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- PDB-4p3d: MT1-MMP:Fab complex (Form II) -

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Basic information

Entry
Database: PDB / ID: 4p3d
TitleMT1-MMP:Fab complex (Form II)
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 / negative regulation of GDF15-GFRAL signaling pathway / positive regulation of macrophage migration / craniofacial suture morphogenesis / macropinosome / response to odorant / chondrocyte proliferation / head development / astrocyte cell migration / TGFBR3 PTM regulation ...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 / astrocyte cell migration / TGFBR3 PTM regulation / 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 / metalloaminopeptidase activity / endodermal cell differentiation / 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 / lung development / skeletal system development / cell motility / protein catabolic process / metalloendopeptidase activity / protein processing / Golgi lumen / response to estrogen / male gonad development / integrin binding / melanosome / positive regulation of cell growth / response to oxidative stress / cytoplasmic vesicle / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / angiogenesis / endopeptidase activity / response to hypoxia / positive regulation of cell migration / serine-type endopeptidase activity / focal adhesion / proteolysis / extracellular space / zinc ion binding / metal 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Neutral zinc metallopeptidases, zinc-binding region signature. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
If kappa light chain / Matrix metalloproteinase-14
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.949 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 7, 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 1.3Sep 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_close_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 1.4Sep 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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
Revision 1.5Oct 30, 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
A: Heavy Chain Fab fragment of antibody LEM-2/15
B: Light Chain Fab fragment of antibody LEM-2/15
C: Matrix metalloproteinase-14
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)98,98716
Polymers98,0456
Non-polymers94210
Water11,854658
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14170 Å2
ΔGint-98 kcal/mol
Surface area37320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.898, 96.226, 81.521
Angle α, β, γ (deg.)90.000, 92.360, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 1 types, 2 molecules CM

#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.: 2 / Fragment: MT1-MMP V-B loop
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, 4 molecules AHBL

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


Mass: 23492.480 Da / Num. of mol.: 2
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: A2NHM3

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Non-polymers , 6 types, 668 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#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


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.83 %
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: 1.949→40 Å / Num. obs: 59340 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 14.85 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.033 / Net I/av σ(I): 17.96 / Net I/σ(I): 8.5 / Num. measured all: 365316
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-1.984.90.3828290.92395.8
1.98-2.025.70.33229450.9299.5
2.02-2.066.20.30329590.965100
2.06-2.16.30.27329610.945100
2.1-2.156.30.22929550.972100
2.15-2.26.20.20530021.021100
2.2-2.256.30.19129301.026100
2.25-2.316.20.17829591.027100
2.31-2.386.30.16629901.063100
2.38-2.466.30.15429411.066100
2.46-2.546.30.13929741.092100
2.54-2.656.30.12329861.13100
2.65-2.776.30.10629521.063100
2.77-2.916.30.09129881.1100
2.91-3.16.30.07729791.087100
3.1-3.336.30.06629741.017100
3.33-3.676.30.06329751.037100
3.67-4.26.10.06329851.051100
4.2-5.296.20.05430191.07100
5.29-406.10.04730371.02999.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DNAdata collection
HKL-2000data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: dev_1603)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YEC

