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- PDB-3t2n: Human hepsin protease in complex with the Fab fragment of an inhi... -

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Basic information

Entry
Database: PDB / ID: 3t2n
TitleHuman hepsin protease in complex with the Fab fragment of an inhibitory antibody
Components
  • Antibody, Fab fragment, Heavy Chain
  • Antibody, Fab fragment, Light Chain
  • Serine protease hepsin
KeywordsHYDROLASE / Type II transmembrane serine protease / SRCR domain / Substrates include pro-hepsin / pro-HGF / Laminin-332 / Transmembrane
Function / homology
Function and homology information


hepsin / pilomotor reflex / Signaling by MST1 / positive regulation of thyroid hormone generation / cochlea morphogenesis / serine-type exopeptidase activity / positive regulation of plasminogen activation / basement membrane disassembly / detection of mechanical stimulus involved in sensory perception of sound / MET Receptor Activation ...hepsin / pilomotor reflex / Signaling by MST1 / positive regulation of thyroid hormone generation / cochlea morphogenesis / serine-type exopeptidase activity / positive regulation of plasminogen activation / basement membrane disassembly / detection of mechanical stimulus involved in sensory perception of sound / MET Receptor Activation / response to thyroid hormone / negative regulation of epithelial to mesenchymal transition / positive regulation by host of viral transcription / positive regulation of hepatocyte proliferation / potassium ion transmembrane transport / serine-type peptidase activity / negative regulation of epithelial cell proliferation / cell-cell junction / peptidase activity / regulation of cell shape / positive regulation of cell growth / apical plasma membrane / serine-type endopeptidase activity / neuronal cell body / positive regulation of gene expression / endoplasmic reticulum membrane / negative regulation of apoptotic process / cell surface / proteolysis / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Hepsin, SRCR domain / Hepsin, SRCR domain / Mac-2 Binding Protein / SRCR-like domain / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family ...Hepsin, SRCR domain / Hepsin, SRCR domain / Mac-2 Binding Protein / SRCR-like domain / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / 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 / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serine protease hepsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKoschubs, T. / Dengl, S. / Duerr, H. / Kaluza, K. / Georges, G. / Hartl, C. / Jennewein, S. / Lanzendoerfer, M. / Auer, J. / Stern, A. ...Koschubs, T. / Dengl, S. / Duerr, H. / Kaluza, K. / Georges, G. / Hartl, C. / Jennewein, S. / Lanzendoerfer, M. / Auer, J. / Stern, A. / Huang, K.-S. / Kostrewa, D. / Ries, S. / Hansen, S. / Kohnert, U. / Cramer, P. / Mundigl, O.
CitationJournal: Biochem.J. / Year: 2012
Title: Allosteric antibody inhibition of human hepsin protease.
Authors: Koschubs, T. / Dengl, S. / Durr, H. / Kaluza, K. / Georges, G. / Hartl, C. / Jennewein, S. / Lanzendorfer, M. / Auer, J. / Stern, A. / Huang, K.S. / Packman, K. / Gubler, U. / Kostrewa, D. / ...Authors: Koschubs, T. / Dengl, S. / Durr, H. / Kaluza, K. / Georges, G. / Hartl, C. / Jennewein, S. / Lanzendorfer, M. / Auer, J. / Stern, A. / Huang, K.S. / Packman, K. / Gubler, U. / Kostrewa, D. / Ries, S. / Hansen, S. / Kohnert, U. / Cramer, P. / Mundigl, O.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine protease hepsin
B: Serine protease hepsin
H: Antibody, Fab fragment, Heavy Chain
I: Antibody, Fab fragment, Heavy Chain
L: Antibody, Fab fragment, Light Chain
M: Antibody, Fab fragment, Light Chain


Theoretical massNumber of molelcules
Total (without water)174,6826
Polymers174,6826
Non-polymers00
Water5,675315
1
A: Serine protease hepsin
H: Antibody, Fab fragment, Heavy Chain
L: Antibody, Fab fragment, Light Chain


Theoretical massNumber of molelcules
Total (without water)87,3413
Polymers87,3413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-32 kcal/mol
Surface area32450 Å2
MethodPISA
2
B: Serine protease hepsin
I: Antibody, Fab fragment, Heavy Chain
M: Antibody, Fab fragment, Light Chain


