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- PDB-5th6: Structure determination of a potent, selective antibody inhibitor... -

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Basic information

Entry
Database: PDB / ID: 5th6
TitleStructure determination of a potent, selective antibody inhibitor of human MMP9 (apo MMP9)
ComponentsMatrix metalloproteinase-9,Matrix metalloproteinase-9
Keywordshydrolase/hydrolase inhibitor / metalloproteinase-9 antibody inhibitor / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / endodermal cell differentiation ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / endodermal cell differentiation / Activation of Matrix Metalloproteinases / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to cadmium ion / collagen binding / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / cellular response to lipopolysaccharide / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
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 ...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. / 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. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAppleby, T.C. / Greenstein, A.E. / Kwon, H.J.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Biochemical characterization and structure determination of a potent, selective antibody inhibitor of human MMP9.
Authors: Appleby, T.C. / Greenstein, A.E. / Hung, M. / Liclican, A. / Velasquez, M. / Villasenor, A.G. / Wang, R. / Wong, M.H. / Liu, X. / Papalia, G.A. / Schultz, B.E. / Sakowicz, R. / Smith, V. / Kwon, H.J.
History
DepositionSep 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Database references
Revision 1.2May 3, 2017Group: Database references
Revision 1.3Oct 4, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix metalloproteinase-9,Matrix metalloproteinase-9
B: Matrix metalloproteinase-9,Matrix metalloproteinase-9
C: Matrix metalloproteinase-9,Matrix metalloproteinase-9
D: Matrix metalloproteinase-9,Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,85324
Polymers103,8484
Non-polymers1,00420
Water16,592921
1
A: Matrix metalloproteinase-9,Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2136
Polymers25,9621
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Matrix metalloproteinase-9,Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2136
Polymers25,9621
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Matrix metalloproteinase-9,Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2136
Polymers25,9621
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Matrix metalloproteinase-9,Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2136
Polymers25,9621
Non-polymers2515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.546, 69.233, 84.093
Angle α, β, γ (deg.)90.000, 101.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Matrix metalloproteinase-9,Matrix metalloproteinase-9 / MMP-9 / 92 kDa gelatinase / 92 kDa type IV collagenase / Gelatinase B / GELB


Mass: 25962.111 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP9, CLG4B / Production host: Escherichia coli (E. coli) / References: UniProt: P14780, gelatinase B
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 921 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 12% (v/v) PEG 8000 0.3 M lithium sulfate 0.1 M sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 93918 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.62 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.041 / Rrim(I) all: 0.08 / Χ2: 0.902 / Net I/σ(I): 11 / Num. measured all: 350236
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.743.70.30665940.9280.1850.3580.80198.6
1.74-1.793.70.24866300.9490.1490.290.84498.6
1.79-1.843.70.19966420.9750.120.2330.87798.9
1.84-1.93.70.16766400.9810.10.1950.999
1.9-1.973.70.14266540.9850.0850.1650.94298.9
1.97-2.053.80.11566890.9880.0690.1350.96299.4
2.05-2.143.80.09766790.990.0580.1130.98999.3
2.14-2.253.80.08866950.9910.0520.1020.9899.4
2.25-2.43.80.07867260.9910.0470.0910.93799.6
2.4-2.583.80.06967250.9940.0410.080.87499.8
2.58-2.843.70.06567650.9940.0390.0760.91899.9
2.84-3.253.70.06867520.9940.0410.081.171100
3.25-4.13.70.05368160.9960.0320.0620.88399.9
4.1-503.70.04169110.9970.0250.0480.54399.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L6J

1l6j


Resolution: 1.7→46.218 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 1999 2.13 %
Rwork0.2075 91692 -
obs0.2081 93691 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.92 Å2 / Biso mean: 16.3579 Å2 / Biso min: 3.76 Å2
Refinement stepCycle: final / Resolution: 1.7→46.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6662 0 20 921 7603
Biso mean--19.22 24.69 -
Num. residues----869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076882
X-RAY DIFFRACTIONf_angle_d0.8369405
X-RAY DIFFRACTIONf_chiral_restr0.051992
X-RAY DIFFRACTIONf_plane_restr0.0071235
X-RAY DIFFRACTIONf_dihedral_angle_d10.5243905
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7002-1.74270.27131380.23656317645596
1.7427-1.78980.25271420.21436494663699
1.7898-1.84250.25081410.21186481662299
1.8425-1.9020.21731410.2056513665499
1.902-1.970.2371430.20266510665399
1.97-2.04880.19211430.20066568671199
2.0488-2.14210.22141410.19456525666699
2.1421-2.2550.2371430.19756556669999
2.255-2.39630.23961440.202965966740100
2.3963-2.58130.24521440.211465766720100
2.5813-2.8410.2461440.211866166760100
2.841-3.2520.23231440.214366046748100
3.252-4.09680.25741450.2016642678799
4.0968-46.23530.21081460.21366694684099

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