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

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Basic information

Entry
Database: PDB / ID: 5ckn
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
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) ...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/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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 1.4Jan 10, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_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 peptidase 2
D: Mannan-binding lectin serine peptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2128
Polymers62,9722
Non-polymers2406
Water1,27971
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-48 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.640, 91.340, 127.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: CA / End label comp-ID: CA / Auth seq-ID: 1 - 302 / Label seq-ID: 1

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA - E
2chain DDB - H

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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: 31485.922 Da / Num. of mol.: 2
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.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3.85 Å3/Da / Density % sol: 68.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-Ac pH 8 + 40% MPD and 80 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.6→63.6 Å / Num. obs: 29893 / % possible obs: 97.6 % / Redundancy: 5 % / Rsym value: 0.082 / Net I/σ(I): 16.04
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.321 / % possible all: 98.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NTO

1nto


Resolution: 2.6→63.545 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1462 4.89 %
Rwork0.2066 28417 -
obs0.2089 29879 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.85 Å2 / Biso mean: 92.7259 Å2 / Biso min: 31.39 Å2
Refinement stepCycle: final / Resolution: 2.6→63.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4428 0 6 71 4505
Biso mean--64.96 59.87 -
Num. residues----556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044586
X-RAY DIFFRACTIONf_angle_d0.9626223
X-RAY DIFFRACTIONf_chiral_restr0.039645
X-RAY DIFFRACTIONf_plane_restr0.004815
X-RAY DIFFRACTIONf_dihedral_angle_d11.3911643
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2620X-RAY DIFFRACTION8.441TORSIONAL
12D2620X-RAY DIFFRACTION8.441TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.69290.31961490.31852847299699
2.6929-2.80080.32931400.28142799293998
2.8008-2.92820.3391480.26892835298399
2.9282-3.08260.28851330.24692837297098
3.0826-3.27570.28341460.23352650279692
3.2757-3.52860.29721560.21052848300498
3.5286-3.88370.23361370.202828913028100
3.8837-4.44550.24261560.18622895305199
4.4455-5.60040.21531390.17342905304498
5.6004-63.5640.22711580.19022910306894
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)
14.0873-2.56112.93073.6741-2.91367.3715-0.0696-0.4571-0.00640.23950.0787-0.2139-0.00340.04490.00740.3779-0.04490.02180.35990.00560.41835.6982-23.4061.6567
21.1701-0.55352.22222.7831-1.12694.1987-0.09290.16940.1858-0.4345-0.1513-0.4890.09461.07580.15840.48820.05790.06710.44860.03790.5570.6997-15.9383-20.1123
32.8226-0.5577-0.43974.3130.98112.61610.45391.32850.1441-2.0441-0.3869-0.7334-0.5531-0.23710.00351.68570.27250.21410.93430.08440.71581.7456-21.3335-57.1417
41.5133-0.2694-1.22874.28853.50618.83390.2281-0.14510.3520.1357-0.01820.1292-0.4204-0.1219-0.18710.3029-0.02610.0260.3587-0.03880.51910.0396-42.6596-30.0321
52.8592-0.53960.08643.0052-4.16847.1381-0.03441.27010.5365-0.20170.42870.2815-1.2179-0.9155-0.37231.2683-0.17330.05521.26960.21430.7475-0.8392-41.7352-85.1212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 109 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 140 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 278 )A0
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 119 )D0
5X-RAY DIFFRACTION5chain 'D' and (resid 120 through 278 )D0

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