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- PDB-4j1y: The X-ray crystal structure of human complement protease C1s zymogen -

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Basic information

Entry
Database: PDB / ID: 4j1y
TitleThe X-ray crystal structure of human complement protease C1s zymogen
ComponentsComplement C1s subcomponent
KeywordsHYDROLASE / C4 / C2 / Hydrolysis / Extracellular
Function / homology
Function and homology information


complement subcomponent C_overbar_1s_ / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / serine-type endopeptidase activity / innate immune response / calcium ion binding / proteolysis ...complement subcomponent C_overbar_1s_ / Classical antibody-mediated complement activation / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / blood microparticle / serine-type endopeptidase activity / innate immune response / calcium ion binding / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
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 / 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. ...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 / 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-type aspartate/asparagine hydroxylation 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 / 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 / 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 C1s subcomponent
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6645 Å
AuthorsPerry, A.J. / Wijeyewickrema, L.C. / Wilmann, P.G. / Gunzburg, M.J. / D'Andrea, L. / Irving, J.A. / Pang, S.S. / Duncan, R.C. / Wilce, J.A. / Whisstock, J.C. / Pike, R.N.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: A Molecular Switch Governs the Interaction between the Human Complement Protease C1s and Its Substrate, Complement C4.
Authors: Perry, A.J. / Wijeyewickrema, L.C. / Wilmann, P.G. / Gunzburg, M.J. / D'Andrea, L. / Irving, J.A. / Pang, S.S. / Duncan, R.C. / Wilce, J.A. / Whisstock, J.C. / Pike, R.N.
History
DepositionFeb 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Jul 3, 2013Group: Structure summary
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C1s subcomponent
B: Complement C1s subcomponent


Theoretical massNumber of molelcules
Total (without water)87,5332
Polymers87,5332
Non-polymers00
Water73941
1
A: Complement C1s subcomponent


Theoretical massNumber of molelcules
Total (without water)43,7661
Polymers43,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C1s subcomponent


Theoretical massNumber of molelcules
Total (without water)43,7661
Polymers43,7661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Complement C1s subcomponent

B: Complement C1s subcomponent


Theoretical massNumber of molelcules
Total (without water)87,5332
Polymers87,5332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
Buried area2190 Å2
ΔGint-4 kcal/mol
Surface area35810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.890, 158.900, 78.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Complement C1s subcomponent / C1 esterase / Complement component 1 subcomponent s / Complement C1s subcomponent heavy chain / ...C1 esterase / Complement component 1 subcomponent s / Complement C1s subcomponent heavy chain / Complement C1s subcomponent light chain


Mass: 43766.457 Da / Num. of mol.: 2 / Fragment: CCP1-CCP2-SPz (UNP Residues 292-698) / Mutation: Q436A, I438A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1S / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star(DE3)pLysS
References: UniProt: P09871, complement subcomponent C_overbar_1s_
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 18% PEG 3350, 0.2M potassium nitrate., pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953695 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2011 / Details: Silicon mirrors (adaptive and U-bent)
RadiationMonochromator: Double crystal monochromator (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953695 Å / Relative weight: 1
ReflectionResolution: 2.66→63.81 Å / Num. all: 27247 / Num. obs: 27108 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Biso Wilson estimate: 73.6 Å2 / Rmerge(I) obs: 0.093
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.66-2.739.31.1252.51957197.8
2.66-63.8112.20.09320.627108199.4
11.92-63.8110.60.0448.9345197

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBES/ MOLREPphasing
PHENIX(phenix.refine: dev_1048)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ELV

