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- PDB-2qy0: Active dimeric structure of the catalytic domain of C1r reveals e... -

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Basic information

Entry
Database: PDB / ID: 2qy0
TitleActive dimeric structure of the catalytic domain of C1r reveals enzyme-product like contacts
Components(Complement C1r subcomponent) x 2
KeywordsHYDROLASE / complement / serine protease / beta barrel / Complement pathway / EGF-like domain / Glycoprotein / Hydroxylation / Immune response / Innate immunity / Phosphorylation / Sushi
Function / homology
Function and homology information


complement subcomponent C_overbar_1r_ / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / molecular sequestering activity / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / blood microparticle / immune response ...complement subcomponent C_overbar_1r_ / zymogen activation / Classical antibody-mediated complement activation / Initial triggering of complement / molecular sequestering activity / complement activation, classical pathway / serine-type peptidase activity / Regulation of Complement cascade / blood microparticle / immune response / innate immune response / serine-type endopeptidase activity / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding
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 / Coagulation Factor Xa inhibitory site / 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 family, serine active site. / Serine proteases, trypsin domain profile. / 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
Complement C1r subcomponent
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKardos, J. / Harmat, V. / Pallo, A. / Barabas, O. / Szilagyi, K. / Graf, L. / Naray-Szabo, G. / Goto, Y. / Zavodszky, P. / Gal, P.
CitationJournal: Mol.Immunol. / Year: 2008
Title: Revisiting the mechanism of the autoactivation of the complement protease C1r in the C1 complex: Structure of the active catalytic region of C1r.
Authors: Kardos, J. / Harmat, V. / Pallo, A. / Barabas, O. / Szilagyi, K. / Graf, L. / Naray-Szabo, G. / Goto, Y. / Zavodszky, P. / Gal, P.
History
DepositionAug 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C1r subcomponent
B: Complement C1r subcomponent
C: Complement C1r subcomponent
D: Complement C1r subcomponent
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,85211
Polymers91,2074
Non-polymers6457
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.541, 92.416, 162.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31A
41C
51A
61C
71A
81C
91A
101C
12B
22D
32B
42D
52B
62D
72B
82D
92B
102D
112B
122D

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ALAALAALAALAAA291 - 3194 - 32
211ALAALAALAALACC291 - 3194 - 32
321CYSCYSPROPROAA321 - 36234 - 75
421CYSCYSPROPROCC321 - 36234 - 75
531LEULEUTHRTHRAA365 - 37578 - 88
631LEULEUTHRTHRCC365 - 37578 - 88
741GLYGLYTHRTHRAA377 - 39890 - 111
841GLYGLYTHRTHRCC377 - 39890 - 111
951GLYGLYARGARGAA408 - 446121 - 159
1051GLYGLYARGARGCC408 - 446121 - 159
112ILEILELYSLYSBB447 - 4901 - 44
212ILEILELYSLYSDD447 - 4901 - 44
322LEULEUARGARGBB500 - 52154 - 75
422LEULEUARGARGDD500 - 52154 - 75
532VALVALLEULEUBB523 - 60777 - 161
632VALVALLEULEUDD523 - 60777 - 161
742GLYGLYTHRTHRBB609 - 671163 - 225
842GLYGLYTHRTHRDD609 - 671163 - 225
952VALVALILEILEBB673 - 680227 - 234
1052VALVALILEILEDD673 - 680227 - 234
1162LYSLYSMETMETBB682 - 684236 - 238
1262LYSLYSMETMETDD682 - 684236 - 238

NCS ensembles :
ID
1
2

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Components

#1: Protein Complement C1r subcomponent


Mass: 18477.934 Da / Num. of mol.: 2 / Fragment: Sushi-1 and Sushi-2 domains, CCP1-CCP2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1R / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P00736, complement subcomponent C_overbar_1r_
#2: Protein Complement C1r subcomponent


Mass: 27125.586 Da / Num. of mol.: 2 / Fragment: Peptidase S1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1R / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P00736, complement subcomponent C_overbar_1r_
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 14% (w/v) PEG 6000, 0.2 M NaCl, 10% (v/v) glycerol, 0.1 M Tris HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 18, 2002 / Details: mirror
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→54.981 Å / Num. all: 35308 / Num. obs: 35308 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 68.122 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 6.1
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2466 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GPZ

1gpz


Resolution: 2.6→54.31 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.901 / SU B: 21.025 / SU ML: 0.224 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.485 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS CONTRIBUTION IS NOT ADDED TO ATOMIC B-VALUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.25938 1768 5 %RANDOM
Rwork0.2106 ---
all0.21306 33537 --
obs0.21306 33537 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.03 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.6→54.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6079 0 42 160 6281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226314
X-RAY DIFFRACTIONr_bond_other_d0.0020.024301
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.9428573
X-RAY DIFFRACTIONr_angle_other_deg1.3663.00510371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3535779
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25823.787301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70215975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9671541
X-RAY DIFFRACTIONr_chiral_restr0.0880.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027103
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021324
X-RAY DIFFRACTIONr_nbd_refined0.1990.21200
X-RAY DIFFRACTIONr_nbd_other0.2070.24370
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22973
X-RAY DIFFRACTIONr_nbtor_other0.0860.23404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2185
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1210.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.21524011
X-RAY DIFFRACTIONr_mcbond_other0.20121589
X-RAY DIFFRACTIONr_mcangle_it1.78436216
X-RAY DIFFRACTIONr_scbond_it0.86522711
X-RAY DIFFRACTIONr_scangle_it1.30832353
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1869medium positional0.250.5
22D2926medium positional0.160.5
11A1869medium thermal0.372
22D2926medium thermal0.332
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 127 -
Rwork0.318 2405 -
obs-2405 100 %
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)
13.346-1.2915-5.54390.58142.28349.94330.18540.59970.0296-0.012-0.06790.1542-0.9654-1.0756-0.11760.23170.43440.18960.10.1201-0.06271.456140.661242.7246
22.48760.048-0.4572.00360.29321.85910.2888-0.0999-0.17820.1289-0.2216-0.0972-0.24750.0715-0.0672-0.168-0.1073-0.0421-0.1080.1156-0.11538.104420.63248.4427
33.34980.7266-4.99940.8303-1.48038.19170.1464-0.430.06230.05150.0054-0.1409-0.73680.7623-0.15180.063-0.33470.0941-0.0362-0.081-0.146239.338439.505738.7415
42.8863-0.1234-0.75052.6801-0.3651.94830.32180.211-0.168-0.2576-0.28350.1591-0.39-0.1852-0.0383-0.11230.1629-0.0193-0.1201-0.0791-0.12380.868821.470272.6109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA290 - 4343 - 147
2X-RAY DIFFRACTION2AA435 - 446148 - 159
3X-RAY DIFFRACTION2BB447 - 6861 - 240
4X-RAY DIFFRACTION3CC290 - 4343 - 147
5X-RAY DIFFRACTION4CC435 - 446148 - 159
6X-RAY DIFFRACTION4DD447 - 6861 - 240

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