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- PDB-4p3c: MT1-MMP:Fab complex (Form I) -

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Basic information

Entry
Database: PDB / ID: 4p3c
TitleMT1-MMP:Fab complex (Form I)
Components
  • Heavy Chain Fab fragment of antibody LEM-2/15
  • Light Chain Fab fragment of antibody LEM-2/15
  • Matrix metalloproteinase-14
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


membrane-type matrix metalloproteinase-1 / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / head development / chondrocyte proliferation / astrocyte cell migration / response to odorant / tissue remodeling / negative regulation of focal adhesion assembly ...membrane-type matrix metalloproteinase-1 / craniofacial suture morphogenesis / positive regulation of macrophage migration / macropinosome / head development / chondrocyte proliferation / astrocyte cell migration / response to odorant / tissue remodeling / negative regulation of focal adhesion assembly / positive regulation of protein processing / endochondral ossification / embryonic cranial skeleton morphogenesis / zymogen activation / endothelial cell proliferation / intermediate filament cytoskeleton / positive regulation of B cell differentiation / branching morphogenesis of an epithelial tube / positive regulation of myotube differentiation / negative regulation of Notch signaling pathway / endodermal cell differentiation / Activation of Matrix Metalloproteinases / metalloaminopeptidase activity / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / regulation of protein localization to plasma membrane / response to mechanical stimulus / ovarian follicle development / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / skeletal system development / cell motility / lung development / response to organic cyclic compound / protein processing / metalloendopeptidase activity / Golgi lumen / response to estrogen / male gonad development / melanosome / integrin binding / cytoplasmic vesicle / positive regulation of cell growth / 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 / 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 ...Peptidase M10A, matrix metallopeptidase, C-terminal / Domain of unknown function (DUF3377) / PGBD superfamily / 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 / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Matrix metalloproteinase-14
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.943 Å
AuthorsRozenberg, H. / Udi, Y. / Sagi, I.
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
DepositionMar 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Feb 18, 2015Group: Refinement description
Revision 1.4Sep 27, 2017Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_symm_contact / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 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 / refine_hist / 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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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.ptnr1_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy Chain Fab fragment of antibody LEM-2/15
L: Light Chain Fab fragment of antibody LEM-2/15
M: Matrix metalloproteinase-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,87015
Polymers49,0233
Non-polymers84812
Water6,810378
1
H: Heavy Chain Fab fragment of antibody LEM-2/15
L: Light Chain Fab fragment of antibody LEM-2/15
M: Matrix metalloproteinase-14
hetero molecules

H: Heavy Chain Fab fragment of antibody LEM-2/15
L: Light Chain Fab fragment of antibody LEM-2/15
M: Matrix metalloproteinase-14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,74030
Polymers98,0456
Non-polymers1,69524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area17270 Å2
ΔGint-79 kcal/mol
Surface area35940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.314, 80.975, 95.568
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11H-433-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules M

#3: Protein/peptide Matrix metalloproteinase-14 / / MMP-14 / MMP-X1 / Membrane-type matrix metalloproteinase 1 / MTMMP1 / Membrane-type-1 matrix ...MMP-14 / MMP-X1 / Membrane-type matrix metalloproteinase 1 / MTMMP1 / Membrane-type-1 matrix metalloproteinase / MT1MMP


Mass: 1566.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP14 / Plasmid: pETR3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P50281, membrane-type matrix metalloproteinase-1

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Antibody , 2 types, 2 molecules HL

#1: Antibody Heavy Chain Fab fragment of antibody LEM-2/15


Mass: 23492.480 Da / Num. of mol.: 1 / Fragment: MT1-MMP V-B loop
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Light Chain Fab fragment of antibody LEM-2/15


Mass: 23963.545 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)

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Non-polymers , 6 types, 390 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25% PEG 3350, 0.2M MgCl.hexahydrate, 0.1M Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.943→40 Å / Num. obs: 30586 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.109 / Χ2: 1.105 / Net I/av σ(I): 22.304 / Net I/σ(I): 8.2 / Num. measured all: 323825
Reflection shell

Diffraction-ID: 1 / Rejects: 0 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2
1.95-1.9810.80.42714870.928
1.98-2.0210.70.38815220.932
2.02-2.0610.80.35414950.939
2.06-2.110.70.31215210.967
2.1-2.1510.70.25714880.971
2.15-2.210.80.22915191.006
2.2-2.2510.70.20914891.047
2.25-2.3110.70.20915071.069
2.31-2.3810.70.1815151.086
2.38-2.4610.70.17415201.155
2.46-2.5410.70.15215251.143
2.54-2.6510.70.13715051.149
2.65-2.7710.70.11815281.158
2.77-2.9110.70.10215331.254
2.91-3.110.70.08715321.239
3.1-3.3310.60.07615251.362
3.33-3.6710.50.07415461.269
3.67-4.210.10.06915651.17
4.2-5.2910.20.05615851.123
5.29-409.70.04916791.121

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DNAdata collection
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: dev_1593)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YEC

