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- PDB-4lor: C1s CUB1-EGF-CUB2 in complex with a collagen-like peptide from C1q -

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Basic information

Entry
Database: PDB / ID: 4lor
TitleC1s CUB1-EGF-CUB2 in complex with a collagen-like peptide from C1q
Components
  • Complement C1s subcomponent heavy chain
  • collagen-like peptide from C1q
KeywordsHYDROLASE/protein binding / CUB domain / EGF-like domain / protein collagen complex / C1 complex / HYDROLASE-protein binding complex
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 / Laminin / Laminin / 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 / 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 / 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: 2.5 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 13, 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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: collagen-like peptide from C1q
C: collagen-like peptide from C1q
D: collagen-like peptide from C1q
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,94210
Polymers38,5554
Non-polymers3876
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-75 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.353, 71.173, 98.393
Angle α, β, γ (deg.)90.000, 111.120, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide / Sugars , 3 types, 5 molecules ABCD

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


Mass: 31115.492 Da / Num. of mol.: 1 / 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: Protein/peptide collagen-like peptide from C1q


Mass: 2479.700 Da / Num. of mol.: 3 / Source method: obtained synthetically
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 50 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Tris, 100 mM NaBr, 24% PEG 3350 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: 2.5→48.57 Å / Num. all: 14978 / Num. obs: 14918 / % possible obs: 93.2 % / Observed criterion σ(I): 2.7 / Biso Wilson estimate: 47.37 Å2
Reflection shellResolution: 2.5→2.69 Å / % possible all: 86.7

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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: 2.5→48.57 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7772 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 28.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 743 4.99 %
Rwork0.1958 --
obs0.1986 14886 92.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.12 Å2 / Biso mean: 47.7734 Å2 / Biso min: 17.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2628 0 19 45 2692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022758
X-RAY DIFFRACTIONf_angle_d0.7413761
X-RAY DIFFRACTIONf_chiral_restr0.044387
X-RAY DIFFRACTIONf_plane_restr0.003501
X-RAY DIFFRACTIONf_dihedral_angle_d10.3731027
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5001-2.69310.38661290.28882623275287
2.6931-2.96410.31941620.24662976313897
2.9641-3.39290.26891870.22282902308997
3.3929-4.27430.21581330.17572766289991
4.2743-48.5810.22341320.16692876300892
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)
12.03590.38580.34351.14950.73340.54740.21120.25190.3380.1014-0.08260.0047-0.339-0.144700.33270.09230.01760.22220.03810.23710.3823-13.941658.0708
21.6440.9431-1.23471.1251-0.13441.15940.05070.8329-0.4749-0.2289-0.20950.04630.1968-0.4654-0.02290.3940.0734-0.0340.4567-0.04550.3993-4.4814-22.305855.4996
30.22150.1218-0.53850.31110.25860.6564-0.13240.2827-0.0184-0.06580.03350.06750.1051-0.4558-00.35070.0294-0.04030.41660.030.271211.5629-18.367838.7099
41.8487-0.57880.61312.297-0.93413.73610.0431-0.0648-0.19090.1383-0.2975-0.32940.04920.03260.00020.2917-0.02690.00150.2362-0.00070.311323.8413-17.1772-0.8094
52.27911.4941-0.01071.96210.83511.90620.1260.18350.1308-0.16490.11450.12610.1634-0.60520.00510.2450.0318-0.01770.27260.01520.264519.5582-16.8864-4.4298
60.4505-0.18520.7050.0755-0.29661.17030.25210.1847-0.04790.13880.055-0.10820.25470.35040.43360.44920.02610.5880.3686-0.38530.9069-15.8906-39.944262.614
70.0714-0.0408-0.10770.9936-0.14550.2397-0.3189-0.19360.36680.0228-0.0220.1909-0.3466-0.4281-0.38190.78550.19240.21360.7254-0.42720.9762-31.3664-13.733373.4046
80.6156-0.70750.42071.01810.16011.84110.6602-0.4625-0.08170.5464-0.14690.3471.0288-0.5770.27980.75220.0703-0.0570.4169-0.13460.6717-15.8523-36.848664.5701
90.3516-0.5131-0.79531.92341.34911.7985-0.34160.5076-1.2201-0.1828-0.2067-0.16150.2853-0.0339-0.76130.15210.09270.0830.7297-0.410.9429-35.2985-11.668271.7893
100.21260.766-0.48852.7578-1.76661.13220.3230.2240.16890.33150.58740.39540.15770.14470.790.58810.0890.23790.4535-0.29770.5474-11.1621-49.580661.3875
110.0540.1540.09060.43840.26820.5316-0.5485-0.1012-0.83380.1005-0.2120.28810.5787-0.142-0.71310.75030.15440.40950.36840.0160.7648-20.5811-32.494568.2401
120.759-0.0630.11270.5665-0.29370.38810.00040.05470.33480.1458-0.19460.4148-0.3055-0.4922-0.67210.39270.35580.23990.8085-0.1540.7488-31.1473-12.03269.9291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 44 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 96 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 158 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 221 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 222 through 277 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 17 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 26 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 17 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 18 through 26 )C0
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 8 )D0
11X-RAY DIFFRACTION11chain 'D' and (resid 9 through 15 )D0
12X-RAY DIFFRACTION12chain 'D' and (resid 16 through 24 )D0

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