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- PDB-8gh4: Complex of Adam 10 disentegrin cysteine rich domains with human m... -

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Basic information

Entry
Database: PDB / ID: 8gh4
TitleComplex of Adam 10 disentegrin cysteine rich domains with human monoclonal antibody
Components
  • Antibody heavy chain
  • Antibody light chain
  • Disintegrin and metalloproteinase domain-containing protein 10
KeywordsIMMUNE SYSTEM / colorectal cancer / adam 10 / human monoclonal antibody
Function / homology
Function and homology information


Degradation of the extracellular matrix / ADAM10 endopeptidase / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of cell adhesion / clathrin-coated vesicle / Neutrophil degranulation / Golgi-associated vesicle / amyloid precursor protein catabolic process ...Degradation of the extracellular matrix / ADAM10 endopeptidase / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / negative regulation of cell adhesion / clathrin-coated vesicle / Neutrophil degranulation / Golgi-associated vesicle / amyloid precursor protein catabolic process / membrane protein ectodomain proteolysis / Notch signaling pathway / synaptic membrane / adherens junction / protein processing / metalloendopeptidase activity / SH3 domain binding / metallopeptidase activity / endopeptidase activity / in utero embryonic development / Golgi membrane / axon / protein phosphorylation / dendrite / protein kinase binding / Golgi apparatus / cell surface / protein homodimerization activity / nucleus / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
: / ADAM10, cysteine-rich domain / ADAM10/ADAM17 catalytic domain / Metallo-peptidase family M12B Reprolysin-like / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin ...: / ADAM10, cysteine-rich domain / ADAM10/ADAM17 catalytic domain / Metallo-peptidase family M12B Reprolysin-like / 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)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsNikolov, D.B. / Saha, N. / Xu, K. / Goldgur, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R21AG08068501 United States
CitationJournal: Biomed Pharmacother / Year: 2023
Title: Fully human monoclonal antibody targeting activated ADAM10 on colorectal cancer cells.
Authors: Saha, N. / Baek, D.S. / Mendoza, R.P. / Robev, D. / Xu, Y. / Goldgur, Y. / De La Cruz, M.J. / de Stanchina, E. / Janes, P.W. / Xu, K. / Dimitrov, D.S. / Nikolov, D.B.
History
DepositionMar 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antibody heavy chain
L: Antibody light chain
E: Disintegrin and metalloproteinase domain-containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9064
Polymers68,4823
Non-polymers4241
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.578, 85.690, 129.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Antibody Antibody heavy chain


Mass: 24089.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Antibody light chain


Mass: 23218.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: 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: 21172.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ADAM10, MADM / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q10741, ADAM10 endopeptidase
#4: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
Has ligand of interestN

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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: 3.21 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M bycine, 20% PEG 10K / Temp details: ambient

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 7903 / % possible obs: 86.9 % / Redundancy: 2.7 % / CC1/2: 0.988 / Rpim(I) all: 0.121 / Net I/σ(I): 7.67
Reflection shellResolution: 3.8→3.87 Å / Redundancy: 2.4 % / Num. unique obs: 305 / CC1/2: 0.724 / Rpim(I) all: 0.451 / % possible all: 67.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→40.69 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3115 382 4.85 %
Rwork0.2878 --
obs0.2889 7875 86.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→40.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4752 0 28 0 4780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034880
X-RAY DIFFRACTIONf_angle_d0.6516605
X-RAY DIFFRACTIONf_dihedral_angle_d12.1841788
X-RAY DIFFRACTIONf_chiral_restr0.042732
X-RAY DIFFRACTIONf_plane_restr0.007855
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.350.34791180.34812168X-RAY DIFFRACTION77
4.35-5.480.33121190.32538X-RAY DIFFRACTION89
5.48-40.690.28331450.25612787X-RAY DIFFRACTION93

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