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- PDB-1os2: Ternary enzyme-product-inhibitor complexes of human MMP12 -

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Basic information

Entry
Database: PDB / ID: 1os2
TitleTernary enzyme-product-inhibitor complexes of human MMP12
ComponentsMacrophage metalloelastase
KeywordsHYDROLASE / MATRIX METALLOPROTEINASE / HYDROXAMIC ACID / MMP12 / ELASTASE / COMPLEX (ELASTASE-INHIBITOR) / METALLO ELASTASE
Function / homology
Function and homology information


macrophage elastase / negative regulation of endothelial cell-matrix adhesion / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / Collagen degradation / collagen catabolic process / positive regulation of interferon-alpha production / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / cellular response to virus / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / extracellular region / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / AZIDE ION / ACETOHYDROXAMIC ACID / Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Mangani, S. / Terni, B.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2003
Title: X-ray Structures of Binary and Ternary Enzyme-Product-Inhibitor Complexes of Matrix Metalloproteinases
Authors: Bertini, I. / Calderone, V. / Fragai, M. / Luchinat, C. / Mangani, S. / Terni, B.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Substrate specificity determinants of human macrophage elastase (MMP-12) based on the 1.1 A crystal structure
Authors: Lang, R. / Kocourek, A. / Braun, M. / Tschesche, H. / Huber, R. / Bode, W. / Maskos, K.
History
DepositionMar 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HET GROUP TRIVIAL NAME: HAE IS ALSO KNOWN AS ACETOHYDROXAMIC ACID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage metalloelastase
B: Macrophage metalloelastase
C: Macrophage metalloelastase
D: Macrophage metalloelastase
E: Macrophage metalloelastase
F: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,84742
Polymers109,9896
Non-polymers1,85936
Water5,549308
1
A: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6587
Polymers18,3311
Non-polymers3266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6427
Polymers18,3311
Non-polymers3106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6257
Polymers18,3311
Non-polymers2936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6587
Polymers18,3311
Non-polymers3266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6427
Polymers18,3311
Non-polymers3106
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6257
Polymers18,3311
Non-polymers2936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
D: Macrophage metalloelastase
E: Macrophage metalloelastase
F: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,92421
Polymers54,9943
Non-polymers92918
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-200 kcal/mol
Surface area23690 Å2
MethodPISA
8
A: Macrophage metalloelastase
B: Macrophage metalloelastase
C: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,92421
Polymers54,9943
Non-polymers92918
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-197 kcal/mol
Surface area23610 Å2
MethodPISA
9
A: Macrophage metalloelastase
hetero molecules

C: Macrophage metalloelastase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,28214
Polymers36,6632
Non-polymers61912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z+2/31
Buried area1750 Å2
ΔGint-123 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.839, 123.839, 69.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsThe protein is monomeric in vivo, while there are six molecules in the crystal asymmetric unit.

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Macrophage metalloelastase / HME / Matrix metalloproteinase-12 / MMP-12 / Macrophage elastase / ME


Mass: 18331.467 Da / Num. of mol.: 6 / Mutation: F171D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12 OR HME / Production host: Escherichia coli (E. coli) / References: UniProt: P39900, macrophage elastase

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Non-polymers , 6 types, 344 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-HAE / ACETOHYDROXAMIC ACID


Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2 / Comment: medication*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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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: 2.71 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Tris, PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.1 MTris-HCl1reservoir
230 %PEG60001reservoir
32 mM1reservoirNaN3
4200 mMAHA1reservoirpH8.0
58 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9322 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 9, 2002 / Details: Si (111) mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9322 Å / Relative weight: 1
ReflectionResolution: 2.15→107 Å / Num. all: 64964 / Num. obs: 64964 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 7.3
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 1.9 / Num. unique all: 9418 / Rsym value: 0.078 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 107 Å / % possible obs: 100 % / Num. measured all: 471410
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.076

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Processing

Software
NameVersionClassification
REFMAC5.1.80refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JK3

1jk3


Resolution: 2.15→69.01 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.894 / SU B: 5.871 / SU ML: 0.153 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.244 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27099 3296 5.1 %RANDOM
Rwork0.21153 ---
all0.21455 61741 --
obs0.21455 61741 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
Displacement parametersBiso mean: 36.148 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.15→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7770 0 54 308 8132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0218016
X-RAY DIFFRACTIONr_angle_refined_deg2.7631.91610852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9635984
X-RAY DIFFRACTIONr_chiral_restr0.2330.21110
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.026334
X-RAY DIFFRACTIONr_nbd_refined0.3120.23395
X-RAY DIFFRACTIONr_metal_ion_refined0.4820.2156
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4520.2116
X-RAY DIFFRACTIONr_mcbond_it1.6671.54884
X-RAY DIFFRACTIONr_mcangle_it2.71827804
X-RAY DIFFRACTIONr_scbond_it4.42533132
X-RAY DIFFRACTIONr_scangle_it6.144.53048
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 230
Rwork0.232 4512
Refinement
*PLUS
Num. reflection all: 64964 / Lowest resolution: 19.8 Å / Num. reflection Rfree: 3250 / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.03
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.6

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