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- PDB-4dd8: ADAM-8 metalloproteinase domain with bound batimastat -

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Basic information

Entry
Database: PDB / ID: 4dd8
TitleADAM-8 metalloproteinase domain with bound batimastat
ComponentsDisintegrin and metalloproteinase domain-containing protein 8
KeywordsHYDROLASE/HYDROLASE INHIBITOR / batimastat / inflammation / alpha/beta motif / metalloproteinase / allergic asthma / tumorigenesis / arthritis / aberrant neural cell signaling / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


positive regulation of fibronectin-dependent thymocyte migration / positive regulation of eosinophil migration / dense core granule membrane / tertiary granule / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / positive regulation of neutrophil extravasation / phagolysosome / neutrophil degranulation / positive regulation of T cell differentiation in thymus / regulation of cell-cell adhesion ...positive regulation of fibronectin-dependent thymocyte migration / positive regulation of eosinophil migration / dense core granule membrane / tertiary granule / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / positive regulation of neutrophil extravasation / phagolysosome / neutrophil degranulation / positive regulation of T cell differentiation in thymus / regulation of cell-cell adhesion / lymphocyte chemotaxis / alpha9-beta1 integrin-ADAM8 complex / positive regulation of protein processing / leukocyte migration involved in inflammatory response / positive regulation of acute inflammatory response / specific granule / positive regulation of innate immune response / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / podosome / positive regulation of membrane protein ectodomain proteolysis / positive regulation of thymocyte apoptotic process / plasma membrane => GO:0005886 / tertiary granule membrane / ficolin-1-rich granule membrane / positive regulation of cell adhesion / extracellular matrix disassembly / positive regulation of bone resorption / specific granule membrane / cell adhesion molecule binding / Degradation of the extracellular matrix / : / positive regulation of protein secretion / positive regulation of MAP kinase activity / cell morphogenesis / metalloendopeptidase activity / cell-cell adhesion / metallopeptidase activity / positive regulation of NF-kappaB transcription factor activity / cellular response to hypoxia / angiogenesis / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / inflammatory response / serine-type endopeptidase activity / calcium ion binding / Neutrophil degranulation / cell surface / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin ...ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BAT / : / Disintegrin and metalloproteinase domain-containing protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHall, T. / Shieh, H.S. / Day, J.E. / Caspers, N. / Chrencik, J.E. / Williams, J.M. / Pegg, L.E. / Pauley, A.M. / Moon, A.F. / Krahn, J.M. ...Hall, T. / Shieh, H.S. / Day, J.E. / Caspers, N. / Chrencik, J.E. / Williams, J.M. / Pegg, L.E. / Pauley, A.M. / Moon, A.F. / Krahn, J.M. / Fischer, D.H. / Kiefer, J.R. / Tomasselli, A.G. / Zack, M.D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of human ADAM-8 catalytic domain complexed with batimastat.
Authors: Hall, T. / Shieh, H.S. / Day, J.E. / Caspers, N. / Chrencik, J.E. / Williams, J.M. / Pegg, L.E. / Pauley, A.M. / Moon, A.F. / Krahn, J.M. / Fischer, D.H. / Kiefer, J.R. / Tomasselli, A.G. / Zack, M.D.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 8
B: Disintegrin and metalloproteinase domain-containing protein 8
C: Disintegrin and metalloproteinase domain-containing protein 8
D: Disintegrin and metalloproteinase domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,15430
Polymers93,4174
Non-polymers2,73626
Water7,476415
1
A: Disintegrin and metalloproteinase domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0979
Polymers23,3541
Non-polymers7438
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Disintegrin and metalloproteinase domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0197
Polymers23,3541
Non-polymers6656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Disintegrin and metalloproteinase domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0197
Polymers23,3541
Non-polymers6656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Disintegrin and metalloproteinase domain-containing protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0197
Polymers23,3541
Non-polymers6656
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.600, 50.900, 93.500
Angle α, β, γ (deg.)90.00, 102.40, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
34
44
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (((resid 197:219 or resid 221:252 or resid...
211chain B and (((resid 197:219 or resid 221:252 or resid...
311chain C and (((resid 197:219 or resid 221:252 or resid...
411chain D and (((resid 197:219 or resid 221:252 or resid...
112chain A and resid 253:257 and backbone
212chain B and resid 253:257 and backbone
312chain C and resid 253:257 and backbone
412chain D and resid 253:257 and backbone
113chain A and resid 258:262
213chain B and resid 258:262
313chain C and resid 258:262
413chain D and resid 258:262
114chain A and resid 263:278 and backbone
214chain B and resid 263:278 and backbone
314chain C and resid 263:278 and backbone
414chain D and resid 263:278 and backbone
115chain B and resid 276:283
215chain D and resid 276:283