1yec


Resolution: 1.943→37.28 Å / FOM work R set: 0.8823 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2001 2000 6.55 %Random
Rwork0.1525 28535 --
obs0.1556 30535 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.15 Å2 / Biso mean: 17.81 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: final / Resolution: 1.943→37.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 57 388 3837
Biso mean--25.41 27.54 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073705
X-RAY DIFFRACTIONf_angle_d1.0625058
X-RAY DIFFRACTIONf_chiral_restr0.046565
X-RAY DIFFRACTIONf_plane_restr0.005653
X-RAY DIFFRACTIONf_dihedral_angle_d11.8071332
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9426-1.99120.20251330.15151903203696
1.9912-2.0450.20171400.153420052145100
2.045-2.10520.22641410.148920092150100
2.1052-2.17320.22161420.14820192161100
2.1732-2.25080.18991410.1520192160100
2.2508-2.34090.19271420.144620122154100
2.3409-2.44740.19451430.151520462189100
2.4474-2.57640.24811410.158320172158100
2.5764-2.73780.21441440.164220472191100
2.7378-2.94910.1881430.153220442187100
2.9491-3.24580.20041440.146520512195100
3.2458-3.71510.17931450.141220782223100
3.7151-4.67910.16591470.137220882235100
4.6791-37.28680.22631540.183821972351100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8094-0.39550.49460.75410.62381.6448-0.1801-0.0443-0.1936-0.08570.1136-0.41130.12180.084-0.10290.07050.00220.01520.1057-0.01870.1167-9.6133-3.1979-21.7393
21.52690.40080.36771.37240.50650.94440.03640.0548-0.0306-0.06670.0324-0.0874-0.03830.0823-0.0270.07510.00810.00880.0746-0.01050.0745-19.0166-6.9813-27.465
31.74880.8611-0.09710.65180.53741.5003-0.01710.1026-0.0132-0.47960.0574-0.1723-0.11220.2435-0.01350.1765-0.02520.04860.1478-0.01120.0867-11.4678-1.0352-29.756
41.27560.58460.69340.61550.54340.52170.0182-0.0466-0.08960.0183-0.0333-0.0686-0.0360.00650.00240.08250.00790.00340.0659-0.00090.0923-16.3793-1.7521-19.9054
50.12780.26320.40260.79480.83941.404-0.081-0.0482-0.07080.1906-0.01920.143-0.1323-0.18280.16780.23130.00740.05260.11180.01920.1068-2.351619.78366.8902
60.5665-0.0295-0.59750.0050.12961.6968-0.07290.0161-0.16980.20220.00740.1270.3193-0.28170.00320.1771-0.03060.04160.10230.0090.1287-3.900810.0948-3.7049
72.5012-0.6715-0.1191.52710.49460.16410.16780.0101-0.11350.1486-0.31430.1770.0752-0.2441-0.190.1509-0.05450.07050.1947-0.04310.1709-8.818712.4681-5.4367
81.13-0.2237-0.86650.0919-0.16182.6301-0.1066-0.1478-0.10810.10690.00770.0520.35050.16090.03970.1770.00570.04520.1052-0.00370.1249-0.828110.15091.8237
90.68750.0399-0.18021.63071.24991.21310.0371-0.04550.0055-0.018-0.05330.0436-0.0158-0.07340.04550.06380.0014-0.00680.0946-0.01010.0759-34.51555.2121-15.673
101.85310.0867-0.29921.0742-0.18761.0034-0.06680.1705-0.0115-0.01070.07160.06680.0426-0.1273-0.00080.0689-0.0139-0.00190.0717-0.0180.0875-7.021224.3219-1.587
112.53031.01960.26831.10120.18681.0146-0.05780.035-0.2217-0.11240.0055-0.03460.0549-0.06550.06880.12850.0166-0.02660.186700.1644-14.61922.5864-5.2297
120.62360.67880.12641.5154-0.04881.09740.10720.03620.20130.0528-0.02610.1473-0.1041-0.1293-0.05650.1230.00940.01260.09910.01330.1494-5.036931.0331-0.5186
130.5865-0.82940.18471.68640.78672.19010.040.2957-0.4465-0.0752-0.0290.27940.4233-0.514-0.05610.1241-0.0229-0.01630.1908-0.04690.1647-32.8657-12.3866-30.8505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )H1 - 17
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 76 )H18 - 76
3X-RAY DIFFRACTION3chain 'H' and (resid 77 through 91 )H77 - 91
4X-RAY DIFFRACTION4chain 'H' and (resid 92 through 124 )H92 - 124
5X-RAY DIFFRACTION5chain 'H' and (resid 125 through 139 )H125 - 139
6X-RAY DIFFRACTION6chain 'H' and (resid 140 through 162 )H140 - 162
7X-RAY DIFFRACTION7chain 'H' and (resid 163 through 178 )H163 - 178
8X-RAY DIFFRACTION8chain 'H' and (resid 179 through 218 )H179 - 218
9X-RAY DIFFRACTION9chain 'L' and (resid 1 through 119 )L1 - 119
10X-RAY DIFFRACTION10chain 'L' and (resid 120 through 156 )L120 - 156
11X-RAY DIFFRACTION11chain 'L' and (resid 157 through 179 )L157 - 179
12X-RAY DIFFRACTION12chain 'L' and (resid 180 through 219 )L180 - 219
13X-RAY DIFFRACTION13chain 'M' and (resid 215 through 227 )M215 - 227

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