[English] 日本語
Yorodumi
- PDB-1gxd: proMMP-2/TIMP-2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gxd
TitleproMMP-2/TIMP-2 complex
Components
  • 72 KDA TYPE IV COLLAGENASE
  • METALLOPROTEINASE INHIBITOR 2
KeywordsHYDROLASE / METALLOPROTEASE / ZYMOGEN / COLLAGEN DEGRADATION / EXTRACELLULAR MATRIX / GELATINASE A / MATRIX METALLOPROTEINASE 2 / PROTEINASE INHIBITOR
Function / homology
Function and homology information


gelatinase A / negative regulation of metallopeptidase activity / intramembranous ossification / peripheral nervous system axon regeneration / blood vessel maturation / luteinization / parturition / negative regulation of membrane protein ectodomain proteolysis / bone trabecula formation / metalloendopeptidase inhibitor activity ...gelatinase A / negative regulation of metallopeptidase activity / intramembranous ossification / peripheral nervous system axon regeneration / blood vessel maturation / luteinization / parturition / negative regulation of membrane protein ectodomain proteolysis / bone trabecula formation / metalloendopeptidase inhibitor activity / TGFBR3 PTM regulation / trophoblast cell migration / tissue remodeling / cellular response to UV-A / peptidase inhibitor activity / ovulation from ovarian follicle / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / prostate gland epithelium morphogenesis / negative regulation of cell adhesion / cellular response to fluid shear stress / face morphogenesis / molecular function inhibitor activity / negative regulation of vasoconstriction / Activation of Matrix Metalloproteinases / macrophage chemotaxis / endodermal cell differentiation / response to amyloid-beta / Collagen degradation / collagen catabolic process / fibronectin binding / extracellular matrix disassembly / response to electrical stimulus / cellular response to interleukin-1 / EPH-ephrin mediated repulsion of cells / response to hyperoxia / ephrin receptor signaling pathway / response to retinoic acid / response to mechanical stimulus / ovarian follicle development / positive regulation of vascular associated smooth muscle cell proliferation / response to hormone / Degradation of the extracellular matrix / response to cytokine / extracellular matrix organization / extracellular matrix / sarcomere / response to activity / cellular response to reactive oxygen species / response to nicotine / cellular response to amino acid stimulus / cellular response to estradiol stimulus / protein catabolic process / response to hydrogen peroxide / metalloendopeptidase activity / response to estrogen / specific granule lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / tertiary granule lumen / cell migration / : / heart development / protease binding / angiogenesis / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / ficolin-1-rich granule lumen / response to hypoxia / Extra-nuclear estrogen signaling / positive regulation of cell migration / response to xenobiotic stimulus / serine-type endopeptidase activity / Neutrophil degranulation / mitochondrion / proteolysis / extracellular space / extracellular region / zinc ion binding / nucleus / plasma membrane
Similarity search - Function
Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Fibronectin, type II, collagen-binding / 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. / 4 Propeller ...Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Tissue inhibitor of metalloproteinase-1. Chain B, domain 1 / Fibronectin, type II, collagen-binding / 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. / 4 Propeller / Hemopexin / Hemopexin-like domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #120 / Seminal Fluid Protein PDC-109 (Domain B) / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / 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 / Kringle-like fold / Ribbon / Neutral zinc metallopeptidases, zinc-binding region signature. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
72 kDa type IV collagenase / Metalloproteinase inhibitor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMorgunova, E. / Tuuttila, A. / Bergmann, U. / Tryggvason, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structural Insight Into the Complex Formation of Latent Matrix Metalloproteinase 2 with Tissue Inhibitor of Metalloproteinase 2
Authors: Morgunova, E. / Tuuttila, A. / Bergmann, U. / Tryggvason, K.
History
DepositionApr 2, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_asym_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 72 KDA TYPE IV COLLAGENASE
B: 72 KDA TYPE IV COLLAGENASE
C: METALLOPROTEINASE INHIBITOR 2
D: METALLOPROTEINASE INHIBITOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,09112
Polymers185,5574
Non-polymers5348
Water00
1
A: 72 KDA TYPE IV COLLAGENASE
C: METALLOPROTEINASE INHIBITOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0456
Polymers92,7782
Non-polymers2674
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 72 KDA TYPE IV COLLAGENASE
D: METALLOPROTEINASE INHIBITOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0456
Polymers92,7782
Non-polymers2674
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)75.696, 374.575, 191.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein 72 KDA TYPE IV COLLAGENASE / GELATINASE A / 72 KDA GELATINASE / MATRIX METALLOPROTEINASE-2 / MMP-2 / TBE-1


