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- PDB-6bdz: ADAM10 Extracellular Domain Bound by the 11G2 Fab -

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Basic information

Entry
Database: PDB / ID: 6bdz
TitleADAM10 Extracellular Domain Bound by the 11G2 Fab
Components
  • 11G2 Fab Heavy Chain
  • 11G2 Fab Light Chain
  • Disintegrin and metalloproteinase domain-containing protein 10
KeywordsMEMBRANE PROTEIN / ADAM10
Function / homology
Function and homology information


ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / marginal zone B cell differentiation / postsynapse organization / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / protein catabolic process at postsynapse ...ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / regulation of vasculature development / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / marginal zone B cell differentiation / postsynapse organization / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / protein catabolic process at postsynapse / perinuclear endoplasmic reticulum / pore complex assembly / positive regulation of T cell chemotaxis / tetraspanin-enriched microdomain / regulation of Notch signaling pathway / NOTCH4 Activation and Transmission of Signal to the Nucleus / adherens junction organization / metallodipeptidase activity / negative regulation of cell adhesion / positive regulation of tumor necrosis factor-mediated signaling pathway / regulation of postsynapse organization / clathrin-coated vesicle / Golgi-associated vesicle / Signaling by EGFR / amyloid precursor protein catabolic process / pore complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / response to tumor necrosis factor / Collagen degradation / membrane protein ectodomain proteolysis / tertiary granule membrane / cochlea development / extracellular matrix disassembly / EPH-ephrin mediated repulsion of cells / specific granule membrane / Degradation of the extracellular matrix / Notch signaling pathway / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / synaptic membrane / Activated NOTCH1 Transmits Signal to the Nucleus / integrin-mediated signaling pathway / adherens junction / Post-translational protein phosphorylation / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein processing / metalloendopeptidase activity / SH3 domain binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / positive regulation of tumor necrosis factor production / cell-cell signaling / positive regulation of cell growth / endopeptidase activity / in utero embryonic development / protein phosphorylation / postsynaptic density / positive regulation of cell migration / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / axon / negative regulation of gene expression / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / dendrite / Neutrophil degranulation / protein kinase binding / glutamatergic synapse / cell surface / Golgi apparatus / protein homodimerization activity / extracellular exosome / metal ion binding / nucleus / membrane / 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. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Disintegrin and metalloproteinase domain-containing protein 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_seq_id / _chem_comp.pdbx_synonyms ..._atom_site.auth_seq_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 11G2 Fab Light Chain
H: 11G2 Fab Heavy Chain
A: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1309
Polymers96,4973
Non-polymers1,6336
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-49 kcal/mol
Surface area39850 Å2
Unit cell
Length a, b, c (Å)79.230, 97.580, 262.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 48943.719 Da / Num. of mol.: 1
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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Antibody , 2 types, 2 molecules LH

#1: Antibody 11G2 Fab Light Chain


Mass: 23455.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody 11G2 Fab Heavy Chain


Mass: 24097.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpN]{[(2+1)][ethyl]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 5 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 2.23M Ammonium Sulfate 100mM Tris pH 8.5 2% PEG400

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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: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 35539 / % possible obs: 99.83 % / Redundancy: 10.6 % / CC1/2: 0.989 / Net I/σ(I): 4.05
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 0.87 / Num. unique obs: 1850 / CC1/2: 0.355 / % possible all: 98.76

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.79 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3173 3582 10.08 %
Rwork0.2612 --
obs0.2669 35539 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6531 0 100 1 6632
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136844
X-RAY DIFFRACTIONf_angle_d0.6939285
X-RAY DIFFRACTIONf_dihedral_angle_d17.942555
X-RAY DIFFRACTIONf_chiral_restr0.0481028
X-RAY DIFFRACTIONf_plane_restr0.0041184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.14080.39831360.38521176X-RAY DIFFRACTION91
3.1408-3.18390.41871280.351149X-RAY DIFFRACTION99
3.1839-3.22930.36851380.35141214X-RAY DIFFRACTION99
3.2293-3.27750.44731400.33331260X-RAY DIFFRACTION100
3.2775-3.32870.37891410.34431228X-RAY DIFFRACTION100
3.3287-3.38330.38321380.34451215X-RAY DIFFRACTION100
3.3833-3.44160.38451360.30551250X-RAY DIFFRACTION100
3.4416-3.50420.38071390.30341247X-RAY DIFFRACTION100
3.5042-3.57160.37061350.28991228X-RAY DIFFRACTION100
3.5716-3.64440.32631400.28821238X-RAY DIFFRACTION100
3.6444-3.72370.30631370.30691227X-RAY DIFFRACTION100
3.7237-3.81020.36041310.26881213X-RAY DIFFRACTION100
3.8102-3.90550.30091420.27191278X-RAY DIFFRACTION100
3.9055-4.0110.3151330.24351217X-RAY DIFFRACTION100
4.011-4.1290.31321420.24231225X-RAY DIFFRACTION100
4.129-4.26220.28661350.22241242X-RAY DIFFRACTION100
4.2622-4.41450.30851400.22551251X-RAY DIFFRACTION100
4.4145-4.59110.28311390.21681220X-RAY DIFFRACTION100
4.5911-4.79980.27351360.21011247X-RAY DIFFRACTION100
4.7998-5.05270.23951430.22781218X-RAY DIFFRACTION100
5.0527-5.36890.30721350.20891244X-RAY DIFFRACTION100
5.3689-5.78280.29471380.22421234X-RAY DIFFRACTION100
5.7828-6.36360.28681410.2491235X-RAY DIFFRACTION100
6.3636-7.28180.32551370.26791217X-RAY DIFFRACTION100
7.2818-9.16440.28671390.2411258X-RAY DIFFRACTION100
9.1644-48.7960.27241430.23851226X-RAY DIFFRACTION100

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