[English] 日本語
Yorodumi
- PDB-6cm1: MT1-MMP HPX Domain with Blade 2 Loop Bound to Nanodiscs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cm1
TitleMT1-MMP HPX Domain with Blade 2 Loop Bound to Nanodiscs
Components
  • Apolipoprotein A-IApolipoprotein AI
  • Matrix metalloproteinase-14
KeywordsLIPID BINDING PROTEIN / MT1-MMP / MMP-14 / Nanodisc / lipids / peripheral membrane protein / protease domain
Function / homology
Function and homology information


membrane-type matrix metalloproteinase-1 / craniofacial suture morphogenesis / positive regulation of macrophage migration / high-density lipoprotein particle receptor binding / macropinosome / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / spherical high-density lipoprotein particle / positive regulation of hydrolase activity ...membrane-type matrix metalloproteinase-1 / craniofacial suture morphogenesis / positive regulation of macrophage migration / high-density lipoprotein particle receptor binding / macropinosome / Defective ABCA1 causes TGD / Scavenging by Class B Receptors / HDL clearance / spherical high-density lipoprotein particle / positive regulation of hydrolase activity / regulation of intestinal cholesterol absorption / response to odorant / negative regulation of response to cytokine stimulus / head development / protein oxidation / chondrocyte proliferation / vitamin transport / phosphatidylcholine-sterol O-acyltransferase activator activity / Chylomicron remodeling / positive regulation of phospholipid efflux / high-density lipoprotein particle binding / cholesterol import / Chylomicron assembly / positive regulation of cholesterol metabolic process / tissue remodeling / negative regulation of heterotypic cell-cell adhesion / high-density lipoprotein particle remodeling / blood vessel endothelial cell migration / astrocyte cell migration / ABC transporters in lipid homeostasis / phospholipid efflux / apolipoprotein receptor binding / high-density lipoprotein particle clearance / negative regulation of cell adhesion molecule production / negative regulation of cytokine production involved in immune response / apolipoprotein A-I receptor binding / HDL assembly / peptidyl-methionine modification / negative regulation of very-low-density lipoprotein particle remodeling / cholesterol transfer activity / reverse cholesterol transport / phosphatidylcholine biosynthetic process / high-density lipoprotein particle assembly / very-low-density lipoprotein particle / lipoprotein biosynthetic process / glucocorticoid metabolic process / positive regulation of CoA-transferase activity / negative regulation of focal adhesion assembly / positive regulation of protein processing / phosphatidylcholine metabolic process / lipid storage / phospholipid homeostasis / high-density lipoprotein particle / endochondral ossification / triglyceride homeostasis / regulation of Cdc42 protein signal transduction / cholesterol transport / chemorepellent activity / HDL remodeling / embryonic cranial skeleton morphogenesis / cholesterol efflux / Scavenging by Class A Receptors / endothelial cell proliferation / zymogen activation / intermediate filament cytoskeleton / cholesterol binding / negative regulation of interleukin-1 beta production / positive regulation of Rho protein signal transduction / positive regulation of B cell differentiation / negative chemotaxis / adrenal gland development / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / cholesterol biosynthetic process / negative regulation of Notch signaling pathway / Activation of Matrix Metalloproteinases / endodermal cell differentiation / metalloaminopeptidase activity / positive regulation of cholesterol efflux / Collagen degradation / endocytic vesicle / collagen catabolic process / extracellular matrix disassembly / negative regulation of tumor necrosis factor-mediated signaling pathway / Scavenging of heme from plasma / Retinoid metabolism and transport / regulation of protein localization to plasma membrane / positive regulation of phagocytosis / response to mechanical stimulus / positive regulation of substrate adhesion-dependent cell spreading / ovarian follicle development / endocytic vesicle lumen / positive regulation of stress fiber assembly / cholesterol metabolic process / heat shock protein binding / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / cholesterol homeostasis / skeletal system development
Similarity search - Function
Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / 4 Propeller / Hemopexin / Hemopexin-like domain / PGBD superfamily / Apolipoprotein A/E / Apolipoprotein A1/A4/E domain / Peptidoglycan binding-like / Hemopexin, conserved site ...Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / 4 Propeller / Hemopexin / Hemopexin-like domain / PGBD superfamily / Apolipoprotein A/E / Apolipoprotein A1/A4/E domain / 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 / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Mainly Beta
Similarity search - Domain/homology
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Apolipoprotein A-I / Matrix metalloproteinase-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsMarcink, T.C. / Van Doren, S.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 CA098799 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10 RR022341 United States
CitationJournal: Structure / Year: 2019
Title: MT1-MMP Binds Membranes by Opposite Tips of Its beta Propeller to Position It for Pericellular Proteolysis.
Authors: Marcink, T.C. / Simoncic, J.A. / An, B. / Knapinska, A.M. / Fulcher, Y.G. / Akkaladevi, N. / Fields, G.B. / Van Doren, S.R.
History
DepositionMar 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Matrix metalloproteinase-14
B: Apolipoprotein A-I
C: Apolipoprotein A-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,023223
Polymers72,9563
Non-polymers148,067220
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: The protein's NMR rotational correlation time increased upon addition of nanodiscs indicating interactions between the molecules. Furthermore, ultra-centrifugation, fluorescence, and ...Evidence: The protein's NMR rotational correlation time increased upon addition of nanodiscs indicating interactions between the molecules. Furthermore, ultra-centrifugation, fluorescence, and mutagenesis were used to demonstrate the association with vesicles in the orientation determined by NMR.
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 15all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

