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- PDB-3bn9: Crystal Structure of MT-SP1 in complex with Fab Inhibitor E2 -

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Basic information

Entry
Database: PDB / ID: 3bn9
TitleCrystal Structure of MT-SP1 in complex with Fab Inhibitor E2
Components
  • E2 Fab Heavy Chain
  • E2 Fab Light Chain
  • Membrane-type serine protease 1
KeywordsHYDROLASE / Antibody-Protease Complex / Protein-Protein Complex / Enzyme-Inhibitor Complex / Disease mutation / Glycoprotein / Membrane / Polymorphism / Serine protease / Signal-anchor / Transmembrane
Function / homology
Function and homology information


matriptase / epithelial cell morphogenesis involved in placental branching / Formation of the cornified envelope / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation ...matriptase / epithelial cell morphogenesis involved in placental branching / Formation of the cornified envelope / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / keratinocyte differentiation / antigen binding / serine-type peptidase activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / neural tube closure / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / protein catabolic process / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / basolateral plasma membrane / blood microparticle / Potential therapeutics for SARS / immune response / external side of plasma membrane / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, matripase / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily ...Peptidase S1A, matripase / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy variable 3-23 / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.173 Å
AuthorsFarady, C.J. / Schneider, E.L. / Egea, P.F. / Goetz, D.H. / Craik, C.S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of an Fab-protease complex reveals a highly specific non-canonical mechanism of inhibition
Authors: Farady, C.J. / Egea, P.F. / Schneider, E.L. / Darragh, M.R. / Craik, C.S.
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 / _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 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Membrane-type serine protease 1
C: E2 Fab Light Chain
D: E2 Fab Heavy Chain
A: Membrane-type serine protease 1
E: E2 Fab Light Chain
F: E2 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,64921
Polymers153,6506
Non-polymers99915
Water14,844824
1
B: Membrane-type serine protease 1
C: E2 Fab Light Chain
D: E2 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,47913
Polymers76,8253
Non-polymers65510
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-14.3 kcal/mol
Surface area27450 Å2
MethodPISA
2
A: Membrane-type serine protease 1
E: E2 Fab Light Chain
F: E2 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1698
Polymers76,8253
Non-polymers3445
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-31 kcal/mol
Surface area27880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.625, 163.279, 201.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Membrane-type serine protease 1 / Serine protease 14 / Matriptase / Suppressor of tumorigenicity protein 14 / MT-SP1 / Prostamin / ...Serine protease 14 / Matriptase / Suppressor of tumorigenicity protein 14 / MT-SP1 / Prostamin / Serine protease TADG-15 / Tumor-associated differentially-expressed gene 15 protein


Mass: 26447.689 Da / Num. of mol.: 2 / Fragment: Peptidase S1 domain / Mutation: C122S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST14, PRSS14, SNC19, TADG15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5Y6, matriptase

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Antibody , 2 types, 4 molecules CEDF

#2: Antibody E2 Fab Light Chain


Mass: 23245.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody E2 Fab Heavy Chain


Mass: 27131.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01764*PLUS

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Non-polymers , 3 types, 839 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 293 K / pH: 8
Details: 16% PEG 5000 MME, 0.21M AmSO4, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 12, 2007 / Details: KOHZU DOUBLE CRYSTAL SI (111)
RadiationMonochromator: KOHZU DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.173→85.64 Å / Num. obs: 74972 / % possible obs: 89.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.5
Reflection shellResolution: 2.173→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.7 / % possible all: 77.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
ELVESdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EAX, 2HFF

