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- PDB-5ckq: CUB1-EGF-CUB2 domains of rat MASP-1 -

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Basic information

Entry
Database: PDB / ID: 5ckq
TitleCUB1-EGF-CUB2 domains of rat MASP-1
ComponentsMannan-binding lectin serine protease 1
KeywordsHYDROLASE / CUB1-EGF-CUB2 / serine protease / lectin pathway / complement
Function / homology
Function and homology information


Scavenging by Class A Receptors / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / Initial triggering of complement / complement activation, lectin pathway / complement activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity ...Scavenging by Class A Receptors / Ficolins bind to repetitive carbohydrate structures on the target cell surface / Lectin pathway of complement activation / Initial triggering of complement / complement activation, lectin pathway / complement activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / protein homodimerization activity / extracellular space
Similarity search - Function
Spermadhesin, CUB domain / Peptidase S1A, complement C1r/C1S/mannan-binding / 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) ...Spermadhesin, CUB domain / Peptidase S1A, complement C1r/C1S/mannan-binding / 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/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Laminin / Laminin / 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 / Jelly Rolls / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mannan-binding lectin serine protease 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.704 Å
AuthorsNan, R. / Furze, C.M. / Wright, D.W. / Gor, J. / Wallis, R. / Perkins, S.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K011715/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/K039121/1 United Kingdom
CitationJournal: Structure / Year: 2017
Title: Flexibility in Mannan-Binding Lectin-Associated Serine Proteases-1 and -2 Provides Insight on Lectin Pathway Activation.
Authors: Nan, R. / Furze, C.M. / Wright, D.W. / Gor, J. / Wallis, R. / Perkins, S.J.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4767
Polymers31,8901
Non-polymers5866
Water0
1
A: Mannan-binding lectin serine protease 1
hetero molecules

A: Mannan-binding lectin serine protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,95114
Polymers63,7802
Non-polymers1,17112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_757-x+2,y,-z+21
Buried area2720 Å2
ΔGint-37 kcal/mol
Surface area30740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.710, 152.710, 152.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23

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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: 31889.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: LIVER / Gene: Masp1, Crarf, Masp3 / Plasmid: PED / Cell line (production host): DXB11 / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: Q8CHN8, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 4.65 Å3/Da / Density % sol: 73.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM imidazole/MOPS pH 6.5 containing 20% ethylene glycol and 10% PEG8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.7→76.4 Å / Num. obs: 6473 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rsym value: 0.082 / Net I/σ(I): 9.2
Reflection shellResolution: 3.7→4.14 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DEM

3dem


Resolution: 3.704→76.355 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2937 301 4.66 %
Rwork0.2475 6160 -
obs0.25 6461 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 453.92 Å2 / Biso mean: 187.1629 Å2 / Biso min: 108.93 Å2
Refinement stepCycle: final / Resolution: 3.704→76.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2239 0 32 0 2271
Biso mean--155.5 --
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022340
X-RAY DIFFRACTIONf_angle_d0.7513175
X-RAY DIFFRACTIONf_chiral_restr0.029331
X-RAY DIFFRACTIONf_plane_restr0.003421
X-RAY DIFFRACTIONf_dihedral_angle_d10.605846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.7038-4.66630.3641470.292230353182
4.6663-76.37120.27581540.235231253279
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)
17.9799-1.28692.53193.8308-0.99942.54790.01420.418-0.0101-0.70640.1158-0.06780.09030.1957-0.11441.2359-0.24950.13811.0487-0.11471.1783146.518101.617128.3244
28.6537-2.33488.15210.5345-2.52147.59150.49730.1905-1.19060.22730.308-0.02370.49640.442-0.83351.05120.08310.03111.5690.10521.3515168.2786102.4126154.8791
36.53741.3894-0.9042.75222.03223.5963-0.23860.20360.08570.80840.0325-0.84960.7426-0.14270.22471.53630.18770.05021.15770.21882.1174199.334998.4928164.593
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 110 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 168 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 169 through 277 )A0

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