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- PDB-1eak: Catalytic domain of proMMP-2 E404Q mutant -

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Basic information

Entry
Database: PDB / ID: 1eak
TitleCatalytic domain of proMMP-2 E404Q mutant
Components
  • 72 KDA TYPE IV COLLAGENASE
  • INHIBITOR PEPTIDE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / HYDROLYSE / MATRIX METALLOPROTEINASE / GELATINASE A / HYDROLASE- HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


gelatinase A / bone trabecula formation / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle ...gelatinase A / bone trabecula formation / peripheral nervous system axon regeneration / blood vessel maturation / parturition / luteinization / tissue remodeling / intramembranous ossification / cellular response to UV-A / ovulation from ovarian follicle / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / prostate gland epithelium morphogenesis / protein metabolic process / cellular response to fluid shear stress / negative regulation of cell adhesion / face morphogenesis / negative regulation of vasoconstriction / macrophage chemotaxis / Activation of Matrix Metalloproteinases / endodermal cell differentiation / response to amyloid-beta / Collagen degradation / fibronectin binding / EPH-ephrin mediated repulsion of cells / collagen catabolic process / extracellular matrix disassembly / response to hyperoxia / ephrin receptor signaling pathway / cellular response to interleukin-1 / response to mechanical stimulus / response to electrical stimulus / response to retinoic acid / ovarian follicle development / embryo implantation / positive regulation of vascular associated smooth muscle cell proliferation / Degradation of the extracellular matrix / extracellular matrix organization / sarcomere / response to activity / response to nicotine / cellular response to estradiol stimulus / cellular response to amino acid stimulus / protein catabolic process / response to hydrogen peroxide / metalloendopeptidase activity / cellular response to reactive oxygen species / response to estrogen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / metallopeptidase activity / heart development / collagen-containing extracellular matrix / angiogenesis / Interleukin-4 and Interleukin-13 signaling / endopeptidase activity / Extra-nuclear estrogen signaling / response to hypoxia / positive regulation of cell migration / response to xenobiotic stimulus / serine-type endopeptidase activity / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular region / nucleus / plasma membrane
Similarity search - Function
Fibronectin, type II, collagen-binding / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / 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 ...Fibronectin, type II, collagen-binding / Muramoyl-pentapeptide Carboxypeptidase; domain 1 / PGBD-like superfamily/PGBD / 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 / 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 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature. / Ribbon / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
72 kDa type IV collagenase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsBergmann, U. / Tuuttila, A. / Tryggvason, K. / Morgunova, E.
CitationJournal: To be Published
Title: Crystal Structure of Human Mmp-2 Reveals a New P
Authors: Bergmann, U. / Tuuttila, A. / Morgunova, E. / Tryggvason, K.
History
DepositionJul 12, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 21, 2016Group: Source and taxonomy
Revision 1.3Jun 13, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Dec 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_beamline / _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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 72 KDA TYPE IV COLLAGENASE
B: 72 KDA TYPE IV COLLAGENASE
C: 72 KDA TYPE IV COLLAGENASE
D: 72 KDA TYPE IV COLLAGENASE
P: INHIBITOR PEPTIDE
R: INHIBITOR PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,88328
Polymers190,4636
Non-polymers1,42022
Water1,964109
1
A: 72 KDA TYPE IV COLLAGENASE
C: 72 KDA TYPE IV COLLAGENASE
P: INHIBITOR PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,94214
Polymers95,2313
Non-polymers71011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 72 KDA TYPE IV COLLAGENASE
D: 72 KDA TYPE IV COLLAGENASE
R: INHIBITOR PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,94214
Polymers95,2313
Non-polymers71011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)117.670, 166.150, 170.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 6 molecules ABCDPR

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


Mass: 47304.348 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN RESIDUES 32-452 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVL1393 / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P08253, gelatinase A
#2: Protein/peptide INHIBITOR PEPTIDE


Mass: 622.671 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 131 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN A, B, C, D ENGINEERED MUTATION GLU404GLN CLEAVES THE COLLAGEN-LIKE SEQUENCE PRO-GLN-GLY-|-ILE- ...CHAIN A, B, C, D ENGINEERED MUTATION GLU404GLN CLEAVES THE COLLAGEN-LIKE SEQUENCE PRO-GLN-GLY-|-ILE-ALA -GLY-GLN.

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.41 Å3/Da / Density % sol: 71.7 %
Crystal growpH: 8.5 / Details: PH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: D2AM / Wavelength: 0.97984
DetectorDate: Oct 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97984 Å / Relative weight: 1
ReflectionResolution: 2.65→37.5 Å / Num. obs: 84612 / % possible obs: 93.7 % / Redundancy: 1.7 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 9.6
Reflection shellResolution: 2.65→2.8 Å / Rmerge(I) obs: 0.036 / Mean I/σ(I) obs: 0.9 / % possible all: 60.8

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
ROTAPREPdata scaling
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CK7

1ck7


Resolution: 2.66→35.58 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1138461.89 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.303 3899 5 %RANDOM
Rwork0.271 ---
obs0.271 77543 80.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.42 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 42.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.54 Å
Luzzati d res low-5 Å
Luzzati sigma a0.72 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 2.66→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13349 0 46 109 13504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.057
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.528 189 4.5 %
Rwork0.499 3970 -
obs--26 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER.PARAM

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