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- PDB-4g0d: Human collagenase 3 (MMP-13) full form with peptides from pro-domain -

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Basic information

Entry
Database: PDB / ID: 4g0d
TitleHuman collagenase 3 (MMP-13) full form with peptides from pro-domain
Components
  • Collagenase 3, pro-domain peptide
  • Collagenase 3
KeywordsHYDROLASE / protein-peptide complex / collagenase / cleavage with mmp3 / pro-peptide / metzincin / Zinc metalloprotease / collagen cleavage / collagen
Function / homology
Function and homology information


growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation ...growth plate cartilage development / RUNX2 regulates genes involved in cell migration / endochondral ossification / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / bone morphogenesis / Assembly of collagen fibrils and other multimeric structures / bone mineralization / Activation of Matrix Metalloproteinases / response to amyloid-beta / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / collagen binding / extracellular matrix / Degradation of the extracellular matrix / extracellular matrix organization / metalloendopeptidase activity / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
4 Propeller / Hemopexin / Hemopexin-like domain / 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 ...4 Propeller / Hemopexin / Hemopexin-like domain / 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 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / S-1,2-PROPANEDIOL / Collagenase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsStura, E.A. / Vera, L. / Visse, R. / Nagase, H. / Dive, V.
CitationJournal: Faseb J. / Year: 2013
Title: Crystal structure of full-length human collagenase 3 (MMP-13) with peptides in the active site defines exosites in the catalytic domain.
Authors: Stura, E.A. / Visse, R. / Cuniasse, P. / Dive, V. / Nagase, H.
History
DepositionJul 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagenase 3
B: Collagenase 3
C: Collagenase 3
D: Collagenase 3
W: Collagenase 3, pro-domain peptide
X: Collagenase 3, pro-domain peptide
Y: Collagenase 3, pro-domain peptide
Z: Collagenase 3, pro-domain peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,08194
Polymers181,5758
Non-polymers5,50586
Water16,141896
1
A: Collagenase 3
W: Collagenase 3, pro-domain peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,70422
Polymers45,3942
Non-polymers1,31020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-96 kcal/mol
Surface area19150 Å2
MethodPISA
2
B: Collagenase 3
X: Collagenase 3, pro-domain peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,71922
Polymers45,3942
Non-polymers1,32520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-125 kcal/mol
Surface area20380 Å2
MethodPISA
3
C: Collagenase 3
Y: Collagenase 3, pro-domain peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,98927
Polymers45,3942
Non-polymers1,59625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-125 kcal/mol
Surface area20200 Å2
MethodPISA
4
D: Collagenase 3
Z: Collagenase 3, pro-domain peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,66823
Polymers45,3942
Non-polymers1,27521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-110 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.260, 105.900, 101.180
Angle α, β, γ (deg.)90.00, 102.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDWXYZ

#1: Protein
Collagenase 3 / / Matrix metalloproteinase-13 / MMP-13


Mass: 42284.617 Da / Num. of mol.: 4 / Fragment: Inactive full form (UNP residues 104-471) / Mutation: E223A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: PET3A / Production host: Escherichia coli (E. coli)
References: UniProt: P45452, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Protein/peptide
Collagenase 3, pro-domain peptide / / Matrix metalloproteinase-13 / MMP-13


Mass: 3109.209 Da / Num. of mol.: 4 / Fragment: pro-domain fragment (UNP residues 25-50)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP13 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / References: UniProt: P45452

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Non-polymers , 7 types, 982 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical...
ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C3H8O2
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 896 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAFTER CLEAVAGE WITH PROTEASE MMP3 TO CUT OFF THE PRO-DOMAIN TO GIVE RISE TO THE MATURE (INACTIVE) ...AFTER CLEAVAGE WITH PROTEASE MMP3 TO CUT OFF THE PRO-DOMAIN TO GIVE RISE TO THE MATURE (INACTIVE) PROTEASE (E223A), A FRAGMENT OF THE PRO-PEPTIDE IS BOUND BACK ONTO THE INACTIVE PROTEASE. THUS CHAIN W BELONGS TO CHAIN A, CHAIN X TO CHAIN B, Y TO C AND Z TO CHAIN D.

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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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 277 K / Method: slow cooling / pH: 7.5
Details: propeptide impurity induces crystallization on cold storage Cryoprotectant: 10% PEG 10K, 5% di-ethylene glycol, 20% 1.2-propanediol, 5% glycerol, .2 M NaCl, 10% PCTP buffer 8:2 ratio, pH 7. ...Details: propeptide impurity induces crystallization on cold storage Cryoprotectant: 10% PEG 10K, 5% di-ethylene glycol, 20% 1.2-propanediol, 5% glycerol, .2 M NaCl, 10% PCTP buffer 8:2 ratio, pH 7.5, SLOW COOLING, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 31, 2011
Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. all: 69045 / Num. obs: 68894 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.05 % / Biso Wilson estimate: 39.978 Å2 / Rmerge(I) obs: 0.258 / Rsym value: 0.224 / Net I/σ(I): 8.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.54-2.694.011.1141.63110790.96599.4
7.54-503.8760.624.2127380.05199.1
5.36-7.544.030.11816.747460.10299.9
4.39-5.364.050.10817.2760700.09499.8
3.8-4.394.080.14614.8871990.12699.8
3.4-3.84.090.24810.8280930.21699.9
3.11-3.44.090.4297.0989830.37399.8
2.88-3.114.080.684.397100.591100
2.69-2.884.020.8042.75104270.69799.9

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FVL

4fvl


Resolution: 2.54→49.503 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / σ(I): -3 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 3442 5 %RANDOM
Rwork0.1689 ---
obs0.1724 68865 99.8 %-
all-68882 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.877 Å2
Refinement stepCycle: LAST / Resolution: 2.54→49.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12779 0 287 896 13962
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813615
X-RAY DIFFRACTIONf_angle_d1.18918442
X-RAY DIFFRACTIONf_dihedral_angle_d15.8784948
X-RAY DIFFRACTIONf_chiral_restr0.0821862
X-RAY DIFFRACTIONf_plane_restr0.0052399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.5401-2.57490.34471350.27212574257498
2.5749-2.61170.39621370.278926112611100
2.6117-2.65070.3861360.271525752575100
2.6507-2.69210.33061370.268226002600100
2.6921-2.73630.40791370.2726162616100
2.7363-2.78340.34581370.251426042604100
2.7834-2.8340.3381380.235726152615100
2.834-2.88860.32831370.224225982598100
2.8886-2.94750.32651370.21126142614100
2.9475-3.01160.33431380.209926172617100
3.0116-3.08160.2631380.176126202620100
3.0816-3.15870.2581370.168226022602100
3.1587-3.24410.241370.168426082608100
3.2441-3.33950.26061380.164926172617100
3.3395-3.44730.25361370.166326062606100
3.4473-3.57050.2511390.153726382638100
3.5705-3.71340.21221360.142625772577100
3.7134-3.88230.18841390.136726472647100
3.8823-4.08690.18471380.131626102610100
4.0869-4.34280.20411380.128726282628100
4.3428-4.67790.16941380.120626302630100
4.6779-5.14820.18941380.128726252625100
5.1482-5.89210.19051400.146626582658100
5.8921-7.41940.19261390.164926382638100
7.4194-49.51270.20411410.1722695269599

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