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- PDB-1pk6: Globular Head of the Complement System Protein C1q -

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Basic information

Entry
Database: PDB / ID: 1pk6
TitleGlobular Head of the Complement System Protein C1q
Components
  • Complement C1q subcomponent, A chain precursor
  • Complement C1q subcomponent, B chain precursor
  • Complement C1q subcomponent, C chain precursor
KeywordsIMMUNE SYSTEM / Complement system / C1q / immunology / jellyroll / IgG
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. / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Jelly Rolls / Sandwich / Mainly Beta
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: 1.85 Å
AuthorsGaboriaud, C. / Juanhuix, J. / Gruez, A. / Lacroix, M. / Darnault, C. / Pignol, D. / Verger, D. / Fontecilla-Camps, J.C. / Arlaud, G.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: The crystal structure of the globular head of complement protein C1q provides a basis for its versatile recognition properties.
Authors: Gaboriaud, C. / Juanhuix, J. / Gruez, A. / Lacroix, M. / Darnault, C. / Pignol, D. / Verger, D. / Fontecilla-Camps, J.C. / Arlaud, G.J.
History
DepositionJun 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_asym_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,2534
Polymers44,2133
Non-polymers401
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-52 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.182, 53.222, 90.880
Angle α, β, γ (deg.)90.00, 112.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Complement C1q subcomponent, A chain precursor / C1Q


Mass: 14914.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human) / References: UniProt: P02745
#2: Protein Complement C1q subcomponent, B chain precursor / C1Q


Mass: 14996.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human) / References: UniProt: P02746
#3: Protein Complement C1q subcomponent, C chain precursor / C1Q


Mass: 14302.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: serum / Source: (natural) Homo sapiens (human) / References: UniProt: P02747
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.03 Å3/Da / Density % sol: 39.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 4000, CaCl2, B-mercaptoethanol, agarose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13-5 mg/mlprotein1drop
250 mMTris-HCl1droppH7.6
3250 mM1dropNaCl
42 %glycerol1drop
5100 mMsulfobetaine1951drop
60.2-0.4 %agarose1drop
728-41 %PEG40001reservoir
8100 mMTris-HCl1reservoirpH7.0
950 mM1reservoirCaCl2
1010 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Jan 28, 1998
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→25.4 Å / Num. all: 26237 / Num. obs: 26090 / % possible obs: 90 % / Redundancy: 4.73 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.1
Reflection shellResolution: 1.86→1.98 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 1.7 / % possible all: 67.2
Reflection
*PLUS
Lowest resolution: 26 Å / Num. measured all: 116591
Reflection shell
*PLUS
Highest resolution: 1.85 Å / % possible obs: 67.2 % / Num. unique obs: 3614 / Num. measured obs: 3946

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 1GR3

1gr3


Resolution: 1.85→25.4 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.396 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A90, A92, A160, B92, B93, B108, B109, B150, B163, B165, C89 HAVE DIFFUSE LATERAL CHAINS
RfactorNum. reflection% reflectionSelection details
Rfree0.23858 1074 4.8 %RANDOM
Rwork0.19869 ---
all0.20057 26237 --
obs0.20057 21245 85.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.877 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.03 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.85→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 1 198 3314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213158
X-RAY DIFFRACTIONr_bond_other_d0.0040.022767
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9354290
X-RAY DIFFRACTIONr_angle_other_deg2.61136428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.065391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023555
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02681
X-RAY DIFFRACTIONr_nbd_refined0.1890.2537
X-RAY DIFFRACTIONr_nbd_other0.2740.23348
X-RAY DIFFRACTIONr_nbtor_other0.1050.21798
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3380.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.961.51956
X-RAY DIFFRACTIONr_mcangle_it1.82323163
X-RAY DIFFRACTIONr_scbond_it1.92531202
X-RAY DIFFRACTIONr_scangle_it3.4284.51127
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.851→1.898 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 19
Rwork0.278 413
Refinement
*PLUS
Lowest resolution: 26 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.98 Å / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.28

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