[English] 日本語
Yorodumi
- PDB-2mqs: Transient Collagen Triple Helix Binding to a Key Metalloproteinas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mqs
TitleTransient Collagen Triple Helix Binding to a Key Metalloproteinase in Invasion and Development: Spin Labels to Structure
Components
  • Matrix metalloproteinase-14
  • THP_L_and_M_chain
  • THP_T_chain
KeywordsHYDROLASE / Protein/Protein
Function / homology
Function and homology information


membrane-type matrix metalloproteinase-1 / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / head development / chondrocyte proliferation / astrocyte cell migration / response to odorant / tissue remodeling / negative regulation of focal adhesion assembly ...membrane-type matrix metalloproteinase-1 / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / head development / chondrocyte proliferation / astrocyte cell migration / response to odorant / tissue remodeling / negative regulation of focal adhesion assembly / positive regulation of protein processing / endochondral ossification / embryonic cranial skeleton morphogenesis / 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 / Collagen degradation / collagen catabolic process / 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 / skeletal system development / cell motility / lung development / response to organic cyclic compound / protein processing / metalloendopeptidase activity / Golgi lumen / response to estrogen / male gonad development / melanosome / integrin binding / cytoplasmic vesicle / positive regulation of cell growth / angiogenesis / endopeptidase activity / response to oxidative stress / response to hypoxia / positive regulation of cell migration / serine-type endopeptidase activity / focal adhesion / proteolysis / extracellular space / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / 4 Propeller / Hemopexin / Hemopexin-like domain / PGBD superfamily / Peptidoglycan binding-like / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain ...Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / 4 Propeller / Hemopexin / Hemopexin-like domain / PGBD superfamily / 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
Matrix metalloproteinase-14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsZhao, Y. / Marcink, T. / Van Doren, S.R.
CitationJournal: Structure / Year: 2015
Title: Transient collagen triple helix binding to a key metalloproteinase in invasion and development.
Authors: Zhao, Y. / Marcink, T.C. / Sanganna Gari, R.R. / Marsh, B.P. / King, G.M. / Stawikowska, R. / Fields, G.B. / Van Doren, S.R.
History
DepositionJun 26, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.formula_weight
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Matrix metalloproteinase-14
B: THP_L_and_M_chain
C: THP_L_and_M_chain
D: THP_T_chain


Theoretical massNumber of molelcules
Total (without water)32,7454
Polymers32,7454
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14514 Å2
ΔGint-31.7 kcal/mol
Surface area7327 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

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


Mass: 23131.346 Da / Num. of mol.: 1
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/peptide THP_L_and_M_chain


Mass: 3293.579 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE PEPTIDE IS DERIVED FROM A SEQUENCE REGION WITHIN HUMAN COLLAGENS I, II, AND III
#3: Protein/peptide THP_T_chain


Mass: 3026.298 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE IS DERIVED FROM A SEQUENCE REGION WITHIN HUMAN COLLAGENS I, II, AND III

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC aromatic
1212D 1H-13C HSQC aliphatic
1313D CBCA(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HN(CO)CA
1813D HN(COCA)CB
1913D 13C-edited NOESY
11013D (H)CCH-TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
1300 uM [U-13C; U-15N; U-2H] Hemopexin-like (HPX) of MT1-MMP, 10 mM Sodium acetate, 1 mM EDTA, 1 mM Sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
20.85 mM THP, 10 mM Sodium acetate, 1 mM EDTA, 1 mM Sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
uMHemopexin-like (HPX) of MT1-MMP-1[U-13C; U-15N; U-2H]200-4001
10 mMSodium acetate-21
1 mMEDTA-31
1 mMSodium azide-41
mMTHP-50.852
10 mMSodium acetate-62
1 mMEDTA-72
1 mMSodium azide-82
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 5 ambient 310 K
210 mM 5.0 ambient 298 K

-
NMR measurement

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

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
HADDOCKBONVINrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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