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- PDB-4qxu: Novel Inhibition Mechanism of Membrane Metalloprotease by an Exos... -

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Basic information

Entry
Database: PDB / ID: 4qxu
TitleNovel Inhibition Mechanism of Membrane Metalloprotease by an Exosite-Swiveling Conformational antibody
Components
  • Matrix metalloproteinase-14
  • anti_MT1-MMP Heavy chain
  • anti_MT1-MMP Light chain
KeywordsIMMUNE SYSTEM / Structural Genomics / PSI-2 / Protein Structure Initiative / Israel Structural Proteomics Center / ISPC / Igg fold
Function / homology
Function and homology information


membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / positive regulation of macrophage migration / craniofacial suture morphogenesis / macropinosome / response to odorant / chondrocyte proliferation / head development / TGFBR3 PTM regulation / astrocyte cell migration ...membrane-type matrix metalloproteinase-1 / negative regulation of GDF15-GFRAL signaling pathway / positive regulation of macrophage migration / craniofacial suture morphogenesis / macropinosome / response to odorant / chondrocyte proliferation / head development / TGFBR3 PTM regulation / astrocyte cell migration / tissue remodeling / negative regulation of focal adhesion assembly / positive regulation of protein processing / endochondral ossification / embryonic cranial skeleton morphogenesis / intermediate filament cytoskeleton / endothelial cell proliferation / zymogen activation / positive regulation of B cell differentiation / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / Activation of Matrix Metalloproteinases / endodermal cell differentiation / metalloaminopeptidase activity / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / negative regulation of Notch signaling pathway / response to mechanical stimulus / regulation of protein localization to plasma membrane / ovarian follicle development / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / skeletal system development / cell motility / lung development / protein catabolic process / metalloendopeptidase activity / protein processing / Golgi lumen / response to estrogen / male gonad development / integrin binding / melanosome / positive regulation of cell growth / cytoplasmic vesicle / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / angiogenesis / endopeptidase activity / response to oxidative stress / response to hypoxia / positive regulation of cell migration / serine-type endopeptidase activity / focal adhesion / proteolysis / extracellular space / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / PGBD superfamily / 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 ...Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / PGBD superfamily / 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 / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Matrix metalloproteinase-14
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUdi, Y. / Grossman, M. / Solomonov, I. / Dym, O. / Rozenberg, H. / Moreno, v. / Cuiniasse, P. / Dive, V. / Arroyo, A.G. / Sagi, I. / Israel Structural Proteomics Center (ISPC)
CitationJournal: Structure / Year: 2015
Title: Inhibition mechanism of membrane metalloprotease by an exosite-swiveling conformational antibody.
Authors: Udi, Y. / Grossman, M. / Solomonov, I. / Dym, O. / Rozenberg, H. / Moreno, V. / Cuniasse, P. / Dive, V. / Arroyo, A.G. / Sagi, I.
History
DepositionJul 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Sep 20, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: anti_MT1-MMP Light chain
H: anti_MT1-MMP Heavy chain
K: Matrix metalloproteinase-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6425
Polymers50,4503
Non-polymers1922
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-66 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.560, 79.560, 93.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody anti_MT1-MMP Light chain


Mass: 24124.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody anti_MT1-MMP Heavy chain


Mass: 24995.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide Matrix metalloproteinase-14 / MMP-14 / MMP-X1 / Membrane-type matrix metalloproteinase 1 / MT-MMP 1 / MTMMP1 / Membrane-type-1 ...MMP-14 / MMP-X1 / Membrane-type matrix metalloproteinase 1 / MT-MMP 1 / MTMMP1 / Membrane-type-1 matrix metalloproteinase / MT1-MMP / MT1MMP


Mass: 1330.422 Da / Num. of mol.: 1 / Fragment: peptide (unp residues 218-228)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP14 / Production host: Escherichia coli (E. coli)
References: UniProt: P50281, membrane-type matrix metalloproteinase-1
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M (NH4)2SO4, 0.01M MgCl2 0.05M MES, 16% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 27071 / Num. obs: 24287 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.42 Å / % possible all: 78.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4OUU

4ouu


Resolution: 2.3→48.26 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.887 / SU B: 8.13 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29336 1229 5.1 %RANDOM
Rwork0.24307 ---
obs0.24567 22973 89.41 %-
all-25694 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.424 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0 Å2
2--0.63 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 10 15 3444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023544
X-RAY DIFFRACTIONr_bond_other_d0.0010.023192
X-RAY DIFFRACTIONr_angle_refined_deg1.7831.954837
X-RAY DIFFRACTIONr_angle_other_deg0.923.0027373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7865457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85724140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63815546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2311516
X-RAY DIFFRACTIONr_chiral_restr0.110.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 77 -
Rwork0.376 1472 -
obs--78.04 %

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