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- PDB-2jg8: Crystallographic structure of human C1q globular heads complexed ... -

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Basic information

Entry
Database: PDB / ID: 2jg8
TitleCrystallographic structure of human C1q globular heads complexed to phosphatidyl-serine
Components(Complement C1q subcomponent subunit ...) x 3
KeywordsIMMUNE SYSTEM / POLYMORPHISM / GLYCOPROTEIN / PHAGOCYTOSIS / DISEASE MUTATION / COMPLEMENT PATHWAY / CELL SURFACE MOLECULE / PYRROLIDONE CARBOXYLIC ACID / HYDROXYLATION / INNATE IMMUNITY / IMMUNE RESPONSE / COLLAGEN / TOLERANCE / APOPOTOSIS / COMPLEMENT
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
PHOSPHOSERINE / 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: 2.05 Å
AuthorsPaidassi, H. / Tacnet-Delorme, P. / Garlatti, V. / Darnault, C. / Ghebrehiwet, B. / Gaboriaud, C. / Arlaud, G.J. / Frachet, P.
CitationJournal: J.Immunol. / Year: 2008
Title: C1Q Binds Phosphatidylserine and Likely Acts as a Multiligand-Bridging Molecule in Apoptotic Cell Recognition.
Authors: Paidassi, H. / Tacnet-Delorme, P. / Garlatti, V. / Darnault, C. / Ghebrehiwet, B. / Gaboriaud, C. / Arlaud, G.J. / Frachet, P.
History
DepositionFeb 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 5, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_nat / pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_atoms / struct_ref / struct_ref_seq
Item: _citation.journal_id_ASTM / _citation.journal_id_CSD ..._citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.page_last / _citation.pdbx_database_id_DOI / _entity.pdbx_description / _entity.src_method / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
B: Complement C1q subcomponent subunit B
C: Complement C1q subcomponent subunit C
D: Complement C1q subcomponent subunit A
E: Complement C1q subcomponent subunit B
F: Complement C1q subcomponent subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,37410
Polymers89,8886
Non-polymers4864
Water5,441302
1
A: Complement C1q subcomponent subunit A
B: Complement C1q subcomponent subunit B
C: Complement C1q subcomponent subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2055
Polymers44,9443
Non-polymers2612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-55.6 kcal/mol
Surface area19240 Å2
MethodPQS
2
D: Complement C1q subcomponent subunit A
E: Complement C1q subcomponent subunit B
F: Complement C1q subcomponent subunit C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1695
Polymers44,9443
Non-polymers2252
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-54.7 kcal/mol
Surface area18990 Å2
MethodPQS
Unit cell
Length a, b, c (Å)48.090, 48.070, 84.700
Angle α, β, γ (deg.)91.34, 93.34, 113.68
Int Tables number1
Space group name H-MP1

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Components

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Complement C1q subcomponent subunit ... , 3 types, 6 molecules ADBECF

#1: Protein Complement C1q subcomponent subunit A


Mass: 14985.883 Da / Num. of mol.: 2 / Fragment: C-TERMINAL GLOBULAR REGION, RESIDUES 112-245 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02745
#2: Protein Complement C1q subcomponent subunit B


Mass: 15398.522 Da / Num. of mol.: 2 / Fragment: C TERMINAL GLOBULAR DOMAIN, RESIDUES 116-251 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02746
#3: Protein Complement C1q subcomponent subunit C


Mass: 14559.454 Da / Num. of mol.: 2 / Fragment: C TERMINAL GLOBULAR DOMAIN, RESIDUES 115-245 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02747

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Sugars , 1 types, 1 molecules

#4: 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

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Non-polymers , 3 types, 305 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SEP / PHOSPHOSERINE / PHOSPHONOSERINE / Phosphoserine


Type: L-peptide linking / Mass: 185.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO6P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.74 Å3/Da / Density % sol: 54.78 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.05→19.95 Å / Num. obs: 38993 / % possible obs: 89.7 % / Observed criterion σ(I): 0 / Redundancy: 1.92 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PK6

1pk6


Resolution: 2.05→19.94 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.888 / SU B: 4.894 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1948 5 %RANDOM
Rwork0.181 ---
obs0.184 37012 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.06 Å20.21 Å2
2---0.95 Å2-0.1 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6239 0 27 302 6568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226403
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0281.9428703
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44523.973297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64915.015990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3641532
X-RAY DIFFRACTIONr_chiral_restr0.0690.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024954
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2310.32951
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.54296
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.5739
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.363
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.522
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.81224036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28636404
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.17632652
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.55342299
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.12 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.277 123
Rwork0.184 2349

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