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- PDB-3tvj: Catalytic fragment of MASP-2 in complex with its specific inhibit... -

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Basic information

Entry
Database: PDB / ID: 3tvj
TitleCatalytic fragment of MASP-2 in complex with its specific inhibitor developed by directed evolution on SGCI scaffold
Components
  • Mannan-binding lectin serine protease 2 A chain
  • Mannan-binding lectin serine protease 2 B chain
  • Protease inhibitor SGPI-2
KeywordsHYDROLASE / in vitro evolution / specific inhibitor / allostery
Function / homology
Function and homology information


mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / complement activation, lectin pathway / Initial triggering of complement / complement activation, classical pathway / serine-type endopeptidase inhibitor activity / calcium-dependent protein binding / peptidase activity ...mannan-binding lectin-associated serine protease-2 / complement component C4b binding / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / complement activation, lectin pathway / Initial triggering of complement / complement activation, classical pathway / serine-type endopeptidase inhibitor activity / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Protease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / Peptidase S1A, complement C1r/C1S/mannan-binding / Complement Module, domain 1 / Complement Module; domain 1 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. ...Protease inhibitor with pacifastin repeats / Pacifastin domain / Pacifastin domain superfamily / Pacifastin inhibitor (LCMII) / Pacifastin domain profile. / Peptidase S1A, complement C1r/C1S/mannan-binding / Complement Module, domain 1 / Complement Module; domain 1 / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / : / Calcium-binding EGF domain / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Mannan-binding lectin serine protease 2 / Serine protease inhibitor I/II
Similarity search - Component
Biological speciesHomo sapiens (human)
Schistocerca gregaria (desert locust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsHeja, D. / Harmat, V. / Dobo, J. / Szasz, R. / Kekesi, K.A. / Zavodszky, P. / Gal, P. / Pal, G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Monospecific Inhibitors Show That Both Mannan-binding Lectin-associated Serine Protease-1 (MASP-1) and -2 Are Essential for Lectin Pathway Activation and Reveal Structural Plasticity of MASP-2.
Authors: Heja, D. / Harmat, V. / Fodor, K. / Wilmanns, M. / Dobo, J. / Kekesi, K.A. / Zavodszky, P. / Gal, P. / Pal, G.
History
DepositionSep 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Sep 13, 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_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 1.4Nov 20, 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: Mannan-binding lectin serine protease 2 A chain
B: Mannan-binding lectin serine protease 2 B chain
I: Protease inhibitor SGPI-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8774
Polymers39,7813
Non-polymers961
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-44 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.916, 62.471, 114.189
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: Protein Mannan-binding lectin serine protease 2 A chain / Mannan-binding lectin serine protease 2 / MBL-associated serine protease 2 / Mannose-binding ...Mannan-binding lectin serine protease 2 / MBL-associated serine protease 2 / Mannose-binding protein-associated serine protease 2 / MASP-2


Mass: 9217.346 Da / Num. of mol.: 1 / Fragment: Sushi 2 domain residues 363-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP2 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 De3
References: UniProt: O00187, mannan-binding lectin-associated serine protease-2
#2: Protein Mannan-binding lectin serine protease 2 B chain / Mannan-binding lectin serine protease 2 / MBL-associated serine protease 2 / Mannose-binding ...Mannan-binding lectin serine protease 2 / MBL-associated serine protease 2 / Mannose-binding protein-associated serine protease 2 / MASP-2


Mass: 26542.971 Da / Num. of mol.: 1 / Fragment: Peptidase S1 domain residues 445-686
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP2 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 De3
References: UniProt: O00187, mannan-binding lectin-associated serine protease-2
#3: Protein/peptide Protease inhibitor SGPI-2 / Schistocerca gregaria chymotrypsin inhibitor / SGCI


Mass: 4020.530 Da / Num. of mol.: 1 / Mutation: A83V, L86K, K87L, A88W, P90N
Source method: isolated from a genetically manipulated source
Details: expressed as MBP fusion protein / Source: (gene. exp.) Schistocerca gregaria (desert locust) / Gene: GenBank: Y09605.1 / Plasmid: pMal-TEV-SGPI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star / References: UniProt: O46162
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24.5% PEG 5000 MME, 0.164 M ammonium sulphate, 82 mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2011
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.28→40 Å / Num. all: 90627 / Num. obs: 90627 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.44 % / Biso Wilson estimate: 16.911 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.28-1.35.060.7522.543960193.3
1.3-1.45.050.5233.6316689194.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: domains of PDB entry 1Q3X, and PDB entry 1GL1

1q3x

1gl1


Resolution: 1.28→38 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.182 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20532 4584 5.1 %RANDOM
Rwork0.15623 ---
all0.15875 85991 --
obs0.15875 85991 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.28→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2753 0 5 509 3267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222995
X-RAY DIFFRACTIONr_bond_other_d0.0010.022002
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.9494103
X-RAY DIFFRACTIONr_angle_other_deg1.1423.0014891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95524.264129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63615481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7641515
X-RAY DIFFRACTIONr_chiral_restr0.1340.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213432
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02610
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3421.51870
X-RAY DIFFRACTIONr_mcbond_other1.3631.5772
X-RAY DIFFRACTIONr_mcangle_it4.45523030
X-RAY DIFFRACTIONr_scbond_it6.42831125
X-RAY DIFFRACTIONr_scangle_it8.5784.51061
X-RAY DIFFRACTIONr_rigid_bond_restr2.93834997
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.28→1.313 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 325 -
Rwork0.272 6092 -
obs--93.39 %
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)
10.09670.03970.20710.0120.07410.5232-0.00570.00360.0034-0.00170.00190.0016-0.01510.00730.00380.00530.0014-0.00070.0061-0.00010.0003-54.44190.2331-4.5642
20.038-0.0144-0.0369-0.00060.00570.0201-0.0026-0.0008-0.0006-0.0010.0015-0.0010.0008-0.00310.00110.00720.0005-0.00020.0076-0.00090.0021-36.328.124823.9264
30.19550.2313-0.10080.2224-0.08620.0279-0.0143-0.0148-0.0396-0.0164-0.0068-0.03460.00340.00620.02110.0061000.00990.0050.0128-9.2477-13.963321.2838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A362 - 433
2X-RAY DIFFRACTION2A434 - 444
3X-RAY DIFFRACTION2B445 - 686
4X-RAY DIFFRACTION3I1 - 35

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