1eax

2hff


Resolution: 2.173→85.64 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 5781 7.72 %
Rwork0.223 --
obs0.226 74902 87.4 %
all-74972 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.62 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 42.28 Å2
Baniso -1Baniso -2Baniso -3
1--2.345 Å20 Å2-0 Å2
2--2.3351 Å2-0 Å2
3----5.7878 Å2
Refinement stepCycle: LAST / Resolution: 2.173→85.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10217 0 62 824 11103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0210551
X-RAY DIFFRACTIONf_angle_d1.44814331
X-RAY DIFFRACTIONf_dihedral_angle_d19.5043701
X-RAY DIFFRACTIONf_chiral_restr0.1341568
X-RAY DIFFRACTIONf_plane_restr0.011861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.173-2.19780.3535920.30821196X-RAY DIFFRACTION46
2.1978-2.22370.34481500.30951965X-RAY DIFFRACTION75
2.2237-2.25080.37511600.30021998X-RAY DIFFRACTION77
2.2508-2.27930.33391680.28681998X-RAY DIFFRACTION77
2.2793-2.30930.36331740.28192076X-RAY DIFFRACTION79
2.3093-2.34090.33751530.27432037X-RAY DIFFRACTION78
2.3409-2.37440.31481680.26872149X-RAY DIFFRACTION82
2.3744-2.40980.32461730.26352187X-RAY DIFFRACTION83
2.4098-2.44750.31441940.26262132X-RAY DIFFRACTION83
2.4475-2.48760.3171810.24662217X-RAY DIFFRACTION85
2.4876-2.53050.31162040.24212205X-RAY DIFFRACTION85
2.5305-2.57650.28991860.24952255X-RAY DIFFRACTION86
2.5765-2.62610.28321880.2492207X-RAY DIFFRACTION86
2.6261-2.67970.3181920.23732289X-RAY DIFFRACTION87
2.6797-2.7380.29061920.23162290X-RAY DIFFRACTION87
2.738-2.80170.30891750.22792284X-RAY DIFFRACTION87
2.8017-2.87170.30731990.23482315X-RAY DIFFRACTION88
2.8717-2.94940.29712070.23312276X-RAY DIFFRACTION89
2.9494-3.03620.31821970.23232396X-RAY DIFFRACTION90
3.0362-3.13420.25311760.22092355X-RAY DIFFRACTION90
3.1342-3.24620.25732100.21562455X-RAY DIFFRACTION92
3.2462-3.37620.26462150.2092428X-RAY DIFFRACTION94
3.3762-3.52980.25182230.19582539X-RAY DIFFRACTION96
3.5298-3.71590.23562150.17922634X-RAY DIFFRACTION98
3.7159-3.94880.21562290.17892606X-RAY DIFFRACTION100
3.9488-4.25360.22152410.16972647X-RAY DIFFRACTION100
4.2536-4.68170.19612150.15852672X-RAY DIFFRACTION100
4.6817-5.3590.19692210.15892718X-RAY DIFFRACTION100
5.359-6.75140.20452430.18552722X-RAY DIFFRACTION100
6.7514-85.70280.22892400.2162873X-RAY DIFFRACTION99
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)
10.4522-0.041-0.49360.24570.01650.7274-0.0741-0.0805-0.01830.02450.1049-0.0184-0.01080.3042-0.03330.106-0.0383-0.00570.4558-0.00360.0707-39.314-34.242834.3929
20.22790.00370.18870.206-0.09430.4442-0.0080.10990.0158-0.07540.05010.0068-0.0998-0.1419-0.05120.0963-0.0207-0.00970.3847-0.02270.0536-17.777134.4401-34.3879
30.38370.38290.40550.21710.30080.24140.2141-0.0382-0.19260.2335-0.0884-0.14150.2698-0.0855-0.15690.2336-0.0472-0.07780.1080.02870.08749.8242011.7524
40.12830.132-0.02120.2656-0.09250.09580.1095-0.0461-0.0230.1673-0.1040.14210.00550.0051-0.03850.1521-0.06570.0180.06170.00830.0739-7.100213.1392.973
50.1188-0.0716-0.20290.05580.05990.10560.0441-0.06530.0225-0.069-0.0399-0.0076-0.20550.1703-0.00750.1393-0.08350.00080.24560.02150.0022-11.4421-20.2017-11.8031
60.34970.2123-0.29490.2812-0.18370.02790.0706-0.14940.02770.0305-0.06890.1243-0.01970.0601-0.0241-0.04-0.08520.01540.0403-0.0052-0.0416-27.9406-13.2175-4.7473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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