[English] 日本語
Yorodumi
- PDB-3v96: Complex of matrix metalloproteinase-10 catalytic domain (MMP-10cd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v96
TitleComplex of matrix metalloproteinase-10 catalytic domain (MMP-10cd) with tissue inhibitor of metalloproteinases-1 (TIMP-1)
Components
  • Metalloproteinase inhibitor 1
  • Stromelysin-2
KeywordsHYDROLASE INHIBITOR/HYDROLASE / Metzincin / OB-fold / Metalloproteinase / Protease inhibitor / HYDROLASE INHIBITOR-HYDROLASE complex
Function / homology
Function and homology information


stromelysin 2 / regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / negative regulation of trophoblast cell migration / negative regulation of membrane protein ectodomain proteolysis / connective tissue replacement involved in inflammatory response wound healing / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / negative regulation of catalytic activity / cellular response to UV-A ...stromelysin 2 / regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / negative regulation of trophoblast cell migration / negative regulation of membrane protein ectodomain proteolysis / connective tissue replacement involved in inflammatory response wound healing / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / negative regulation of catalytic activity / cellular response to UV-A / cellular response to peptide / negative regulation of endopeptidase activity / peptidase inhibitor activity / cartilage development / Interleukin-10 signaling / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / basement membrane / extracellular matrix disassembly / response to hormone / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / response to cytokine / platelet alpha granule lumen / cytokine activity / Post-translational protein phosphorylation / growth factor activity / metalloendopeptidase activity / response to peptide hormone / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / protease binding / Interleukin-4 and Interleukin-13 signaling / endoplasmic reticulum lumen / serine-type endopeptidase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding
Similarity search - Function
Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Netrin domain ...Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Protease inhibitor I35 (TIMP) / Proteinase inhibitor I35b (TIMP), C-terminal / Tissue inhibitor of metalloproteinase, conserved site / Tissue inhibitor of metalloproteinase / Tissue inhibitors of metalloproteinases signature. / Tissue inhibitor of metalloproteinase family. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Metalloproteinase inhibitor 1 / Stromelysin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBatra, J. / Soares, A.S. / Radisky, E.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Matrix metalloproteinase-10 (MMP-10) interaction with tissue inhibitors of metalloproteinases TIMP-1 and TIMP-2: binding studies and crystal structure.
Authors: Batra, J. / Robinson, J. / Soares, A.S. / Fields, A.P. / Radisky, D.C. / Radisky, E.S.
History
DepositionDec 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Metalloproteinase inhibitor 1
B: Stromelysin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7019
Polymers39,2602
Non-polymers4417
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-94 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)231.720, 37.682, 39.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Metalloproteinase inhibitor 1 / Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor / ...Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor / Tissue inhibitor of metalloproteinases 1 / TIMP-1


Mass: 20689.822 Da / Num. of mol.: 1 / Fragment: unp residues 24-207 / Mutation: N30A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLGI, TIMP, TIMP1 / Plasmid: pTT/TIMP1 / Cell line (production host): HEK 293E / Production host: HOMO SAPIENS (human) / References: UniProt: P01033
#2: Protein Stromelysin-2 / SL-2 / Matrix metalloproteinase-10 / MMP-10 / Transin-2


Mass: 18570.561 Da / Num. of mol.: 1 / Fragment: unp residues 99-263
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP10, STMY2 / Plasmid: MMP-10cdna / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09238, stromelysin 2

-
Non-polymers , 4 types, 195 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 0.1 M sodium dihydrogen phosphate solution, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 26365 / % possible obs: 91.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 23.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 1.4

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.288 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1326 5 %RANDOM
Rwork0.215 ---
obs0.218 26280 91.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20 Å2
2---1.12 Å20 Å2
3---2.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 15 188 2781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222682
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.9483650
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7635325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.70923.44125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88415426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5731514
X-RAY DIFFRACTIONr_chiral_restr0.1370.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212055
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
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_it0.9981.51616
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58322609
X-RAY DIFFRACTIONr_scbond_it2.58231066
X-RAY DIFFRACTIONr_scangle_it3.6644.51038
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 54 -
Rwork0.341 1115 -
obs--57.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.849-0.81520.42233.1743-1.45122.62080.1152-0.143-0.24860.04-0.1971-0.2640.01330.40610.08180.2115-0.0346-0.03760.3275-0.00950.0592158.7765.191-5.856
230.236614.71737.830210.049711.437922.2167-1.89192.06043.4614-2.0630.63151.8326-3.4196-0.33811.26040.93320.1055-0.30740.6550.14560.427145.80710.813-22.757
38.18340.01493.05095.0951-1.09042.3825-0.09440.61280.5933-0.5493-0.0406-0.3795-0.12610.58840.1350.3489-0.07260.04440.5179-0.00150.1049161.86613.253-15.362
49.1928-3.6256-1.23977.5496-0.17173.9154-0.05592.8351-0.4035-2.129-1.6552-2.85160.29791.61061.7110.92730.23070.98022.33410.64392.1048168.5974.579-13.629
54.30530.3840.12572.6229-0.90352.32640.05490.0229-0.0269-0.0099-0.1798-0.1433-0.1750.35790.1250.2121-0.0459-0.01650.32420.00030.0196158.2428.662-7.488
629.2786-8.54125.19849.7264-6.32014.4308-0.1032-0.6395-3.41010.54390.42930.965-0.0342-0.1148-0.32610.537-0.0070.12690.49520.24170.8007151.38-8.3138.545
73.7472.6101-1.14466.3883-1.42295.78760.1914-0.8205-0.68031.4147-0.3192-0.2347-1.14550.78540.12770.5977-0.0205-0.0280.79560.26420.261159.3061.1589.732
84.8534-2.84131.41326.1795-0.55171.31980.0409-0.0166-1.15480.23310.16951.3874-0.04590.0945-0.21050.1399-0.02510.03230.12130.02450.4902132.8012.524-5.369
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 35
3X-RAY DIFFRACTION3A36 - 46
4X-RAY DIFFRACTION4A47 - 58
5X-RAY DIFFRACTION5A59 - 130
6X-RAY DIFFRACTION6A131 - 144
7X-RAY DIFFRACTION7A145 - 178
8X-RAY DIFFRACTION8B105 - 468

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more