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- PDB-3gov: Crystal structure of the catalytic region of human MASP-1 -

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Basic information

Entry
Database: PDB / ID: 3gov
TitleCrystal structure of the catalytic region of human MASP-1
Components(MASP-1) x 2
KeywordsHYDROLASE / Complement / serine protease / beta barrel / Hydroxylation / Immune response / Innate immunity / Sushi / Coagulation / Complement pathway / Disulfide bond / EGF-like domain / Glycoprotein / Protease
Function / homology
Function and homology information


Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / negative regulation of complement activation / complement activation, lectin pathway / zymogen activation / Scavenging by Class A Receptors / Initial triggering of complement / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity ...Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / negative regulation of complement activation / complement activation, lectin pathway / zymogen activation / Scavenging by Class A Receptors / Initial triggering of complement / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / extracellular space / extracellular region / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
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 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) ...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 / 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-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 / EGF-like domain signature 2. / EGF-like domain / Ribbon / 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 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsHarmat, V. / Dobo, J. / Beinrohr, L. / Sebestyen, E. / Zavodszky, P. / Gal, P.
CitationJournal: J.Immunol. / Year: 2009
Title: MASP-1, a promiscuous complement protease: structure of its catalytic region reveals the basis of its broad specificity.
Authors: Dobo, J. / Harmat, V. / Beinrohr, L. / Sebestyen, E. / Zavodszky, P. / Gal, P.
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Sep 6, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MASP-1
B: MASP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7214
Polymers45,5372
Non-polymers1842
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-13 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.418, 70.412, 121.413
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MASP-1 / Ra-reactive factor serine protease p100 / RaRF / Mannan-binding lectin serine protease 1 / Mannose- ...Ra-reactive factor serine protease p100 / RaRF / Mannan-binding lectin serine protease 1 / Mannose-binding protein-associated serine protease / MASP-1 / Serine protease 5 / Complement-activating component of Ra-reactive factor heavy chain / Complement-activating component of Ra-reactive factor light chain


Mass: 17508.240 Da / Num. of mol.: 1
Fragment: Sushi-1 and Sushi-2 domains, CCP1-CCP2, residues 298-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRARF, CRARF1, MASP1, PRSS5 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)plyss
References: UniProt: P48740, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein MASP-1 / Ra-reactive factor serine protease p100 / RaRF / Mannan-binding lectin serine protease 1 / Mannose- ...Ra-reactive factor serine protease p100 / RaRF / Mannan-binding lectin serine protease 1 / Mannose-binding protein-associated serine protease / MASP-1 / Serine protease 5 / Complement-activating component of Ra-reactive factor heavy chain / Complement-activating component of Ra-reactive factor light chain


Mass: 28028.900 Da / Num. of mol.: 1 / Fragment: serine protease domain, residues 449-699
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRARF, CRARF1, MASP1, PRSS5 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)plyss
References: UniProt: P48740, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAINS A AND B ARE PRODUCTS OF SPECIFIC CLEAVAGE OF THE ARG448-ILE449 BOND DURING SPONTANEOUS ...CHAINS A AND B ARE PRODUCTS OF SPECIFIC CLEAVAGE OF THE ARG448-ILE449 BOND DURING SPONTANEOUS AUTOACTIVATION OF MASP-1
Has protein modificationY
Sequence detailsTHE RESIDUE AT POSITION 499 IS A NATURAL VARIANT OF THE ENZYME

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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: 3.27 Å3/Da / Density % sol: 62.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: well solution: 11%(w/v) PEG3350, 0.1 M MES; protein solution: 50 mM NaCl, 5 mM Tris, 0.5 mM EDTA, 20 mM benzamidine-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 2007 / Details: mirrors
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.55→45.98 Å / Num. obs: 19349 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 30.892 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.96
Reflection shellResolution: 2.55→2.6 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 6216 / Num. unique all: 1066 / Num. unique obs: 1066 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MASP-1 serine protease domain(unpublished), CCP1 and CCP2 modules of PDB entry 1zjk

1zjk


Resolution: 2.55→45.98 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.859 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 24.172 / SU ML: 0.252 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.453 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 989 5.1 %RANDOM
Rwork0.229 ---
all0.231 ---
obs0.231 19342 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.76 Å2 / Biso mean: 48.887 Å2 / Biso min: 23.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 12 90 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223196
X-RAY DIFFRACTIONr_bond_other_d0.0020.022174
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9594352
X-RAY DIFFRACTIONr_angle_other_deg0.8243.0065319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4195406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27824.887133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92915529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5821511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023546
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02600
X-RAY DIFFRACTIONr_nbd_refined0.190.2543
X-RAY DIFFRACTIONr_nbd_other0.1880.22115
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21477
X-RAY DIFFRACTIONr_nbtor_other0.0810.21701
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0970.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1570.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.26
X-RAY DIFFRACTIONr_mcbond_it0.62322057
X-RAY DIFFRACTIONr_mcbond_other0.0962810
X-RAY DIFFRACTIONr_mcangle_it1.04633230
X-RAY DIFFRACTIONr_scbond_it0.42921319
X-RAY DIFFRACTIONr_scangle_it0.67431117
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 78 -
Rwork0.337 1318 -
all-1396 -
obs-1438 97.08 %
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)
10.7489-1.2185-0.32312.04723.17691.2885-0.0639-0.07210.04010.34080.2322-0.55490.10620.0449-0.1683-0.20630.00410.0003-0.10740.0042-0.169.953541.585825.6109
22.4316-0.47951.57991.5227-0.21064.20390.01010.2328-0.24-0.1640.0511-0.0310.25730.2418-0.0612-0.1533-0.01120.0252-0.1738-0.0149-0.1291-0.6742-8.14832.0919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A298 - 435
2X-RAY DIFFRACTION2A436 - 699

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