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- PDB-4igd: Crystal structure of the zymogen catalytic region of Human MASP-1 -

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Basic information

Entry
Database: PDB / ID: 4igd
TitleCrystal structure of the zymogen catalytic region of Human MASP-1
ComponentsMannan-binding lectin serine protease 1
KeywordsHYDROLASE / Complement / Immune response / Innate immunity / beta barrel / serine protease / Glycosylation
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 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHarmat, V. / Megyeri, M. / Vegh, A. / Dobo, J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Quantitative characterization of the activation steps of mannan-binding lectin (MBL)-associated serine proteases (MASPs) points to the central role of MASP-1 in the initiation of the complement lectin pathway
Authors: Megyeri, M. / Harmat, V. / Major, B. / Vegh, A. / Balczer, J. / Heja, D. / Szilagyi, K. / Datz, D. / Pal, G. / Zavodszky, P. / Gal, P. / Dobo, J.
History
DepositionDec 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mannan-binding lectin serine protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6743
Polymers45,4901
Non-polymers1842
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.310, 69.610, 117.680
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 1 / Complement factor MASP-3 / Complement-activating component of Ra-reactive factor / Mannose-binding ...Complement factor MASP-3 / Complement-activating component of Ra-reactive factor / Mannose-binding lectin-associated serine protease 1 / MASP-1 / Mannose-binding protein-associated serine protease / Ra-reactive factor serine protease p100 / RaRF / Serine protease 5


Mass: 45489.918 Da / Num. of mol.: 1 / Fragment: CCP1-CCP2-SP fragment, residues 298-699 / Mutation: R448Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MASP1 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21
References: UniProt: P48740, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20%(v/v) PEG400, 0.1M imidazole, pH 7.0, 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 / Details: Sagitally focusing Ge(220) and a multilayer
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: 2.5→20 Å / Num. all: 18608 / Num. obs: 18608 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.84 % / Biso Wilson estimate: 53.502 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.75
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.14 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 3.37 / Num. unique all: 1358 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INDIVIDUAL DOMAINS OF PDB ENTRY 3GOV

3gov


Resolution: 2.5→19.971 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 24.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 878 5.08 %random
Rwork0.2193 ---
all0.2207 17273 --
obs0.2207 17273 93.01 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.001 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.2295 Å2-0 Å20 Å2
2---7.7581 Å20 Å2
3---2.5286 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 12 91 3132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023150
X-RAY DIFFRACTIONf_angle_d0.5694291
X-RAY DIFFRACTIONf_chiral_restr0.04472
X-RAY DIFFRACTIONf_plane_restr0.003563
X-RAY DIFFRACTIONf_dihedral_angle_d11.7931133
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.65630.38031240.35132324244881
2.6563-2.86090.34981380.32534267288
2.8609-3.14780.33051530.26722698285193
3.1478-3.60090.26141710.23992827299897
3.6009-4.52810.20991580.18532933309199
4.5281-19.97170.18811340.1793079321399
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)
10.38770.1229-0.22980.3229-0.00920.426-0.1485-0.57130.59630.56120.0810.21440.35110.1621-0.02940.66670.0141-0.08360.1270.1250.054523.2774-59.48433.0209
20.0643-0.051-0.08280.06460.03530.15490.04830.16320.35480.1797-0.0893-0.16710.27350.34060.04220.3942-0.24140.0427-0.2616-0.10740.411718.6078-24.246122.7929
31.30270.0547-1.26090.9916-0.43081.50110.04760.4755-0.036-0.1098-0.1449-0.1444-0.0354-0.3514-0.00070.16480.0392-0.02630.32460.02980.220726.53156.37392.1378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 298:364)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 365:435)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 436:699)

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