[English] 日本語
Yorodumi
- PDB-2mzi: NMR Solution Structure of the PRO Form of Human Matrilysin (proMM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mzi
TitleNMR Solution Structure of the PRO Form of Human Matrilysin (proMMP-7) in Complex with Anionic Membrane
ComponentsMatrilysinMMP7
KeywordsHYDROLASE / zymogen / membrane-bound form / metalloenzyme / anionic
Function / homology
Function and homology information


matrilysin / membrane protein intracellular domain proteolysis / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / membrane protein ectodomain proteolysis / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / extracellular matrix / Degradation of the extracellular matrix ...matrilysin / membrane protein intracellular domain proteolysis / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / membrane protein ectodomain proteolysis / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / metallopeptidase activity / endopeptidase activity / Extra-nuclear estrogen signaling / positive regulation of cell migration / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region
Similarity search - Function
Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase ...Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / 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. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CHOLEST-5-EN-3-YL HYDROGEN SULFATE / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Matrilysin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsfewest violations, model1
AuthorsPrior, S.H. / Van Doren, S.R.
CitationJournal: Structure / Year: 2015
Title: Charge-Triggered Membrane Insertion of Matrix Metalloproteinase-7, Supporter of Innate Immunity and Tumors.
Authors: Prior, S.H. / Fulcher, Y.G. / Koppisetti, R.K. / Jurkevich, A. / Van Doren, S.R.
History
DepositionFeb 12, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_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: Matrilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,470137
Polymers27,9131
Non-polymers88,558136
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 10000structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Matrilysin / MMP7 / Matrin / Matrix metalloproteinase-7 / MMP-7 / Pump-1 protease / Uterine metalloproteinase


Mass: 27912.572 Da / Num. of mol.: 1 / Mutation: E195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP7, MPSL1, PUMP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09237, matrilysin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical...
ChemComp-PX4 / 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Dimyristoylphosphatidylcholine


Mass: 678.940 Da / Num. of mol.: 126 / Source method: obtained synthetically / Formula: C36H73NO8P / Comment: DMPC, phospholipid*YM
#5: Chemical
ChemComp-C3S / CHOLEST-5-EN-3-YL HYDROGEN SULFATE / CHOLESTEROL-SULFATE / Cholesterol sulfate


Mass: 466.717 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H46O4S

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY
1322D 1H-15N HSQC, CPMG
1422D 1H-13C HSQC, CPMG

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 15N, U-100% 13CH3 (ILV)] proMMP-7(E195A), 50 mM 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 100 mM 1,2-DIHEXANEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 3 mM CHOLEST-5-EN-3-YL HYDROGEN SULFATE, 20 mM imidazole, 10 mM CaCl2, 20 uM ZnCl2, 10 mM beta-mercaptoethanol, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-100% 15N, U-100% 13CH3 (ILV)] proMMP-7(E195A), 50 mM 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 100 mM 1,2-DIHEXANEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE, 3 mM CHOLEST-5-EN-3-YL HYDROGEN SULFATE, 20 mM imidazole, 10 mM CaCl2, 20 uM ZnCl2, 10 mM beta-mercaptoethanol, 0.02 % sodium azide, 1.5 mM 1-palmitoyl-2-stearoyl-(14-doxyl)-sn-glycero-3-phosphocholine, 1.5 mM 1,2-dipalmitoyl-sn-glycero-3-phospho(tempo)choline, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMproMMP-7(E195A)-1[U-100% 15N, U-100% 13CH3 (ILV)]1
50 mM1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE-21
100 mM1,2-DIHEXANEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE-31
3 mMCHOLEST-5-EN-3-YL HYDROGEN SULFATE-41
20 mMimidazole-51
10 mMCaCl2-61
20 uMZnCl2-71
10 mMbeta-mercaptoethanol-81
0.02 %sodium azide-91
0.4 mMproMMP-7(E195A)-10[U-100% 15N, U-100% 13CH3 (ILV)]2
50 mM1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE-112
100 mM1,2-DIHEXANEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE-122
3 mMCHOLEST-5-EN-3-YL HYDROGEN SULFATE-132
20 mMimidazole-142
10 mMCaCl2-152
20 uMZnCl2-162
10 mMbeta-mercaptoethanol-172
0.02 %sodium azide-182
1.5 mM1-palmitoyl-2-stearoyl-(14-doxyl)-sn-glycero-3-phosphocholine-192
1.5 mM1,2-dipalmitoyl-sn-glycero-3-phospho(tempo)choline-202
Sample conditionspH: 6.6 / Temperature: 310 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
Analysis2.4CCPNpeak picking
Analysis2.4CCPNchemical shift assignment
HADDOCK2.1Alexandre Bonvinstructure solution
GROMOS4.5.7van Gunsteren and Berendsenrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Energy minimisation. 100ps NVT equilibration. 1ns NPT equilibration. 20ns time-averaged restrained MD.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 10000 / Conformers submitted total number: 20

+
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