1yec


Resolution: 1.949→39.657 Å / FOM work R set: 0.8669 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2096 3001 5.06 %
Rwork0.1584 56302 -
obs0.161 59303 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.76 Å2 / Biso mean: 16.69 Å2 / Biso min: 0.82 Å2
Refinement stepCycle: final / Resolution: 1.949→39.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6800 0 57 662 7519
Biso mean--27.54 24.04 -
Num. residues----898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097457
X-RAY DIFFRACTIONf_angle_d1.18710215
X-RAY DIFFRACTIONf_chiral_restr0.0531138
X-RAY DIFFRACTIONf_plane_restr0.0061327
X-RAY DIFFRACTIONf_dihedral_angle_d12.8552692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9488-1.98080.29051190.20192489260893
1.9808-2.01490.25641530.18082649280299
2.0149-2.05160.22461450.168326872832100
2.0516-2.0910.20121370.166826862823100
2.091-2.13370.23931390.165326992838100
2.1337-2.18010.21791460.154626512797100
2.1801-2.23080.22141520.156426732825100
2.2308-2.28660.21271350.163527102845100
2.2866-2.34840.25581470.164526832830100
2.3484-2.41750.2511350.168227082843100
2.4175-2.49550.21881450.159426642809100
2.4955-2.58470.2291510.171726552806100
2.5847-2.68820.26091430.176226942837100
2.6882-2.81050.25051430.172827242867100
2.8105-2.95860.21331470.168826682815100
2.9586-3.14390.18241500.161327032853100
3.1439-3.38650.20541350.152926812816100
3.3865-3.72710.17661410.145127092850100
3.7271-4.26590.20331440.135827002844100
4.2659-5.37240.15751420.131327272869100
5.3724-39.6650.17971520.164327422894100
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)
10.8316-0.0734-0.0730.43090.40860.5950.12950.01760.0197-0.1062-0.12450.0916-0.1244-0.03930.02780.08080.03150.00050.0528-0.00310.079715.386226.007127.3523
20.2346-0.0898-0.29960.43030.31620.67770.0654-0.0360.0422-0.255-0.13570.0629-0.3204-0.19770.01760.11680.1187-0.05130.06710.00920.06511.496715.799815.6744
30.70260.14340.39671.05540.46130.2660.0437-0.4175-0.13290.2369-0.1613-0.2202-0.0561-0.2654-0.46750.14190.0932-0.00130.2210.01610.06383.26130.8878.1557
40.7398-0.44530.05860.60650.33770.45520.10030.01420.0436-0.0463-0.0458-0.0184-0.050.08460.14890.07970.00860.01550.06950.00850.04433.942715.142416.4691
50.5293-0.05420.0640.07130.18090.4231-0.0634-0.0295-0.03570.00690.0079-0.01-0.1039-0.0396-0.03150.10710.0205-0.01930.11660.0170.09929.27671.587-7.1539
60.4784-0.335-0.64610.27370.39320.8864-0.1191-0.310.22220.3670.0226-0.1379-0.0180.29350.01220.1786-0.02250.02190.0963-0.01960.155931.329130.519633.895
70.6236-0.1845-0.21970.2930.0360.2378-0.03450.0280.0148-0.01350.00190.04930.0265-0.018100.059-0.0136-0.00570.0758-0.01250.064515.652-25.603614.8104
80.01530.02090.01550.1267-0.03980.0760.0911-0.14390.30540.2897-0.0309-0.0722-0.1194-0.0921-0.02650.1899-0.01610.0660.0716-0.1070.2030.4426.348339.8488
90.48180.27910.25750.60860.48870.1892-0.03150.01840.0575-0.23570.041-0.1327-0.0576-0.0054-0.03270.0729-0.02080.02370.0478-0.00260.07941.9305-1.759730.3897
100.39690.06780.09040.40210.2550.73420.02240.015-0.0401-0.00960.0030.05840.0133-0.003300.05650.00760.00440.0745-0.01140.075534.3642-17.986322.8975
110.20950.1104-0.24011.2469-0.18450.2153-0.0313-0.1529-0.1367-0.0848-0.006-0.3613-0.01620.0647-0.01170.0506-0.0144-0.01290.06780.00650.099641.2118-18.490625.3274
120.465-0.2862-0.22570.12260.24050.24720.0123-0.05810.03840.01230.0167-0.01710.01520.01340.11740.0526-0.01010.01680.08270.0020.086417.684-7.487836.1027
130.2301-0.15350.14790.1726-0.02790.1084-0.16240.1074-0.1848-0.0147-0.001-0.05990.1706-0.0284-0.00090.15010.01620.02970.14830.01140.174413.3175-6.091342.3137
140.16020.30330.06610.4970.06860.3351-0.0341-0.1624-0.27130.3177-0.0309-0.13820.17780.13030.1610.1378-0.04120.05290.09760.02640.0963-2.885-7.070148.4115
150.39450.22270.02240.7702-0.35340.3023-0.1145-0.34190.3090.27670.24730.085-0.06210.1760.17940.0706-0.0092-0.030.234-0.0740.07236.91142.0152.3278
160.0423-0.00880.0514-0.0006-0.00840.0155-0.00310.2042-0.0426-0.1175-0.009-0.02510.03690.1199-0.00210.1273-0.0019-0.00410.1095-0.01820.11132.6209-31.64187.4586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 83 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 139 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 140 through 218 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 119 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 120 through 218 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 215 through 227 )C0
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 124 )H0
8X-RAY DIFFRACTION8chain 'H' and (resid 125 through 139 )H0
9X-RAY DIFFRACTION9chain 'H' and (resid 140 through 218 )H0
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 66 )L0
11X-RAY DIFFRACTION11chain 'L' and (resid 67 through 80 )L0
12X-RAY DIFFRACTION12chain 'L' and (resid 81 through 156 )L0
13X-RAY DIFFRACTION13chain 'L' and (resid 157 through 179 )L0
14X-RAY DIFFRACTION14chain 'L' and (resid 180 through 194 )L0
15X-RAY DIFFRACTION15chain 'L' and (resid 195 through 218 )L0
16X-RAY DIFFRACTION16chain 'M' and (resid 215 through 227 )M0

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