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

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Basic information

Entry
Database: PDB / ID: 5hzf
TitleSingle Chain Recombinant Globular Head of the Complement System Protein C1q in complex with magnesium
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 / microglial cell activation / synapse organization / cell-cell signaling / amyloid-beta binding / collagen-containing extracellular matrix / blood microparticle / postsynapse / 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: 1.55 Å
AuthorsMoreau, C.P. / Gaboriaud, C.P.
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
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 2.0Aug 30, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jun 12, 2019Group: Data collection / Structure summary
Category: audit_author / database_PDB_rev / database_PDB_rev_record
Item: _audit_author.name
Revision 2.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 16, 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 C1q subcomponent subunit A,Complement C1q subcomponent subunit C,Complement C1q subcomponent subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7222
Polymers45,6981
Non-polymers241
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-9 kcal/mol
Surface area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.996, 52.911, 89.894
Angle α, β, γ (deg.)90.00, 115.19, 90.00
Int Tables number5
Space group name H-MC121

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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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 1.94 Å3/Da / Density % sol: 36.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30% PEG 8000, 0.1M HEPES, pH 7.5

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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: 1.55→100 Å / Num. obs: 49348 / % possible obs: 98.4 % / Redundancy: 4.9 % / Rsym value: 0.056 / Net I/σ(I): 14.85
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.95 / Rsym value: 0.0753 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PK6

1pk6


Resolution: 1.55→42.901 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.03
RfactorNum. reflection% reflection
Rfree0.1856 2507 5.08 %
Rwork0.169 --
obs0.1699 49342 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→42.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 1 315 3480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113347
X-RAY DIFFRACTIONf_angle_d1.1884562
X-RAY DIFFRACTIONf_dihedral_angle_d13.0421983
X-RAY DIFFRACTIONf_chiral_restr0.077496
X-RAY DIFFRACTIONf_plane_restr0.007601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5501-1.57990.3091040.33982514X-RAY DIFFRACTION95
1.5799-1.61210.3231490.32052608X-RAY DIFFRACTION99
1.6121-1.64720.29831390.28942578X-RAY DIFFRACTION99
1.6472-1.68550.29211630.26872560X-RAY DIFFRACTION99
1.6855-1.72770.24651310.22772643X-RAY DIFFRACTION99
1.7277-1.77440.25991290.21862576X-RAY DIFFRACTION99
1.7744-1.82660.21381460.19742567X-RAY DIFFRACTION98
1.8266-1.88550.21171240.18982600X-RAY DIFFRACTION99
1.8855-1.95290.2131240.18462616X-RAY DIFFRACTION98
1.9529-2.03110.19371370.17022592X-RAY DIFFRACTION98
2.0311-2.12360.19981340.16372605X-RAY DIFFRACTION99
2.1236-2.23550.20441450.16412584X-RAY DIFFRACTION99
2.2355-2.37560.18711700.16392593X-RAY DIFFRACTION99
2.3756-2.5590.19571570.16572599X-RAY DIFFRACTION98
2.559-2.81640.18451270.17032616X-RAY DIFFRACTION99
2.8164-3.22390.18751390.1542646X-RAY DIFFRACTION99
3.2239-4.06120.1421380.13692652X-RAY DIFFRACTION99
4.0612-42.91730.14311510.14232686X-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)
12.8829-0.7294-0.14522.513-0.12231.7331-0.0693-0.2136-0.09330.11350.04270.16660.079-0.16360.01580.105-0.00470.02120.15170.00060.1773.05832.30718.9523
22.1618-0.1215-0.83291.60520.01222.84210.04360.09760.3621-0.10820.03870.0028-0.23750.04420.00440.0964-0.0199-0.02980.1147-0.00630.203785.374911.80588.7263
32.6036-0.25560.19391.865-0.27721.2437-0.0087-0.0080.270.04970.0042-0.1078-0.09170.1176-0.01980.1044-0.00880.01750.1351-0.03570.179292.081410.361511.6542
42.38990.4876-0.01852.58790.64711.993-0.0816-0.6690.03550.39560.0771-0.13710.07060.1354-0.01310.21920.0719-0.03150.3729-0.05270.169791.58334.869630.9992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 125 )
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 165 )
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 279 )
4X-RAY DIFFRACTION4chain 'A' and (resid 280 through 407 )

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