Mass: 70995.406 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVL1393 / Cell line (production host): H5 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P08253, gelatinase A
#2: Protein METALLOPROTEINASE INHIBITOR 2 / TISSUE INHIBITOR OF METALLOPROTEINASES-2 / TIMP-2


Mass: 21783.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVL1393 / Cell line (production host): H5 / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P16035
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 67.5 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.25 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
111 mg/mlprotein1drop
20.2 M1reservoirLi2SO4
30.2 mMreduced1reservoir
40.2 mMoxidized glutathione1reservoir
54 %PEG40001reservoir
60.1 Mammonium acetate1reservoirpH6.25

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8342
DetectorDetector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8342 Å / Relative weight: 1
ReflectionResolution: 3.1→12.9 Å / Num. obs: 46264 / % possible obs: 94.1 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.011 / Net I/σ(I): 10
Reflection
*PLUS
Lowest resolution: 12.94 Å / Num. all: 46286 / Num. measured all: 475848 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.2 Å / % possible obs: 70.8 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
BLANCphasing
FFFEARphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CK7,1BR9

1ck7

1br9


Resolution: 3.1→8 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.783 / SU B: 27.95 / SU ML: 0.508 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.585 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.333 2207 5 %RANDOM
Rwork0.275 ---
obs0.278 41759 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12929 0 16 0 12945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02113344
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.94318092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.15431623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.697152324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.21820
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210416
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3320.37373
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.51053
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2820.518
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4170.3144
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6480.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3391.58105
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.642213037
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.73135239
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2634.55055
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.17 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.426 106
Rwork0.341 1943
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.565-0.2389-0.21343.3071-0.09671.7927-0.0524-0.4507-0.2670.43380.1292-0.4350.33570.2838-0.07670.13870.0436-0.09850.36110.050.220954.878173.132626.4229
24.7892-1.46753.06213.11390.15925.79140.50780.1558-0.8425-1.0428-0.06721.5411.20970.0197-0.44061.27050.0189-0.49510.37860.17031.110553.773636.085424.2933
31.0598-0.2871-0.21741.91510.48712.15950.14730.01940.0004-0.0770.0122-0.0034-0.3243-0.1135-0.15950.0083-0.00750.03110.1851-0.02220.11751.7346116.821624.1683
43.8565-0.7366-2.085524.1959-1.66486.82160.74260.83380.7442-5.5894-0.3382-1.8991-1.2587-0.3433-0.40432.39020.1580.77570.39050.03950.824448.2663153.569716.8929
55.53192.296-0.68614.2127-5.30354.31030.7106-0.7724-1.0106-0.10670.10930.95381.8349-0.5787-0.81992.4714-0.0849-0.46530.74450.26851.851957.8321-6.85843.7018
615.332.72151.941612.63581.441-1.62051.008-1.181-1.2163-0.5785-0.24621.09940.597-0.4408-0.76182.0530.0169-0.69450.50020.1361.230661.748413.095830.1679
72.6795-0.2699-0.712210.88593.57477.509-0.0034-0.2321-0.0016-1.10920.5223-1.31340.53791.0475-0.51881.92510.2817-0.11880.6969-0.00151.214546.0171199.431829.7501
85.02361.5678-4.367242.9768-1.99974.90540.1821-0.6289-0.0642-0.9390.36881.3989-0.35090.5685-0.55091.84660.2626-0.1590.7666-0.02341.455440.6637176.492121.7937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 420
2X-RAY DIFFRACTION2A431 - 631
3X-RAY DIFFRACTION3B2 - 420
4X-RAY DIFFRACTION4B433 - 631
5X-RAY DIFFRACTION5C1 - 127
6X-RAY DIFFRACTION6C128 - 182
7X-RAY DIFFRACTION7D1 - 127
8X-RAY DIFFRACTION8D128 - 182
Refinement
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 12.94 Å / Num. reflection obs: 43921 / Num. reflection Rfree: 2314 / % reflection Rfree: 5 % / Rfactor Rfree: 0.335 / Rfactor Rwork: 0.282
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.639

+
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