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- PDB-2mzi: NMR Solution Structure of the PRO Form of Human Matrilysin (proMM... -

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Basic information

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


matrilysin / antibacterial peptide secretion / antibacterial peptide biosynthetic process / membrane protein intracellular domain proteolysis / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / membrane protein ectodomain proteolysis / extracellular matrix disassembly ...matrilysin / antibacterial peptide secretion / antibacterial peptide biosynthetic process / membrane protein intracellular domain proteolysis / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / Collagen degradation / collagen catabolic process / membrane protein ectodomain proteolysis / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / metallopeptidase activity / regulation of cell population proliferation / endopeptidase activity / defense response to Gram-negative bacterium / Extra-nuclear estrogen signaling / defense response to Gram-positive bacterium / positive regulation of cell migration / response to xenobiotic stimulus / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding
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
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,470137
Polymers27,9131
Non-polymers88,558136
Water00
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

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Components

#1: Protein Matrilysin / 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


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


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

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Experimental details

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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

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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

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NMR measurement

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

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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

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