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- PDB-4lmf: C1s CUB1-EGF-CUB2 -

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Basic information

Entry
Database: PDB / ID: 4lmf
TitleC1s CUB1-EGF-CUB2
ComponentsComplement C1s subcomponent heavy chain
KeywordsHYDROLASE / CUB domain / EGF-like domain / Complement C1s
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
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 / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain ...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 / 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 / Laminin / Laminin / 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 / 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
Complement C1s subcomponent
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.921 Å
AuthorsWallis, R. / Venkatraman Girija, U. / Moody, P.C.E. / Marshall, J.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis of the C1q/C1s interaction and its central role in assembly of the C1 complex of complement activation.
Authors: Venkatraman Girija, U. / Gingras, A.R. / Marshall, J.E. / Panchal, R. / Sheikh, M.A. / Gal, P. / Schwaeble, W.J. / Mitchell, D.A. / Moody, P.C. / Wallis, R.
History
DepositionJul 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Oct 23, 2013Group: Database references
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C1s subcomponent heavy chain
B: Complement C1s subcomponent heavy chain
C: Complement C1s subcomponent heavy chain
D: Complement C1s subcomponent heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,03520
Polymers124,4624
Non-polymers57316
Water0
1
A: Complement C1s subcomponent heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2595
Polymers31,1151
Non-polymers1434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Complement C1s subcomponent heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2595
Polymers31,1151
Non-polymers1434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Complement C1s subcomponent heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2595
Polymers31,1151
Non-polymers1434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Complement C1s subcomponent heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2595
Polymers31,1151
Non-polymers1434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Complement C1s subcomponent heavy chain
hetero molecules

D: Complement C1s subcomponent heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,51710
Polymers62,2312
Non-polymers2868
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2150 Å2
ΔGint-44 kcal/mol
Surface area28920 Å2
MethodPISA
6
B: Complement C1s subcomponent heavy chain
C: Complement C1s subcomponent heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,51710
Polymers62,2312
Non-polymers2868
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-69 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.876, 71.668, 157.723
Angle α, β, γ (deg.)90.000, 95.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain D) / NCS domain segments: (Selection details: chain 'D')

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Components

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


Mass: 31115.492 Da / Num. of mol.: 4 / Fragment: CUB1-EGF-CUB2 fragment (unp residues 17-292)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1S / Production host: Cricetulus griseus (Chinese hamster)
References: UniProt: P09871, complement subcomponent C_overbar_1s_
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca

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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: 59.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.92→67.51 Å / Num. all: 32700 / Num. obs: 32566 / % possible obs: 98.9 % / Observed criterion σ(I): 2.1 / Biso Wilson estimate: 55.15 Å2
Reflection shellResolution: 2.92→3 Å / % possible all: 91

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.921→67.51 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7744 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 28.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2521 1652 5.08 %
Rwork0.2083 --
obs0.2106 32535 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.86 Å2 / Biso mean: 46.501 Å2 / Biso min: 2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.921→67.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8752 0 16 0 8768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039028
X-RAY DIFFRACTIONf_angle_d0.77312240
X-RAY DIFFRACTIONf_chiral_restr0.0311256
X-RAY DIFFRACTIONf_plane_restr0.0041648
X-RAY DIFFRACTIONf_dihedral_angle_d12.313268
Refine LS restraints NCSNumber: 5325 / Type: POSITIONAL / Rms dev position: 9.245 Å
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9205-3.00650.35881260.32662373249991
3.0065-3.10350.33181370.29492539267698
3.1035-3.21440.37511320.27142569270199
3.2144-3.34310.27871460.25162553269999
3.3431-3.49530.26171410.23132570271199
3.4953-3.67950.27051460.21212597274399
3.6795-3.910.27681320.21452581271399
3.91-4.21190.27191490.193526022751100
4.2119-4.63570.20491450.16682576272199
4.6357-5.30620.19051310.15872627275899
5.3062-6.68440.22111290.19662638276799
6.6844-67.530.2181380.19342658279698
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)
10.2433-0.12370.08110.3287-0.19420.26120.08610.20620.044-0.19940.0531-0.0376-0.0750.10210.42580.0855-0.10340.09490.1457-0.0015-0.0315-19.800115.0363-82.1177
20.02-0.01880.02970.1562-0.06390.0531-0.0350.0380.01480.07870.0363-0.083-0.00690.01540.00050.1135-0.08390.00150.2583-0.10570.1101-3.212518.1998-48.635
30.10820.03080.01120.08340.05540.0821-0.08210.0015-0.0073-0.0625-0.00950.04460.0007-0.0418-0.26690.04660.01620.0226-0.065-0.11830.002421.712822.1206-33.1896
40.02820.0406-0.00360.0721-0.00030.0011-0.04070.19630.0512-0.0628-0.04420.0284-0.05120.1783-0.11630.1431-0.116-0.0650.66460.12180.1925-6.5412-19.3032-43.1988
50.0166-0.039-0.00280.09790.01210.0066-0.09950.02460.040.0970.12520.03340.05960.0222-0.00160.1314-0.0773-0.04350.2472-0.04190.23339.4994-13.2305-9.827
60.0053-0.01360.0050.11210.01020.0409-0.03480.0692-0.0971-0.08060.0098-0.0806-0.0235-0.0112-0.09540.1568-0.0196-0.0158-0.0226-0.06530.098334.2962-9.06145.9347
70.03050.0062-0.03810.0270.00170.0495-0.1783-0.42120.07250.10380.03670.0093-0.1603-0.1326-0.00750.22140.1465-0.04620.5357-0.09530.2074-6.2101-12.3523.5878
80.00270.01390.00490.1060.03360.0502-0.0457-0.00220.1015-0.07410.01310.04390.0062-0.0034-0.01670.0733-0.0392-0.04870.28090.0080.2894-23.094-15.2462-31.083
90.23790.1923-0.11010.30580.11280.3452-0.12150.0195-0.1254-0.0653-0.03190.0266-0.0729-0.0039-0.30460.07930.0012-0.0010.0215-0.0160.1247-47.338-13.6799-45.3295
100.13220.01180.01240.2757-0.10010.54050.0896-0.0698-0.00540.10730.08380.0956-0.0244-0.17050.08050.1489-0.00640.03910.1312-0.00410.113144.812217.3599-43.9379
110.32610.1294-0.07230.10620.02350.1239-0.0229-0.1668-0.16970.0276-0.0747-0.1066-0.06350.035-0.37980.0816-0.0153-0.04150.0340.12810.11237.867718.5435-84.0001
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 116 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 117 through 158 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 277 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 116 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 117 through 158 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 159 through 277 )B0
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 116 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 117 through 162 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 163 through 277 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 158 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 159 through 277 )D0

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