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- PDB-2wnv: Complex between C1q globular heads and deoxyribose -

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Basic information

Entry
Database: PDB / ID: 2wnv
TitleComplex between C1q globular heads and deoxyribose
Components(COMPLEMENT C1Q SUBCOMPONENT SUBUNIT ...) x 3
KeywordsIMMUNE SYSTEM / C1Q / SECRETED / COLLAGEN / COMPLEMENT / RECOGNITION / DISULFIDE BOND / INNATE IMMUNITY / IMMUNE RESPONSE / PYRROLIDONE CARBOXYLIC ACID / DISEASE MUTATION / COMPLEMENT PATHWAY / GLYCOPROTEIN / HYDROXYLATION
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
2-deoxy-beta-D-erythro-pentofuranose / 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: 1.25 Å
AuthorsGarlatti, V. / Chouquet, A. / Lunardi, T. / Thielens, N.M. / Arlaud, G.J. / Gaboriaud, C.
CitationJournal: J.Immunol. / Year: 2010
Title: Cutting Edge: C1Q Binds Deoxyribose and Heparan Sulfate Through Neighboring Sites of its Recognition Domain.
Authors: Garlatti, V. / Chouquet, A. / Lunardi, T. / Vives, R. / Paidassi, H. / Lortat-Jacob, H. / Thielens, N.M. / Arlaud, G.J. / Gaboriaud, C.
History
DepositionJul 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 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 1.4Dec 13, 2023Group: Data collection / Database references ...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
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)90,54411
Polymers89,8886
Non-polymers6575
Water18,9881054
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)45,3396
Polymers44,9443
Non-polymers3953
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-52.8 kcal/mol
Surface area15490 Å2
MethodPISA
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)45,2055
Polymers44,9443
Non-polymers2612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-50.9 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.350, 48.330, 88.060
Angle α, β, γ (deg.)92.39, 92.60, 113.57
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 / C1Q CHAIN 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 / C1Q CHAIN 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 / C1Q CHAIN 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 , 2 types, 3 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.: 2
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
#6: Sugar ChemComp-2DR / 2-deoxy-beta-D-erythro-pentofuranose / 2-deoxy-beta-D-ribofuranose / 2-deoxy-beta-D-erythro-pentose / 2-deoxy-D-erythro-pentose / 2-deoxy-erythro-pentose


Type: D-saccharide, beta linking / Mass: 134.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O4

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Non-polymers , 2 types, 1056 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1054 / 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: 2.14 Å3/Da / Density % sol: 42.28 % / 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 QUANTUM 4 / Detector: CCD / Date: May 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 167366 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.15
Reflection shellResolution: 1.25→1.4 Å / Redundancy: 1.05 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5.4 / % possible all: 72.1

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PK6

1pk6


Resolution: 1.25→19.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.545 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20176 8368 5 %RANDOM
Rwork0.17496 ---
obs0.17629 158977 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.543 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0.17 Å20.21 Å2
2---0.62 Å20.15 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.25→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6120 0 41 1054 7215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226693
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.9449159
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3395859
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56623.834313
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.193151044
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2781538
X-RAY DIFFRACTIONr_chiral_restr0.070.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025260
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.23469
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24562
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21050
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.263
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6441.54211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06826718
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.43332790
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9184.52431
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.76137001
X-RAY DIFFRACTIONr_sphericity_free1.95831056
X-RAY DIFFRACTIONr_sphericity_bonded2.31436492
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 510 -
Rwork0.199 9694 -
obs--100 %

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