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- PDB-1zjk: Crystal structure of the zymogen catalytic region of human MASP-2 -

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Basic information

Entry
Database: PDB / ID: 1zjk
TitleCrystal structure of the zymogen catalytic region of human MASP-2
ComponentsMannan-binding lectin serine protease 2
KeywordsHYDROLASE / beta barrel / modular protein
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 / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase 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 / 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
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsGal, P. / Harmat, V. / Kocsis, A. / Bian, T. / Barna, L. / Ambrus, G. / Vegh, B. / Balczer, J. / Sim, R.B. / Naray-Szabo, G. / Zavodszky, P.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: A True Autoactivating Enzyme: Structural insight into mannose-binding lectin-associated serine protease-2 activations
Authors: Gal, P. / Harmat, V. / Kocsis, A. / Bian, T. / Barna, L. / Ambrus, G. / Vegh, B. / Balczer, J. / Sim, R.B. / Naray-Szabo, G. / Zavodszky, P.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: The Structure of MBL-Associated Serine Protease-2 Reveals that Identical Substrate Specificities of C1s and MASP-2 are Realized Through Different Sets of Enzyme-Substrate Interactions
Authors: Harmat, V. / Gal, P. / Kardos, J. / Szilagyi, K. / Ambrus, G. / Vegh, B. / Naray-Szabo, G. / Zavodszky, P.
History
DepositionApr 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannan-binding lectin serine protease 2


Theoretical massNumber of molelcules
Total (without water)44,0321
Polymers44,0321
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.665, 72.689, 110.989
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 / Mannose-binding protein associated serine protease 2 / MASP-2 / MBL- associated serine protease 2


Mass: 44031.715 Da / Num. of mol.: 1
Fragment: complement control protein modules 1,2 and serine protease domain
Mutation: R444Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP2 / Plasmid: pET-17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O00187, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.2 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000, sodium chloride, TRIS/HCl buffer, pH 8.0, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9392 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2003 / Details: toroidal focusing mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9392 Å / Relative weight: 1
ReflectionResolution: 2.18→28.9 Å / Num. all: 18330 / Num. obs: 18330 / % possible obs: 88.1 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.13
Reflection shellResolution: 2.18→2.25 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 1.9 / Num. unique all: 800 / % possible all: 43.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SP domain of PDB ENTRY 1Q3X

1q3x


Resolution: 2.18→28.9 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.011 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.352 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25285 938 5.1 %RANDOM
Rwork0.20491 ---
all0.20733 17391 --
obs0.20733 17391 88.18 %-
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: 25.915 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---2.56 Å20 Å2
3---2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.18→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 0 84 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212996
X-RAY DIFFRACTIONr_bond_other_d0.0010.022605
X-RAY DIFFRACTIONr_angle_refined_deg0.8751.9444091
X-RAY DIFFRACTIONr_angle_other_deg0.63936045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.195388
X-RAY DIFFRACTIONr_chiral_restr0.0560.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023408
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02610
X-RAY DIFFRACTIONr_nbd_refined0.2010.3717
X-RAY DIFFRACTIONr_nbd_other0.2390.32956
X-RAY DIFFRACTIONr_nbtor_other0.1190.52061
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.5130
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.372
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.513
X-RAY DIFFRACTIONr_mcbond_it1.2921924
X-RAY DIFFRACTIONr_mcangle_it2.13533075
X-RAY DIFFRACTIONr_scbond_it0.98821072
X-RAY DIFFRACTIONr_scangle_it1.49131016
LS refinement shellResolution: 2.18→2.237 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 27
Rwork0.309 615
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)
18.1843-7.5141-2.461319.70676.71545.04780.19420.31190.5193-0.5264-0.57680.9744-0.5584-0.51780.38260.24010.1266-0.02940.2142-0.0380.2412-31.43346.50952.769
24.8401-3.0045-0.96036.27611.84491.9652-0.02310.05060.00470.1939-0.1193-0.12150.1490.11710.14240.24530.03450.04360.23320.02430.0157-11.1317.23348.055
33.94990.3759-1.11983.30760.4012.7452-0.14790.01680.05060.11780.2136-0.29280.13350.1127-0.06580.08520.0441-0.04090.1179-0.03250.067914.4272.94627.462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA296 - 36513 - 82
2X-RAY DIFFRACTION2AA366 - 43383 - 150
3X-RAY DIFFRACTION3AA434 - 686151 - 403

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