Theoretical massNumber of molelcules
Total (without water)87,3413
Polymers87,3413
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-28 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.980, 66.580, 108.330
Angle α, β, γ (deg.)88.71, 94.30, 104.53
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serine protease hepsin / Transmembrane protease serine 1 / Serine protease hepsin non-catalytic chain / Serine protease ...Transmembrane protease serine 1 / Serine protease hepsin non-catalytic chain / Serine protease hepsin catalytic chain


Mass: 40491.793 Da / Num. of mol.: 2 / Fragment: Extracellular domain (UNP residues 46-417)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPN, TMPRSS1 / Plasmid: pTT5 / Cell line (production host): FreeStyle 293 cells / Production host: Homo sapiens (human) / References: UniProt: P05981, hepsin
#2: Antibody Antibody, Fab fragment, Heavy Chain


Mass: 23967.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#3: Antibody Antibody, Fab fragment, Light Chain


Mass: 22881.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 18% PEG 3350, 0.15 M MgSO4 and 0.01 M barium chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9188 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2010
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 2.55→47.33 Å / Num. obs: 54655 / Redundancy: 3.4 % / Biso Wilson estimate: 59.85 Å2 / Net I/σ(I): 7.96
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.13

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.9.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→47.33 Å / Cor.coef. Fo:Fc: 0.8657 / Cor.coef. Fo:Fc free: 0.8363 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.767 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.67 / SU Rfree Blow DPI: 0.314 / SU Rfree Cruickshank DPI: 0.326
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 2772 5.07 %RANDOM
Rwork0.2425 ---
obs0.2442 54655 98.67 %-
Displacement parametersBiso max: 138 Å2 / Biso mean: 47.6298 Å2 / Biso min: 12.27 Å2
Baniso -1Baniso -2Baniso -3
1-12.1847 Å23.8432 Å23.0041 Å2
2---8.2036 Å2-1.5295 Å2
3----3.9811 Å2
Refine analyzeLuzzati coordinate error obs: 0.479 Å
Refinement stepCycle: LAST / Resolution: 2.55→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11434 0 0 315 11749
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5193SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes232HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1725HARMONIC5
X-RAY DIFFRACTIONt_it11739HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1526SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13093SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11739HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg16007HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion3.02
LS refinement shellResolution: 2.55→2.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3126 211 5.19 %
Rwork0.2705 3851 -
all0.2726 4062 -
obs--98.67 %
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)
11.24210.3169-0.65081.4582-0.55751.8896-0.06350.1489-0.05690.0506-0.0518-0.03130.03450.3520.1154-0.1132-0.02050.0776-0.0299-0.0287-0.218446.4924-36.9479-7.5503
21.3891-0.5504-0.36661.06640.30221.3322-0.2023-0.10360.0109-0.09050.07610.04870.032-0.33130.1263-0.1372-0.00750.09660.031-0.08-0.203616.9024-36.074817.9916
32.1839-0.21160.8070.6383-0.39581.35150.13110.027-0.13350.0498-0.0339-0.05910.0319-0.1297-0.0972-0.1278-0.04680.08180.0864-0.066-0.24373.4298-16.3837-38.3121
42.1410.05430.22030.2917-0.12330.95060.0806-0.0009-0.07620.0756-0.02760.1365-0.0358-0.0007-0.053-0.13410.05370.0690.0837-0.0419-0.216460.4595-15.542148.328
52.8583-0.38480.37580.3383-0.14610.48010.0556-0.06040.35480.1086-0.0877-0.00610.0349-0.05550.0321-0.0797-0.07770.08360.0617-0.0505-0.15145.9257-3.5204-25.2884
63.85830.635-0.14010.39710.25660.57880.06370.16890.3036-0.0151-0.0652-0.0069-0.048-0.01050.0014-0.11730.1210.05380.07480.0301-0.178757.5915-2.678435.6988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A48 - 472
2X-RAY DIFFRACTION2{ B|* }B48 - 485
3X-RAY DIFFRACTION3{ H|* }H1 - 315
4X-RAY DIFFRACTION4{ I|* }I1 - 308
5X-RAY DIFFRACTION5{ L|* }L1 - 302
6X-RAY DIFFRACTION6{ M|* }M1 - 281

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