1elv


Resolution: 2.6645→54.273 Å / SU ML: 0.33 / Phase error: 29.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1361 5.02 %RANDOM
Rwork0.2005 ---
all0.2034 27108 --
obs0.2034 27096 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6645→54.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5581 0 0 41 5622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115790
X-RAY DIFFRACTIONf_angle_d1.5247886
X-RAY DIFFRACTIONf_dihedral_angle_d14.1282060
X-RAY DIFFRACTIONf_chiral_restr0.088844
X-RAY DIFFRACTIONf_plane_restr0.0081039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6645-2.75970.33961100.28442504X-RAY DIFFRACTION98
2.7597-2.87020.32541260.26112583X-RAY DIFFRACTION100
2.8702-3.00080.32451320.24532550X-RAY DIFFRACTION100
3.0008-3.1590.32871360.24012536X-RAY DIFFRACTION100
3.159-3.35690.2921390.23072570X-RAY DIFFRACTION100
3.3569-3.61610.30971400.21432546X-RAY DIFFRACTION99
3.6161-3.97990.27911200.19532525X-RAY DIFFRACTION98
3.9799-4.55550.21961470.17162598X-RAY DIFFRACTION100
4.5555-5.73850.20871470.16422612X-RAY DIFFRACTION100
5.7385-54.28430.24151640.19582711X-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)
13.3687-2.29652.22214.8685-2.37782.0542-0.5006-0.31790.5330.41730.2192-1.6825-0.1267-0.1930.33720.94090.06390.01140.68930.03531.1838149.126152.3254106.1252
22.4882-3.92820.90368.5131-1.84280.62650.04020.03910.32380.2687-0.1342-0.7210.0075-0.09450.06220.7919-0.02220.00160.74440.01780.9896158.381523.9648107.6407
32.23860.0730.06175.2480.5751.92380.01890.3148-0.0524-0.83280.0105-0.7728-0.09650.2521-0.01060.74460.01490.17780.51990.0010.7649173.1234-15.608497.507
43.7751-1.25621.53025.1483-0.19341.71230.18890.37880.8278-1.1094-0.23-0.1643-0.32310.1578-0.05711.20730.17720.30420.6896-0.09050.7991227.189-49.20286.9128
53.408-3.9650.3834.111-0.4248-0.52650.38880.47030.1531-0.7121-0.62840.2235-0.0838-0.03550.1990.99920.0480.05080.7340.06220.9478216.8529-37.114894.0556
66.438-3.0479-1.32413.967-0.22962.21780.65610.80470.4085-2.1337-0.88320.46490.22630.07190.26061.37640.1356-0.15060.87410.08081.0533207.4295-13.169187.7064
73.1335-4.0541.98948.9285-0.561.81850.10890.16890.752-1.7565-0.479-0.5357-0.01540.02430.10331.16220.0763-0.03520.85430.09821.2916205.1717-0.590290.279
85.34661.27392.13783.56960.37832.23780.1677-1.17480.87540.5691-0.89162.1738-0.0476-1.03340.61421.0267-0.05230.09771.0573-0.23021.795197.950816.3868107.7617
90.88350.13510.93840.06360.42333.6996-0.4561.00510.3752-0.8298-0.0931.1527-1.90380.98390.40611.4148-0.1624-0.39270.64670.16961.5171205.365519.056592.1349
102.74765.21041.52232.04492.67735.6984-0.7732-0.11581.74890.142-0.24141.0415-1.5414-0.69850.74861.37670.1713-0.50990.90610.09862.3813193.078628.106697.6416
113.6419-0.37580.20523.24420.64714.8775-0.1225-0.05540.8912-1.5414-0.25271.2448-0.5983-0.3707-0.02491.22570.0145-0.38950.75520.00651.7336204.542325.257999.058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 292 through 331 )
2X-RAY DIFFRACTION2chain 'A' and (resid 332 through 439 )
3X-RAY DIFFRACTION3chain 'A' and (resid 440 through 684 )
4X-RAY DIFFRACTION4chain 'B' and (resid 292 through 315 )
5X-RAY DIFFRACTION5chain 'B' and (resid 316 through 370 )
6X-RAY DIFFRACTION6chain 'B' and (resid 371 through 407 )
7X-RAY DIFFRACTION7chain 'B' and (resid 408 through 445 )
8X-RAY DIFFRACTION8chain 'B' and (resid 446 through 540 )
9X-RAY DIFFRACTION9chain 'B' and (resid 541 through 569 )
10X-RAY DIFFRACTION10chain 'B' and (resid 570 through 594 )
11X-RAY DIFFRACTION11chain 'B' and (resid 595 through 683 )

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