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- PDB-2v4b: Crystal Structure of Human ADAMTS-1 catalytic Domain and Cysteine... -

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Basic information

Entry
Database: PDB / ID: 2v4b
TitleCrystal Structure of Human ADAMTS-1 catalytic Domain and Cysteine- Rich Domain (apo-form)
ComponentsADAMTS-1
KeywordsHYDROLASE / ZYMOGEN / PROTEASE / ADAMTS-1 / METALLOPROTEASE / HEPARIN-BINDING / METALLOPROTEINASE / METZINCIN / GLYCOPROTEIN / METAL-BINDING / EXTRACELLULAR MATRIX / CLEAVAGE ON PAIR OF BASIC RESIDUES
Function / homology
Function and homology information


Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / ovulation from ovarian follicle / heart trabecula formation / positive regulation of vascular associated smooth muscle cell migration / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / basement membrane / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix ...Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / ovulation from ovarian follicle / heart trabecula formation / positive regulation of vascular associated smooth muscle cell migration / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / basement membrane / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / negative regulation of angiogenesis / integrin-mediated signaling pathway / kidney development / metalloendopeptidase activity / metallopeptidase activity / heparin binding / cytoplasmic vesicle / negative regulation of cell population proliferation / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
Peptidase M12B, ADAM-TS1 / YefM-like fold - #60 / Thrombospondin type 1 domain / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / : / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 ...Peptidase M12B, ADAM-TS1 / YefM-like fold - #60 / Thrombospondin type 1 domain / ADAMTS/ADAMTS-like, Spacer 1 / ADAMTS/ADAMTS-like / ADAMTS, cysteine-rich domain 2 / ADAMTS/ADAMTS-like, cysteine-rich domain 3 / : / ADAM-TS Spacer 1 / ADAMTS cysteine-rich domain 2 / ADAMTS cysteine-rich domain / YefM-like fold / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Thrombospondin type 1 domain / Thrombospondin type-1 (TSP1) repeat superfamily / Thrombospondin type-1 (TSP1) repeat profile. / Thrombospondin type 1 repeats / Thrombospondin type-1 (TSP1) repeat / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICKEL (II) ION / A disintegrin and metalloproteinase with thrombospondin motifs 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGerhardt, S. / Hassall, G. / Hawtin, P. / McCall, E. / Flavell, L. / Minshull, C. / Hargreaves, D. / Ting, A. / Pauptit, R.A. / Parker, A.E. / Abbott, W.M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structures of Human Adamts-1 Reveal a Conserved Catalytic Domain and a Disintegrin-Like Domain with a Fold Homologous to Cysteine-Rich Domains.
Authors: Gerhardt, S. / Hassall, G. / Hawtin, P. / Mccall, E. / Flavell, L. / Minshull, C. / Hargreaves, D. / Ting, A. / Pauptit, R.A. / Parker, A.E. / Abbott, W.M.
History
DepositionJun 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 24, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADAMTS-1
B: ADAMTS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,39129
Polymers65,8242
Non-polymers1,56727
Water3,855214
1
A: ADAMTS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,82517
Polymers32,9121
Non-polymers91316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ADAMTS-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,56612
Polymers32,9121
Non-polymers65411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.579, 64.396, 113.524
Angle α, β, γ (deg.)90.00, 90.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.02465, 0.02414), (0.1001, 0.9947, -0.006286), (0.995, -0.09997)
Vector: 0.8263, -27.98, 31.44)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ADAMTS-1 / A DISINTEGRIN AND METALLOPROTEINASE WITH THROMBOSPONDIN MOTIFS 1 / ADAM-TS 1 / ADAM-TS1 / METH-1


Mass: 32911.938 Da / Num. of mol.: 2
Fragment: CATALYTIC DOMAIN INCL. CYSTEINE-RICH DOMAIN, RESIDUES 253-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q9UHI8, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 6 types, 241 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCLEAVES AGGRECAN, A CARTILAGE PROTEOGLYCAN
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: 2.96 Å3/Da / Density % sol: 58.06 % / Description: NONE
Crystal growpH: 7
Details: 0.2-0.6M SODIUM ACETATE, 0.05M CADMIUM SULPHATE, 0.1M HEPES PH 7.0, 12-22% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.41→40.26 Å / Num. obs: 50457 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.64 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 4.17
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.63 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.06 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→40.26 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 14.081 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 421-427 AND 433-437 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2565 5.1 %RANDOM
Rwork0.22 ---
obs0.222 47875 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.06 Å2
2--1.97 Å20 Å2
3----2.05 Å2
Refinement stepCycle: LAST / Resolution: 2→40.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4315 0 27 214 4556
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214430
X-RAY DIFFRACTIONr_bond_other_d0.0030.023766
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9326018
X-RAY DIFFRACTIONr_angle_other_deg0.838833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1124.9200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9315709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4981515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024929
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02840
X-RAY DIFFRACTIONr_nbd_refined0.210.2918
X-RAY DIFFRACTIONr_nbd_other0.1690.23528
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22078
X-RAY DIFFRACTIONr_nbtor_other0.0820.22365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2190
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1170.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5621.52788
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05124486
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.431703
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2724.51532
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 185
Rwork0.301 3511
Refinement TLS params.Method: refined / Origin x: 0.9936 Å / Origin y: 1.5114 Å / Origin z: 29.697 Å
111213212223313233
T-0.1388 Å20.0036 Å2-0.0007 Å2--0.1001 Å2-0.007 Å2---0.0632 Å2
L0.5558 °20.0266 °20.0071 °2-0.954 °2-0.6649 °2--1.9877 °2
S0.001 Å °-0.2039 Å °-0.0058 Å °-0.0847 Å °-0.0131 Å °-0.0109 Å °0.0152 Å °0.0319 Å °0.0121 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B256 - 552
2X-RAY DIFFRACTION1A256 - 551

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