryo-EM structure of gamma secretase in complex with a Notch fragment
Components
  • (Gamma-secretase subunit ...Gamma secretase) x 2
  • Nicastrin
  • Notch1
  • Presenilin-1PSEN1
KeywordsMEMBRANE PROTEIN / complex
Function / homologyNicastrin small lobe / Presenilin enhancer-2 subunit of gamma secretase / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / NRIF signals cell death from the nucleus / Regulated proteolysis of p75NTR / Degradation of the extracellular matrix / Nuclear signaling by ERBB4 / Aph-1 protein / NOTCH2 Activation and Transmission of Signal to the Nucleus ...Nicastrin small lobe / Presenilin enhancer-2 subunit of gamma secretase / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / NRIF signals cell death from the nucleus / Regulated proteolysis of p75NTR / Degradation of the extracellular matrix / Nuclear signaling by ERBB4 / Aph-1 protein / NOTCH2 Activation and Transmission of Signal to the Nucleus / Nicastrin / Presenilin / Gamma-secretase aspartyl protease complex, presenilin enhancer-2 subunit / Gamma-secretase subunit Aph-1 / Nicastrin / Peptidase A22A, presenilin 1 / Peptidase A22A, presenilin / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Presenilin/signal peptide peptidase / EPH-ephrin mediated repulsion of cells / Neutrophil degranulation / Amyloid fiber formation / Noncanonical activation of NOTCH3 / NOTCH4 Activation and Transmission of Signal to the Nucleus / NOTCH3 Activation and Transmission of Signal to the Nucleus / Cajal-Retzius cell differentiation / positive regulation of L-glutamate import across plasma membrane / positive regulation of coagulation / regulation of resting membrane potential / 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 / regulation of phosphorylation / endoplasmic reticulum calcium ion homeostasis / myeloid dendritic cell differentiation / positive regulation of receptor recycling / regulation of canonical Wnt signaling pathway / 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 / negative regulation of ubiquitin-dependent protein catabolic process / activation of MAPKK activity / neuron development / 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
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single 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 Report
SummaryFull reportAbout validation report
DateDeposition: Sep 9, 2018 / Release: Dec 26, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 26, 2018Structure modelrepositoryInitial release
1.1Jan 16, 2019Structure modelData collection / Database referencescitation / citation_author_citation.pdbx_database_id_PubMed / _citation_author.name

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Assembly

Deposited unit
A: Nicastrin
B: Presenilin-1
C: Gamma-secretase subunit APH-1A
D: Gamma-secretase subunit PEN-2
E: Notch1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,78533
Polyers186,9435
Non-polymers8,84328
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)26970
ΔGint (kcal/M)-112
Surface area (Å2)62150

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Components

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Protein/peptide , 3 types, 3 molecules ABE

#1: Protein/peptide Nicastrin /


Mass: 78483.570 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: NCSTN / Production host: Homo sapiens (human) / References: UniProt: Q92542
#2: Protein/peptide Presenilin-1 / PSEN1 / PS-1


Mass: 52644.543 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PS1 / Production host: Homo sapiens (human)
References: UniProt: P49768, Hydrolases, Acting on peptide bonds (peptidases), Aspartic endopeptidases
#5: Protein/peptide Notch1


Mass: 14758.500 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Gamma-secretase subunit ... , 2 types, 2 molecules CD

#3: Protein/peptide Gamma-secretase subunit APH-1A / Gamma secretase / APH-1a


Mass: 29017.943 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: APH1A / Production host: Homo sapiens (human) / References: UniProt: Q96BI3
#4: Protein/peptide Gamma-secretase subunit PEN-2 / Gamma secretase / Presenilin enhancer protein 2


Mass: 12038.029 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PEN2 / Production host: Homo sapiens (human) / References: UniProt: Q9NZ42

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Non-polymers , 4 types, 28 molecules

#6: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 18 / Formula: C8H15NO6 / N-Acetylglucosamine
#7: Chemical ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 3 / Formula: C6H12O6
#8: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 4 / Formula: C44H88NO8P / Comment: phospholipid *YM
#9: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Formula: C27H46O / Cholesterol

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: gamma-secretaseGamma secretase / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.5625 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 476853 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00511489
ELECTRON MICROSCOPYf_angle_d0.98215687
ELECTRON MICROSCOPYf_dihedral_angle_d8.4326693
ELECTRON MICROSCOPYf_chiral_restr0.0571869
ELECTRON MICROSCOPYf_plane_restr0.0071895

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