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- PDB-6be6: ADAM10 Extracellular Domain -

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Basic information

Entry
Database: PDB / ID: 6be6
TitleADAM10 Extracellular Domain
ComponentsDisintegrin and metalloproteinase domain-containing protein 10
KeywordsMEMBRANE PROTEIN / ADAM10
Function / homology
Function and homology information


constitutive protein ectodomain proteolysis / ADAM10 endopeptidase / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / postsynapse organization / protein catabolic process at postsynapse / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / pore complex assembly ...constitutive protein ectodomain proteolysis / ADAM10 endopeptidase / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / postsynapse organization / protein catabolic process at postsynapse / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / pore complex assembly / regulation of Notch signaling pathway / perinuclear endoplasmic reticulum / positive regulation of T cell chemotaxis / tetraspanin-enriched microdomain / metallodipeptidase activity / NOTCH4 Activation and Transmission of Signal to the Nucleus / negative regulation of cell adhesion / adherens junction organization / clathrin-coated vesicle / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of postsynapse organization / Golgi-associated vesicle / cochlea development / Signaling by EGFR / pore complex / amyloid precursor protein catabolic process / tertiary granule membrane / Collagen degradation / membrane protein ectodomain proteolysis / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / response to tumor necrosis factor / specific granule membrane / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / Degradation of the extracellular matrix / NOTCH2 Activation and Transmission of Signal to the Nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / synaptic membrane / integrin-mediated signaling pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / adherens junction / Post-translational protein phosphorylation / protein processing / metalloendopeptidase activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SH3 domain binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / integrin binding / cell-cell signaling / positive regulation of cell growth / endopeptidase activity / in utero embryonic development / molecular adaptor activity / postsynaptic density / positive regulation of cell migration / protein phosphorylation / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / axon / negative regulation of gene expression / intracellular membrane-bounded organelle / signaling receptor binding / focal adhesion / glutamatergic synapse / dendrite / positive regulation of cell population proliferation / Neutrophil degranulation / protein kinase binding / Golgi apparatus / cell surface / protein homodimerization activity / extracellular exosome / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / Metallo-peptidase family M12B Reprolysin-like / ADAM10, cysteine-rich domain / ADAM10/ADAM17 catalytic domain / : / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily ...: / Metallo-peptidase family M12B Reprolysin-like / ADAM10, cysteine-rich domain / ADAM10/ADAM17 catalytic domain / : / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Disintegrin and metalloproteinase domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSeegar, T.C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41 GM103403 United States
CitationJournal: Cell / Year: 2017
Title: Structural Basis for Regulated Proteolysis by the alpha-Secretase ADAM10.
Authors: Seegar, T.C.M. / Killingsworth, L.B. / Saha, N. / Meyer, P.A. / Patra, D. / Zimmerman, B. / Janes, P.W. / Rubinstein, E. / Nikolov, D.B. / Skiniotis, G. / Kruse, A.C. / Blacklow, S.C.
History
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disintegrin and metalloproteinase domain-containing protein 10
B: Disintegrin and metalloproteinase domain-containing protein 10
C: Disintegrin and metalloproteinase domain-containing protein 10
D: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,79823
Polymers198,2494
Non-polymers5,54819
Water6,900383
1
A: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7406
Polymers49,5621
Non-polymers1,1785
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0305
Polymers49,5621
Non-polymers1,4674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8367
Polymers49,5621
Non-polymers1,2746
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1925
Polymers49,5621
Non-polymers1,6294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.420, 188.780, 86.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Disintegrin and metalloproteinase domain-containing protein 10 / ADAM 10 / CDw156 / Kuzbanian protein homolog / Mammalian disintegrin-metalloprotease


Mass: 49562.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM10, KUZ, MADM / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O14672, ADAM10 endopeptidase

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Sugars , 4 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-alpha-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
DManpa1-3DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-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
DManpa1-2DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 398 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.26M Ammonium Sulfate 100mM HEPES pH 7.5 21.75 % PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→47.476 Å / Num. obs: 52456 / % possible obs: 97.37 % / Redundancy: 3.1 % / CC1/2: 0.959 / Net I/av σ(I): 4.8 / Net I/σ(I): 4.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.35 / Num. unique obs: 5184 / CC1/2: 0.323 / % possible all: 97.99

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKC

1bkc


Resolution: 2.8→47.476 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2845 4849 5.04 %
Rwork0.2363 --
obs0.2387 52448 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.476 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13275 0 342 383 14000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414096
X-RAY DIFFRACTIONf_angle_d0.50619034
X-RAY DIFFRACTIONf_dihedral_angle_d19.0515488
X-RAY DIFFRACTIONf_chiral_restr0.0412045
X-RAY DIFFRACTIONf_plane_restr0.0032461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.42781430.37362748X-RAY DIFFRACTION87
2.8318-2.86510.39551800.34433189X-RAY DIFFRACTION96
2.8651-2.90010.37791690.3143158X-RAY DIFFRACTION98
2.9001-2.93680.31811690.3083171X-RAY DIFFRACTION98
2.9368-2.97540.37181710.323176X-RAY DIFFRACTION98
2.9754-3.01620.38961700.32673188X-RAY DIFFRACTION98
3.0162-3.05920.40171680.32043156X-RAY DIFFRACTION97
3.0592-3.10490.37441670.32443182X-RAY DIFFRACTION97
3.1049-3.15340.37561650.3163125X-RAY DIFFRACTION97
3.1534-3.20510.35381670.30533130X-RAY DIFFRACTION95
3.2051-3.26030.33641550.28473011X-RAY DIFFRACTION95
3.2603-3.31960.33731610.27653046X-RAY DIFFRACTION93
3.3196-3.38340.36621500.27482971X-RAY DIFFRACTION91
3.3834-3.45250.29821560.26342746X-RAY DIFFRACTION84
3.4525-3.52750.29471540.25352911X-RAY DIFFRACTION91
3.5275-3.60960.27361730.24953165X-RAY DIFFRACTION97
3.6096-3.69980.31951660.25163130X-RAY DIFFRACTION97
3.6998-3.79980.30991680.22623129X-RAY DIFFRACTION97
3.7998-3.91160.3091630.22393132X-RAY DIFFRACTION96
3.9116-4.03770.27261590.21113133X-RAY DIFFRACTION96
4.0377-4.1820.20531620.19433042X-RAY DIFFRACTION95
4.182-4.34930.28981560.18122998X-RAY DIFFRACTION91
4.3493-4.54710.22611390.16982720X-RAY DIFFRACTION84
4.5471-4.78660.20581630.17013001X-RAY DIFFRACTION93
4.7866-5.08620.21831660.17643115X-RAY DIFFRACTION96
5.0862-5.47840.25911590.19233103X-RAY DIFFRACTION96
5.4784-6.02870.24711600.18653048X-RAY DIFFRACTION94
6.0287-6.89880.18241470.1992763X-RAY DIFFRACTION85
6.8988-8.68310.19761640.1923088X-RAY DIFFRACTION95
8.6831-47.4830.23141590.20692961X-RAY DIFFRACTION91

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