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- PDB-5hkj: Single Chain Recombinant Globular Head of the Complement System P... -

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Basic information

Entry
Database: PDB / ID: 5hkj
TitleSingle Chain Recombinant Globular Head of the Complement System Protein C1q
ComponentsComplement C1q subcomponent subunit A,Complement C1q subcomponent subunit C,Complement C1q subcomponent subunit B
KeywordsSIGNALING PROTEIN / gC1q domain / complement / C1q
Function / homology
Function and homology information


complement component C1 complex / complement component C1q complex / negative regulation of macrophage differentiation / synapse pruning / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer / complement activation / Classical antibody-mediated complement activation ...complement component C1 complex / complement component C1q complex / negative regulation of macrophage differentiation / synapse pruning / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer / complement activation / Classical antibody-mediated complement activation / neuron remodeling / Initial triggering of complement / complement activation, classical pathway / Regulation of Complement cascade / astrocyte activation / synapse organization / microglial cell activation / cell-cell signaling / amyloid-beta binding / postsynapse / collagen-containing extracellular matrix / blood microparticle / immune response / innate immune response / synapse / extracellular space / extracellular region
Similarity search - Function
C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies)
Similarity search - Domain/homology
Complement C1q subcomponent subunit A / Complement C1q subcomponent subunit B / Complement C1q subcomponent subunit C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMoreau, C.P. / Gaboriaud, C.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR 09-PIRI-0021 France
CitationJournal: Front Immunol / Year: 2016
Title: Structural and Functional Characterization of a Single-Chain Form of the Recognition Domain of Complement Protein C1q.
Authors: Moreau, C. / Bally, I. / Chouquet, A. / Bottazzi, B. / Ghebrehiwet, B. / Gaboriaud, C. / Thielens, N.
History
DepositionJan 14, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
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 / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C1q subcomponent subunit A,Complement C1q subcomponent subunit C,Complement C1q subcomponent subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9593
Polymers45,6981
Non-polymers2612
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-11 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.115, 52.729, 89.930
Angle α, β, γ (deg.)90.00, 115.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-831-

HOH

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Components

#1: Protein Complement C1q subcomponent subunit A,Complement C1q subcomponent subunit C,Complement C1q subcomponent subunit B


Mass: 45697.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1QA, C1QC, C1QG, C1QB / Plasmid: pcDNA3.1 / Cell line (production host): HEK 293-F / Production host: Homo sapiens (human)
References: UniProt: P02745, UniProt: P02747, UniProt: P02746
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


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
#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 / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 23% PEG 3350, 0.1 M Tris, 0.2 M NaCl, 50 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.35→100 Å / Num. obs: 74618 / % possible obs: 98.7 % / Redundancy: 4.8 % / Rsym value: 0.07 / Net I/σ(I): 11.2
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.53 / Rsym value: 0.671 / % possible all: 85.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHASERphasing
Cootmodel building
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2wnv

2wnv


Resolution: 1.35→42.821 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 3748 5.02 %
Rwork0.175 --
obs0.1763 74612 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→42.821 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 16 231 3409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133452
X-RAY DIFFRACTIONf_angle_d1.4714720
X-RAY DIFFRACTIONf_dihedral_angle_d15.0621269
X-RAY DIFFRACTIONf_chiral_restr0.122516
X-RAY DIFFRACTIONf_plane_restr0.009626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36710.3591400.32052338X-RAY DIFFRACTION90
1.3671-1.38510.33051210.28392607X-RAY DIFFRACTION97
1.3851-1.40410.27571500.26152546X-RAY DIFFRACTION99
1.4041-1.42420.29491390.25832668X-RAY DIFFRACTION99
1.4242-1.44540.23921380.2382573X-RAY DIFFRACTION99
1.4454-1.4680.26681510.22552655X-RAY DIFFRACTION99
1.468-1.49210.23791200.22322590X-RAY DIFFRACTION99
1.4921-1.51780.27911210.21942656X-RAY DIFFRACTION99
1.5178-1.54540.23481450.20952589X-RAY DIFFRACTION99
1.5454-1.57510.25741420.19842635X-RAY DIFFRACTION99
1.5751-1.60730.22411470.18832626X-RAY DIFFRACTION99
1.6073-1.64220.20661300.17972638X-RAY DIFFRACTION100
1.6422-1.68040.21511290.17222646X-RAY DIFFRACTION99
1.6804-1.72250.17471430.17622624X-RAY DIFFRACTION99
1.7225-1.7690.22971470.17052621X-RAY DIFFRACTION99
1.769-1.82110.19421350.16072622X-RAY DIFFRACTION99
1.8211-1.87990.19691310.16082633X-RAY DIFFRACTION99
1.8799-1.94710.17761510.16012634X-RAY DIFFRACTION99
1.9471-2.0250.191550.16062640X-RAY DIFFRACTION100
2.025-2.11720.19651400.16262642X-RAY DIFFRACTION100
2.1172-2.22880.20721550.16762621X-RAY DIFFRACTION100
2.2288-2.36840.17991330.16832641X-RAY DIFFRACTION99
2.3684-2.55130.21711230.17912694X-RAY DIFFRACTION100
2.5513-2.8080.2061360.18332656X-RAY DIFFRACTION100
2.808-3.21420.18691410.17782673X-RAY DIFFRACTION99
3.2142-4.0490.16341520.15212669X-RAY DIFFRACTION99
4.049-42.84270.18081330.15342727X-RAY DIFFRACTION99
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)
13.41460.11310.05462.8825-0.06623.83550.0283-0.42280.00520.4492-0.12940.23590.0671-0.31070.04770.07120.02310.04980.1657-0.01370.114270.69944.073225.009
21.9923-0.6255-0.14922.27470.17460.6356-0.0151-0.09-0.03450.0464-0.00320.12410.031-0.1020.00980.0784-0.00430.02610.10970.00050.121373.50812.464417.5814
32.0854-0.0557-0.7151.26640.01242.06310.01210.14510.2388-0.11570.0271-0.0223-0.110.00390.04760.0881-0.0203-0.00670.08120.00010.138685.795710.58498.444
41.8339-0.1501-0.01211.6066-0.10880.76570.00210.01990.16440.01590.0143-0.1342-0.06820.1019-0.01670.0739-0.00820.02850.092-0.02010.119293.16969.377110.4935
51.9272-0.1502-0.01882.53010.21721.39870.0292-0.11890.25550.06040.0178-0.0725-0.10650.0098-0.00830.0716-0.00870.01970.1016-0.01130.142389.541911.601114.3756
61.95040.1558-0.31762.19060.49061.2248-0.0445-0.49420.0590.30270.0539-0.13380.01840.17650.0070.14930.0334-0.01470.2636-0.02740.115691.76315.325230.8331
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 124 )
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 164 )
4X-RAY DIFFRACTION4chain 'A' and (resid 165 through 245 )
5X-RAY DIFFRACTION5chain 'A' and (resid 246 through 278 )
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 407 )

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