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


Mass: 23131.346 Da / Num. of mol.: 1 / Fragment: residues 316-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP14 / Production host: Escherichia coli (E. coli)
References: UniProt: P50281, membrane-type matrix metalloproteinase-1
#2: Protein Apolipoprotein A-I / Apolipoprotein AI / ApoA-I / Apolipoprotein A1


Mass: 24912.156 Da / Num. of mol.: 2 / Fragment: residues 79-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02647
#3: Chemical...
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 218 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1HMQC
121isotropic1TROSY
131isotropic1CPMG-HMQC

-
Sample preparation

DetailsType: solution
Contents: 20 mM Tri-HCl, 300 mM NaCl, 0.02 % sodium azide, 93 % H2O, 7 % [U-100% 2H] D2O, 90 uM 2H, 13C, 15N MT1-MMP hemopexin-like domain, 180 uM MSP1D1, 14.4 mM PX4, 93% H2O/7% D2O
Details: 300 mM NaCl was used to reduce affinity of the HPX domain to the nanodisc. NMR shaped tubes were used to obtain a better spectra
Label: 2H, 13C, 15N / Solvent system: 93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTri-HClnatural abundance1
300 mMNaClnatural abundance1
0.02 %sodium azidenatural abundance1
93 %H2Onatural abundance1
7 %D2O[U-100% 2H]1
90 uMMT1-MMP hemopexin-like domain2H, 13C, 15N1
180 uMMSP1D1natural abundance1
14.4 mMPX4natural abundance1
Sample conditionsDetails: MT1-MMP hemopexin-like domain along with the MSP1D1 and PX4 complex were suspended in a buffer containing 300 mM NaCl, 0.02% sodium azide, 93% water, 7% D2O, and 20 mM Tris pH 7.2
Ionic strength: 300 mM / Label: NMR Buffer / pH: 7.2 / Pressure: 1 atm / Temperature: 303 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospinprocessing
Analysis2.4CCPNdata analysis
HADDOCKHADDOCK2.1Bonvinstructure calculation
NAMDNAMD2.1 with CUDA GPU processingTheoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaignrefinement
NAMDNAMD2.1 with CUDA GPU processingTheoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaignstructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 15 / Conformers submitted total number: 15

+
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