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

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Entry
Database: PDB / ID: 6idf
TitleCryo-EM structure of gamma secretase in complex with a Notch fragment
Components
  • (Gamma-secretase subunit ...) x 2
  • Nicastrin
  • Notch1
  • Presenilin-1
KeywordsMEMBRANE PROTEIN / complex
Function / homology
Function and homology information


Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / growth involved in heart morphogenesis / regulation of cardioblast proliferation / mesenchymal cell development / cell differentiation in spinal cord / venous endothelial cell differentiation / arterial endothelial cell differentiation / collecting duct development ...Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / growth involved in heart morphogenesis / regulation of cardioblast proliferation / mesenchymal cell development / cell differentiation in spinal cord / venous endothelial cell differentiation / arterial endothelial cell differentiation / collecting duct development / cell migration involved in endocardial cushion formation / negative regulation of pro-B cell differentiation / Pre-NOTCH Processing in the Endoplasmic Reticulum / mitral valve formation / : / endocardium morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / cardiac chamber formation / cardiac atrium morphogenesis / negative regulation of endothelial cell chemotaxis / atrioventricular node development / cardiac ventricle morphogenesis / positive regulation of transcription of Notch receptor target / pericardium morphogenesis / Cajal-Retzius cell differentiation / cellular response to tumor cell / positive regulation of smooth muscle cell differentiation / positive regulation of L-glutamate import across plasma membrane / amyloid precursor protein biosynthetic process / glomerular mesangial cell development / positive regulation of endopeptidase activity / vasculogenesis involved in coronary vascular morphogenesis / negative regulation of extracellular matrix constituent secretion / gamma-secretase complex / regulation of extracellular matrix assembly / positive regulation of apoptotic process involved in morphogenesis / chemical synaptic transmission, postsynaptic / endocardial cell differentiation / aspartic endopeptidase activity, intramembrane cleaving / positive regulation of amyloid precursor protein biosynthetic process / epithelial to mesenchymal transition involved in endocardial cushion formation / left/right axis specification / smooth endoplasmic reticulum calcium ion homeostasis / Noncanonical activation of NOTCH3 / protein catabolic process at postsynapse / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / : / T-helper 17 type immune response / positive regulation of endothelial cell differentiation / cardiac left ventricle morphogenesis / TGFBR3 PTM regulation / coronary vein morphogenesis / negative regulation of myotube differentiation / cardiac vascular smooth muscle cell development / : / Notch receptor processing / endocardium development / positive regulation of coagulation / negative regulation of axonogenesis / neuronal stem cell population maintenance / positive regulation of astrocyte differentiation / negative regulation of cell adhesion molecule production / cardiac muscle cell myoblast differentiation / tissue regeneration / skin morphogenesis / membrane protein intracellular domain proteolysis / positive regulation of cardiac epithelial to mesenchymal transition / negative regulation of oligodendrocyte differentiation / cardiac epithelial to mesenchymal transition / heart trabecula morphogenesis / central nervous system myelination / regulation of cell adhesion involved in heart morphogenesis / short-term synaptic potentiation / interleukin-17-mediated signaling pathway / Pre-NOTCH Processing in Golgi / T cell activation involved in immune response / negative regulation of catalytic activity / negative regulation of myoblast differentiation / negative regulation of collagen biosynthetic process / cellular response to follicle-stimulating hormone stimulus / NOTCH4 Activation and Transmission of Signal to the Nucleus / myeloid dendritic cell differentiation / negative regulation of cardiac muscle hypertrophy / ciliary rootlet / choline transport / negative regulation of stem cell differentiation / regulation of resting membrane potential / luteolysis / metanephros development / neural retina development / pulmonary valve morphogenesis / tube formation / brain morphogenesis / determination of left/right symmetry / Regulated proteolysis of p75NTR / cardiac muscle tissue morphogenesis / embryonic limb morphogenesis / coronary artery morphogenesis / negative regulation of cell migration involved in sprouting angiogenesis
Similarity search - Function
Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / : / Notch / Peptidase A22A, presenilin 1 / Gamma-secretase subunit Aph-1 / Notch, NOD domain / Notch, NODP domain / Gamma-secretase aspartyl protease complex, presenilin enhancer-2 subunit ...Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / : / Notch / Peptidase A22A, presenilin 1 / Gamma-secretase subunit Aph-1 / Notch, NOD domain / Notch, NODP domain / Gamma-secretase aspartyl protease complex, presenilin enhancer-2 subunit / Aph-1 protein / NOTCH protein / NOTCH protein / Presenilin enhancer-2 subunit of gamma secretase / NOD / NODP / Peptidase A22A, presenilin / Presenilin, C-terminal / Presenilin / Nicastrin / Nicastrin, small lobe / Nicastrin large lobe / Nicastrin small lobe / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. / Presenilin/signal peptide peptidase / Presenilin, signal peptide peptidase, family / LNR domain / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / : / Calcium-binding EGF domain / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Ankyrin repeat / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
CHOLESTEROL / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Neurogenic locus notch homolog protein 1 / Presenilin-1 / Nicastrin / Gamma-secretase subunit APH-1A / Gamma-secretase subunit PEN-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsYang, G. / Zhou, R. / Zhou, Q. / Guo, X. / Yan, C. / Ke, M. / Lei, J. / Shi, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31621092 China
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 /
Abstract: Aberrant cleavage of Notch by γ-secretase leads to several types of cancer, but how γ-secretase recognizes its substrate remains unknown. Here we report the cryo-electron microscopy structure of ...Aberrant cleavage of Notch by γ-secretase leads to several types of cancer, but how γ-secretase recognizes its substrate remains unknown. Here we report the cryo-electron microscopy structure of human γ-secretase in complex with a Notch fragment at a resolution of 2.7 Å. The transmembrane helix of Notch is surrounded by three transmembrane domains of PS1, and the carboxyl-terminal β-strand of the Notch fragment forms a β-sheet with two substrate-induced β-strands of PS1 on the intracellular side. Formation of the hybrid β-sheet is essential for substrate cleavage, which occurs at the carboxyl-terminal end of the Notch transmembrane helix. PS1 undergoes pronounced conformational rearrangement upon substrate binding. These features reveal the structural basis of Notch recognition and have implications for the recruitment of the amyloid precursor protein by γ-secretase.
History
DepositionSep 9, 2018Deposition site: PDBJ / Processing site: PDBJ
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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)195,62324
Polymers186,9435
Non-polymers8,68119
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area26970 Å2
ΔGint-112 kcal/mol
Surface area62150 Å2

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Components

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Protein , 3 types, 3 molecules ABE

#1: Protein Nicastrin


Mass: 78483.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCSTN / Production host: Homo sapiens (human) / References: UniProt: Q92542
#2: Protein Presenilin-1 / PS-1


Mass: 52644.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 Notch1


Mass: 14758.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P46531*PLUS

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

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


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


Mass: 12038.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEN2 / Production host: Homo sapiens (human) / References: UniProt: Q9NZ42

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Sugars , 3 types, 12 molecules

#6: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#7: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 7 molecules

#9: Chemical
ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#10: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H46O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: gamma-secretase / Type: COMPLEX / Entity ID: #1-#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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
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
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. 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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