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- PDB-3pob: Crystal structure of MASP-1 CUB2 domain in complex with the colla... -

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Basic information

Entry
Database: PDB / ID: 3pob
TitleCrystal structure of MASP-1 CUB2 domain in complex with the collagen-like domain of MBL
Components
  • MBL collagen-like peptide
  • Mannan-binding lectin serine protease 1
KeywordsHYDROLASE / collagen complex / MASP / CUB domain / MBL / MBP / Collagen peptide / Calcium binding site / Complement proteins / lectin pathway of complement / MASP-1 / Bloodstream
Function / homology
Function and homology information


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 / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding ...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 / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / calcium-dependent protein binding / peptidase activity / serine-type endopeptidase activity / calcium ion binding / protein homodimerization activity / 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 / 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 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / Resolution: 1.801 Å
AuthorsGingras, A.R. / Moody, P.C.E. / Wallis, R.
CitationJournal: Structure / Year: 2011
Title: Structural Basis of Mannan-Binding Lectin Recognition by Its Associated Serine Protease MASP-1: Implications for Complement Activation.
Authors: Gingras, A.R. / Girija, U.V. / Keeble, A.H. / Panchal, R. / Mitchell, D.A. / Moody, P.C. / Wallis, R.
History
DepositionNov 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Sep 6, 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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 1
B: MBL collagen-like peptide
C: MBL collagen-like peptide
D: MBL collagen-like peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5715
Polymers20,5314
Non-polymers401
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.200, 52.560, 57.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 / Mannan-binding lectin serine protease 1 heavy chain / Mannan-binding lectin serine protease 1 light chain


Mass: 13091.511 Da / Num. of mol.: 1 / Fragment: MASP-1 CUB2 domain (UNP Residues 188-301)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Crarf, MASP-1/-3, Masp1, Masp3 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8CHN8, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein/peptide MBL collagen-like peptide


Mass: 2479.700 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: peptide
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 28% PEG 8000, 50mM Tris, pH 8.0, 4mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2010
RadiationMonochromator: multi-layer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 17822 / Num. obs: 17755 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 25.76
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 5.38 / Num. unique all: 2795 / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DEM

3dem


Resolution: 1.801→26.44 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.029 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25213 888 5 %RANDOM
Rwork0.19801 ---
all0.20069 17822 --
obs0.20069 16865 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.129 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2---0.75 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.801→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1424 0 1 184 1609
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221498
X-RAY DIFFRACTIONr_angle_refined_deg2.1942.1762087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4995189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24424.22245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5115164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.942155
X-RAY DIFFRACTIONr_chiral_restr0.1510.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0261235
X-RAY DIFFRACTIONr_mcbond_it1.3361.5994
X-RAY DIFFRACTIONr_mcangle_it2.27521632
X-RAY DIFFRACTIONr_scbond_it3.6053504
X-RAY DIFFRACTIONr_scangle_it5.944.5455
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 63 -
Rwork0.27 1196 -
obs--100 %

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