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- PDB-5ckm: The CUB1-EGF-CUB2 domains of rat MBL-associated serine protease-2... -

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Basic information

Entry
Database: PDB / ID: 5ckm
TitleThe CUB1-EGF-CUB2 domains of rat MBL-associated serine protease-2 (MASP-2) bound to Ca2+
ComponentsMannan-binding lectin serine peptidase 2
KeywordsHYDROLASE / MASP / CUB1-EGF-CUB2 / Complement activation / lectin pathway
Function / homology
Function and homology information


mannan-binding lectin-associated serine protease-2 / Ficolins bind to repetitive carbohydrate structures on the target cell surface / complement component C4b binding / Lectin pathway of complement activation / Initial triggering of complement / complement activation, lectin pathway / complement activation / complement activation, classical pathway / calcium-dependent protein binding / peptidase activity ...mannan-binding lectin-associated serine protease-2 / Ficolins bind to repetitive carbohydrate structures on the target cell surface / complement component C4b binding / Lectin pathway of complement activation / Initial triggering of complement / complement activation, lectin pathway / complement activation / complement activation, classical pathway / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region
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 / 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 / Jelly Rolls / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Sandwich / Mainly Beta
Similarity search - Domain/homology
MBL associated serine protease 2 / Mannan-binding lectin serine protease 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.73 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 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 21, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.6Jul 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_conn_type / 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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Jan 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

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Assembly

Deposited unit
A: Mannan-binding lectin serine peptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7405
Polymers31,3991
Non-polymers3414
Water2,540141
1
A: Mannan-binding lectin serine peptidase 2
hetero molecules

A: Mannan-binding lectin serine peptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,48110
Polymers62,7982
Non-polymers6838
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2600 Å2
ΔGint-61 kcal/mol
Surface area29750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.900, 119.390, 104.020
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

21A-510-

HOH

31A-515-

HOH

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Components

#1: Protein Mannan-binding lectin serine peptidase 2 / Mannan-binding lectin serine peptidase 2 / isoform CRA_b / Mannan-binding lectin serine protease 2


Mass: 31398.844 Da / Num. of mol.: 1 / Fragment: residues 21-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Masp2, rCG_31002 / Plasmid: PED / Cell (production host): OVARY / Cell line (production host): DXB11 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A2VCV7, UniProt: Q9JJS8*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: 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.: 1
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 4.1 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-Ac pH 8 containing 40% MPD and 200 mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: PIXEL / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.73→22.9 Å / Num. obs: 14031 / % possible obs: 99.4 % / Redundancy: 2 % / Rsym value: 0.167 / Net I/σ(I): 6.4
Reflection shellResolution: 2.73→2.82 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.06 / % possible all: 94.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NTO

1nto


Resolution: 2.73→22.9 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 704 5.02 %
Rwork0.204 13324 -
obs0.2069 14028 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.12 Å2 / Biso mean: 34.7302 Å2 / Biso min: 9.79 Å2
Refinement stepCycle: final / Resolution: 2.73→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 17 141 2369
Biso mean--65.88 26.76 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042302
X-RAY DIFFRACTIONf_angle_d0.833124
X-RAY DIFFRACTIONf_chiral_restr0.035326
X-RAY DIFFRACTIONf_plane_restr0.003408
X-RAY DIFFRACTIONf_dihedral_angle_d11.946824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7252-2.93530.31981410.2742565X-RAY DIFFRACTION97
2.9353-3.22990.32681470.23942620X-RAY DIFFRACTION100
3.2299-3.69560.26761480.2062650X-RAY DIFFRACTION100
3.6956-4.64970.20611230.1712704X-RAY DIFFRACTION100
4.6497-22.940.25761450.18442785X-RAY DIFFRACTION100
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)
12.92270.37130.94112.81340.28835.5505-0.0427-0.24270.03760.14660.0591-0.2093-0.07110.1629-0.00870.18950.04630.0180.08310.01250.162110.7563-1.390723.0122
21.9760.0769-2.76236.47942.97915.3151-0.2936-0.208-0.57820.4211-0.067-0.45410.51050.40480.32540.45490.06030.07340.10190.05840.284810.4394-15.8348-9.974
34.3333-0.4044-0.85884.64761.04066.88170.20260.2589-0.34430.129-0.25630.41060.1043-0.39080.06690.32130.07440.04190.1552-0.05480.374615.7676-38.4327-27.7954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 119 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 163 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 278 )A0

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