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- PDB-1q3x: Crystal structure of the catalytic region of human MASP-2 -

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Basic information

Entry
Database: PDB / ID: 1q3x
TitleCrystal structure of the catalytic region of human MASP-2
ComponentsMannan-binding lectin serine protease 2
KeywordsHYDROLASE / complement / serine protease / modular structure / hinge bending / autoactivation
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 / Sushi repeat (SCR repeat) ...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 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 / 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: 2.23 Å
AuthorsHarmat, V. / Gal, P. / Kardos, J. / Szilagyi, K. / Ambrus, G. / Naray-Szabo, G. / Zavodszky, P.
Citation
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. / Zavodsky, P.
#1: Journal: J.Immunol. / Year: 2003
Title: Natural substrates and inhibitors of mannan-binding lectin-associated serine protease 1 and 2: A study on recombinant catalytic fragments
Authors: Ambrus, G. / Gal, P. / Kojima, M. / Szilagyi, K. / Balczer, J. / Antal, J. / Graf, L. / Laich, A. / Moffat, B.E. / Schwaelbe, W. / Sim, R.B. / Zvodszky, P.
#2: Journal: Embo J. / Year: 2000
Title: Crystal structure of the catalytic domain of human complement C1s: a serine protease with a handle
Authors: Gaboriaud, C. / Rossi, V. / Bally, I. / Arlaud, G.J. / Fontecilla-Camps, J.C.
History
DepositionAug 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: Mannan-binding lectin serine protease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,20311
Polymers71,5132
Non-polymers6919
Water6,521362
1
A: Mannan-binding lectin serine protease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1486
Polymers35,7561
Non-polymers3915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mannan-binding lectin serine protease 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0565
Polymers35,7561
Non-polymers2994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.950, 41.521, 102.994
Angle α, β, γ (deg.)96.44, 91.77, 119.52
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSALAALAAA434 - 43876 - 80
21CYSCYSALAALABB434 - 43876 - 80
32ILEILEHISHISAA445 - 49087 - 132
42ILEILEHISHISBB445 - 49087 - 132
53ALAALAVALVALAA492 - 542134 - 184
63ALAALAVALVALBB492 - 542134 - 184
74ILEILEPROPROAA544 - 554186 - 196
84ILEILEPROPROBB544 - 554186 - 196
95GLUGLUGLNGLNAA557 - 596199 - 238
105GLUGLUGLNGLNBB557 - 596199 - 238
116CYSCYSTYRTYRAA598 - 602240 - 244
126CYSCYSTYRTYRBB598 - 602240 - 244
137PROPROCYSCYSAA605 - 629247 - 271
147PROPROCYSCYSBB605 - 629247 - 271
158GLYGLYPHEPHEAA631 - 686273 - 328
168GLYGLYPHEPHEBB631 - 686273 - 328

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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: 35756.309 Da / Num. of mol.: 2 / Fragment: CCP2-SP
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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 293 K / pH: 7.5
Details: PEG 6000, sodium chloride, glycerol, Tris-HCl , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9474
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 14, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9474 Å / Relative weight: 1
ReflectionResolution: 2.23→50.64 Å / Num. obs: 27022 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.6
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.9 / % possible all: 74.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ELV

1elv


Resolution: 2.23→50.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.758 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1356 5 %RANDOM
Rwork0.174 ---
obs0.176 25664 94.8 %-
all-27020 --
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: 18.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20.18 Å20.19 Å2
2---0.7 Å2-0.26 Å2
3---1.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.292 Å0.221 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.23→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 44 362 5224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214994
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9041.9496789
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1395631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023826
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.32252
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.5554
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.3100
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.545
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.36523137
X-RAY DIFFRACTIONr_mcangle_it2.21335017
X-RAY DIFFRACTIONr_scbond_it1.59321857
X-RAY DIFFRACTIONr_scangle_it2.30531772
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1819 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.040.05
tight thermal0.060.5
LS refinement shellResolution: 2.23→2.29 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.273 84
Rwork0.233 1555
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)
11.0322-0.2737-0.10071.10340.09941.23030.0105-0.02490.0365-0.00920.01250.0121-0.04390.0395-0.02290.2266-0.00850.00650.24740.01590.2307-6.08315.24956.689
21.16650.1304-0.05530.9940.00971.11940.00630.00440.02290.01090.01290.01180.0350.0336-0.01920.2303-0.0156-0.00840.24510.0020.2225-6.151-18.35292.957
34.1175-7.51250.677823.84880.071522.78420.2186-0.49580.4766-0.2423-0.0865-2.47780.97870.4213-0.1320.38630.12220.02810.12370.04950.279312.003-8.01531.051
415.152225.32540.9925128.160227.575847.07540.71510.53560.23131.0003-0.4254-2.9066-0.76351.7232-0.28970.2301-0.0879-0.00870.25820.00890.21798.1994.307119.809
54.1952-3.9835-3.90611.00527.904114.40580.3152-0.03320.0689-0.8435-0.3815-0.0240.0836-0.44280.06620.50950.03790.02760.0908-0.02020.0214.919-3.77226.595
60.78162.54280.140923.99476.24716.56120.4456-0.378-0.02192.196-0.52220.1685-1.46060.70130.07670.7235-0.2029-0.03280.3939-0.13970.07281.406-1.539122.904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA434 - 68676 - 328
2X-RAY DIFFRACTION2BB434 - 68676 - 328
3X-RAY DIFFRACTION3AA405 - 42847 - 70
4X-RAY DIFFRACTION4BB405 - 42847 - 70
5X-RAY DIFFRACTION5AA362 - 4044 - 46
6X-RAY DIFFRACTION5AA429 - 43171 - 73
7X-RAY DIFFRACTION6BB366 - 4048 - 46
8X-RAY DIFFRACTION6BB429 - 43171 - 73

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