NCS ensembles :
ID
1
2
3
4
5

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Disintegrin and metalloproteinase domain-containing protein 8 / ADAM 8 / Cell surface antigen MS2


Mass: 23354.297 Da / Num. of mol.: 4 / Fragment: UNP Residues 196-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM8, MS2 / Plasmid: pcDNAmychisB / Cell line (production host): HEK-293 Freestyle / Production host: Homo sapiens (human)
References: UniProt: P78325, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 7 types, 441 molecules

#2: Chemical
ChemComp-BAT / 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE / BATIMASTAT / BB94


Mass: 477.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H31N3O4S2 / Comment: inhibitor*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Purified ADAM-8/batimastat complex (10mg/mL) was crystallized by the sitting-drop vapor diffusion method, mixing 1uL complex with 1uL of 0.1M Tris pH 8.0, 1M sodium formate, 10% methanol. ...Details: Purified ADAM-8/batimastat complex (10mg/mL) was crystallized by the sitting-drop vapor diffusion method, mixing 1uL complex with 1uL of 0.1M Tris pH 8.0, 1M sodium formate, 10% methanol. Crystals reached usable size in 10 days. Crystals were then transferred to a cryo solution containing 0.1M Tris pH 8.0, 1.2M sodium formate, 10% methanol, and 10% glycerol. The crystals were harvested and flash frozen in liquid nitrogen for data collection., VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Details: mirrors
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.26
ReflectionResolution: 2.1→50 Å / Num. all: 49827 / Num. obs: 49479 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.106 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.92 / Num. unique all: 4746 / Rsym value: 0.365 / % possible all: 95.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R55

1r55


Resolution: 2.1→44.745 Å / Cross valid method: R-free / σ(F): 1 / Phase error: 36.91 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2368 4.97 %random
Rwork0.1881 ---
obs0.1916 47689 96.04 %-
all-49479 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.471 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3066 Å2-0 Å2-12.629 Å2
2---4.8035 Å20 Å2
3---1.4969 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 150 415 6835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086718
X-RAY DIFFRACTIONf_angle_d0.6828982
X-RAY DIFFRACTIONf_dihedral_angle_d12.892340
X-RAY DIFFRACTIONf_chiral_restr0.049990
X-RAY DIFFRACTIONf_plane_restr0.0021200
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A674X-RAY DIFFRACTIONPOSITIONAL
12B674X-RAY DIFFRACTIONPOSITIONAL0.155
13C682X-RAY DIFFRACTIONPOSITIONAL0.122
14D670X-RAY DIFFRACTIONPOSITIONAL0.151
21A20X-RAY DIFFRACTIONPOSITIONAL
22B20X-RAY DIFFRACTIONPOSITIONAL0.237
23C20X-RAY DIFFRACTIONPOSITIONAL0.127
24D20X-RAY DIFFRACTIONPOSITIONAL0.145
31A41X-RAY DIFFRACTIONPOSITIONAL
32B41X-RAY DIFFRACTIONPOSITIONAL0.138
33C41X-RAY DIFFRACTIONPOSITIONAL0.118
34D41X-RAY DIFFRACTIONPOSITIONAL0.145
41A60X-RAY DIFFRACTIONPOSITIONAL
42B60X-RAY DIFFRACTIONPOSITIONAL0.211
43C60X-RAY DIFFRACTIONPOSITIONAL0.187
44D60X-RAY DIFFRACTIONPOSITIONAL0.209
51B65X-RAY DIFFRACTIONPOSITIONAL
52D65X-RAY DIFFRACTIONPOSITIONAL0.078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14290.3006970.23612354X-RAY DIFFRACTION82
2.1429-2.18940.28971180.22652506X-RAY DIFFRACTION87
2.1894-2.24030.26341200.22532514X-RAY DIFFRACTION87
2.2403-2.29630.32881220.22762554X-RAY DIFFRACTION88
2.2963-2.35830.27031460.2272589X-RAY DIFFRACTION90
2.3583-2.42760.29531410.21812653X-RAY DIFFRACTION91
2.4276-2.50590.29911460.20942619X-RAY DIFFRACTION91
2.5059-2.59530.30291330.21112709X-RAY DIFFRACTION92
2.5953-2.69910.27081600.21242683X-RAY DIFFRACTION93
2.6991-2.82170.28061500.20382700X-RAY DIFFRACTION93
2.8217-2.97020.3241260.22745X-RAY DIFFRACTION94
2.9702-3.15580.2571150.1842764X-RAY DIFFRACTION95
3.1558-3.39880.25681270.17142783X-RAY DIFFRACTION95
3.3988-3.73950.22431430.16462749X-RAY DIFFRACTION94
3.7395-4.27750.21961550.14662746X-RAY DIFFRACTION93
4.2775-5.37750.19231390.15142791X-RAY DIFFRACTION95
5.3775-22.83110.2491690.19452873X-RAY DIFFRACTION94

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