[English] 日本語
Yorodumi
- PDB-3ma2: Complex membrane type-1 matrix metalloproteinase (MT1-MMP) with t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ma2
TitleComplex membrane type-1 matrix metalloproteinase (MT1-MMP) with tissue inhibitor of metalloproteinase-1 (TIMP-1)
Components
  • Matrix metalloproteinase-14
  • Metalloproteinase inhibitor 1Matrix metalloproteinase inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Protein - protein complex / Cleavage on pair of basic residues / Disulfide bond / Membrane / Metal-binding / Metalloprotease / Protease / Transmembrane / Zymogen / Erythrocyte maturation / Glycoprotein / Metalloenzyme inhibitor / Metalloprotease inhibitor / Secreted / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


membrane-type matrix metalloproteinase-1 / craniofacial suture morphogenesis / regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / positive regulation of macrophage migration / macropinosome / peptidase inhibitor activity / head development / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing ...membrane-type matrix metalloproteinase-1 / craniofacial suture morphogenesis / regulation of integrin-mediated signaling pathway / negative regulation of metallopeptidase activity / positive regulation of macrophage migration / macropinosome / peptidase inhibitor activity / head development / negative regulation of trophoblast cell migration / connective tissue replacement involved in inflammatory response wound healing / negative regulation of membrane protein ectodomain proteolysis / chondrocyte proliferation / astrocyte cell migration / metalloendopeptidase inhibitor activity / response to odorant / tissue remodeling / cellular response to UV-A / negative regulation of catalytic activity / negative regulation of focal adhesion assembly / positive regulation of protein processing / negative regulation of endopeptidase activity / endochondral ossification / embryonic cranial skeleton morphogenesis / cartilage development / zymogen activation / endothelial cell proliferation / intermediate filament cytoskeleton / positive regulation of B cell differentiation / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / negative regulation of Notch signaling pathway / endodermal cell differentiation / Activation of Matrix Metalloproteinases / metalloaminopeptidase activity / Interleukin-10 signaling / Collagen degradation / collagen catabolic process / basement membrane / extracellular matrix disassembly / regulation of protein localization to plasma membrane / response to mechanical stimulus / ovarian follicle development / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / platelet alpha granule lumen / response to hormone / skeletal system development / response to cytokine / cytokine activity / cell motility / Post-translational protein phosphorylation / growth factor activity / lung development / response to organic cyclic compound / protein processing / metalloendopeptidase activity / response to peptide hormone / Golgi lumen / response to estrogen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / male gonad development / melanosome / integrin binding / Platelet degranulation / cytoplasmic vesicle / positive regulation of cell growth / Interleukin-4 and Interleukin-13 signaling / angiogenesis / endopeptidase activity / protease binding / response to oxidative stress / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / focal adhesion / positive regulation of cell population proliferation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / 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 / PGBD superfamily ...Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / 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 / PGBD superfamily / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / 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) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Metalloproteinase inhibitor 1 / Matrix metalloproteinase-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGrossman, M. / Tworowski, D. / Dym, O. / Lee, M.-H. / Levy, Y. / Sagi, I.
CitationJournal: Biochemistry / Year: 2010
Title: The Intrinsic Protein Flexibility of Endogenous Protease Inhibitor TIMP-1 Controls Its Binding Interface and Affects Its Function.
Authors: Grossman, M. / Tworowski, D. / Dym, O. / Lee, M.H. / Levy, Y. / Murphy, G. / Sagi, I.
History
DepositionMar 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 28, 2015Group: Structure summary
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Matrix metalloproteinase-14
A: Matrix metalloproteinase-14
B: Metalloproteinase inhibitor 1
C: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,79812
Polymers69,3764
Non-polymers4228
Water2,612145
1
D: Matrix metalloproteinase-14
C: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8996
Polymers34,6882
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-12 kcal/mol
Surface area14000 Å2
MethodPISA
2
A: Matrix metalloproteinase-14
B: Metalloproteinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8996
Polymers34,6882
Non-polymers2114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-13 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.690, 63.649, 87.158
Angle α, β, γ (deg.)90.00, 105.86, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Matrix metalloproteinase-14 / / MMP-14 / Membrane-type matrix metalloproteinase 1 / MT-MMP 1 / MTMMP1 / Membrane-type-1 matrix ...MMP-14 / Membrane-type matrix metalloproteinase 1 / MT-MMP 1 / MTMMP1 / Membrane-type-1 matrix metalloproteinase / MT1-MMP / MT1MMP / MMP-X1


Mass: 20561.676 Da / Num. of mol.: 2 / Fragment: Residues 112-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP14 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P50281, membrane-type matrix metalloproteinase-1
#2: Protein Metalloproteinase inhibitor 1 / Matrix metalloproteinase inhibitor / Tissue inhibitor of metalloproteinases 1 / TIMP-1 / Erythroid-potentiating activity / EPA / ...Tissue inhibitor of metalloproteinases 1 / TIMP-1 / Erythroid-potentiating activity / EPA / Fibroblast collagenase inhibitor / Collagenase inhibitor


Mass: 14126.209 Da / Num. of mol.: 2 / Fragment: Residues 24-148 / Mutation: V27A,P29V,T121L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIMP1, CLGI, TIMP / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01033
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris pH 5.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 28, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 39106 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 24.36 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.103 / Net I/σ(I): 19.5
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1787 / Rsym value: 0.237 / % possible all: 90.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BQQ

1bqq


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.507 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24707 1961 5 %RANDOM
Rwork0.19644 ---
obs0.19905 37132 98.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.357 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-1.05 Å2
2---0.88 Å20 Å2
3---1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4556 0 8 145 4709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0224695
X-RAY DIFFRACTIONr_angle_refined_deg2.4111.9236379
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8335568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15723.404235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8915692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2491526
X-RAY DIFFRACTIONr_chiral_restr0.2480.2661
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213702
X-RAY DIFFRACTIONr_mcbond_it1.4931.52852
X-RAY DIFFRACTIONr_mcangle_it2.43924571
X-RAY DIFFRACTIONr_scbond_it3.78231843
X-RAY DIFFRACTIONr_scangle_it5.4544.51808
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 111 -
Rwork0.243 2420 -
obs--87.01 %

+
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