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- PDB-5l0q: Crystal structure of the complex between ADAM10 D+C domain and a ... -

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Basic information

Entry
Database: PDB / ID: 5l0q
TitleCrystal structure of the complex between ADAM10 D+C domain and a conformation specific mAb 8C7.
Components
  • Disintegrin and metalloproteinase domain-containing protein 10
  • mAb 8C7 heavy chain
  • mAb 8C7 light chain
KeywordsHYDROLASE/IMMUNE SYSTEM / ADAM protease / mAb / 8C7 / Notch signaling / therapeutic antibody / cancer stem cell / drug resistance / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Degradation of the extracellular matrix / ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / regulation of vasculature development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / marginal zone B cell differentiation ...Degradation of the extracellular matrix / ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / regulation of vasculature development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / marginal zone B cell differentiation / postsynapse organization / protein catabolic process at postsynapse / pore complex assembly / perinuclear endoplasmic reticulum / positive regulation of T cell chemotaxis / tetraspanin-enriched microdomain / regulation of Notch signaling pathway / adherens junction organization / metallodipeptidase activity / negative regulation of cell adhesion / regulation of postsynapse organization / clathrin-coated vesicle / Neutrophil degranulation / Golgi-associated vesicle / amyloid precursor protein catabolic process / pore complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / response to tumor necrosis factor / membrane protein ectodomain proteolysis / cochlea development / Notch signaling pathway / synaptic membrane / adherens junction / protein processing / metalloendopeptidase activity / SH3 domain binding / metallopeptidase activity / positive regulation of cell growth / endopeptidase activity / in utero embryonic development / protein phosphorylation / postsynaptic density / Golgi membrane / negative regulation of gene expression / axon / positive regulation of cell population proliferation / dendrite / protein kinase binding / glutamatergic synapse / cell surface / Golgi apparatus / protein homodimerization activity / metal ion binding / nucleus / 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 speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.759 Å
AuthorsXu, K. / Saha, N. / Nikolov, D.B.
CitationJournal: J.Exp.Med. / Year: 2016
Title: An activated form of ADAM10 is tumor selective and regulates cancer stem-like cells and tumor growth.
Authors: Atapattu, L. / Saha, N. / Chheang, C. / Eissman, M.F. / Xu, K. / Vail, M.E. / Hii, L. / Llerena, C. / Liu, Z. / Horvay, K. / Abud, H.E. / Kusebauch, U. / Moritz, R.L. / Ding, B.S. / Cao, Z. ...Authors: Atapattu, L. / Saha, N. / Chheang, C. / Eissman, M.F. / Xu, K. / Vail, M.E. / Hii, L. / Llerena, C. / Liu, Z. / Horvay, K. / Abud, H.E. / Kusebauch, U. / Moritz, R.L. / Ding, B.S. / Cao, Z. / Rafii, S. / Ernst, M. / Scott, A.M. / Nikolov, D.B. / Lackmann, M. / Janes, P.W.
History
DepositionJul 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Disintegrin and metalloproteinase domain-containing protein 10
B: mAb 8C7 light chain
C: mAb 8C7 heavy chain
D: Disintegrin and metalloproteinase domain-containing protein 10
E: mAb 8C7 light chain
F: mAb 8C7 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,02925
Polymers138,8476
Non-polymers2,18219
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15470 Å2
ΔGint-233 kcal/mol
Surface area59510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.326, 141.679, 268.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules BECF

#2: Antibody mAb 8C7 light chain


Mass: 23712.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody mAb 8C7 heavy chain


Mass: 23930.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 6 molecules AD

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


Mass: 21780.699 Da / Num. of mol.: 2 / Fragment: UNP residues 455-646
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ADAM10, MADM / Production host: Homo sapiens (human) / References: UniProt: Q10741, ADAM10 endopeptidase
#4: 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.: 4
Source method: isolated from a genetically manipulated source
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 , 3 types, 349 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 3.66 Å3/Da / Density % sol: 66.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES, 0.2M NaCl, and 1.6 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.759→125.262 Å / Num. all: 52855 / Num. obs: 52855 / % possible obs: 99.1 % / Redundancy: 4.4 % / Rpim(I) all: 0.071 / Rrim(I) all: 0.155 / Rsym value: 0.125 / Net I/av σ(I): 5.556 / Net I/σ(I): 10.3 / Num. measured all: 234255
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.76-2.914.40.6751.1198.9
2.91-3.084.60.4891.6199.8
3.08-3.34.50.2962.6199.4
3.3-3.564.30.1834.1198.6
3.56-3.94.60.1345.6199.8
3.9-4.364.40.0819.1199.5
4.36-5.044.40.06111.3198
5.04-6.174.40.06311.2199.8
6.17-8.734.30.05113.3197.6
8.73-125.2624.20.03316.1196.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AO7

2ao7


Resolution: 2.759→125.262 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2514 2689 5.1 %
Rwork0.2028 --
obs0.2052 52755 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.759→125.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9485 0 123 334 9942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099847
X-RAY DIFFRACTIONf_angle_d1.26113313
X-RAY DIFFRACTIONf_dihedral_angle_d17.9582304
X-RAY DIFFRACTIONf_chiral_restr0.0871449
X-RAY DIFFRACTIONf_plane_restr0.0071717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7593-2.80950.38881480.35322576X-RAY DIFFRACTION97
2.8095-2.86350.34191160.29812570X-RAY DIFFRACTION99
2.8635-2.92190.33171300.26722632X-RAY DIFFRACTION100
2.9219-2.98550.32031600.26282622X-RAY DIFFRACTION100
2.9855-3.05490.32221390.26682599X-RAY DIFFRACTION100
3.0549-3.13130.31241480.24892658X-RAY DIFFRACTION100
3.1313-3.2160.27881480.24332603X-RAY DIFFRACTION99
3.216-3.31070.28411530.24442620X-RAY DIFFRACTION99
3.3107-3.41750.25711250.2222569X-RAY DIFFRACTION98
3.4175-3.53970.24251480.19872614X-RAY DIFFRACTION98
3.5397-3.68140.23171370.18512611X-RAY DIFFRACTION100
3.6814-3.8490.23921410.17812687X-RAY DIFFRACTION100
3.849-4.05190.23071310.16792641X-RAY DIFFRACTION99
4.0519-4.30580.21111390.16122656X-RAY DIFFRACTION100
4.3058-4.63820.19731360.15392574X-RAY DIFFRACTION96
4.6382-5.1050.22061530.16372673X-RAY DIFFRACTION99
5.105-5.84370.23341360.17082734X-RAY DIFFRACTION100
5.8437-7.36240.24981450.19832653X-RAY DIFFRACTION96
7.3624-125.39080.21521560.20952774X-RAY DIFFRACTION95

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