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- PDB-2wnu: Complex between c1q globular heads and heparan sulfate -

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Basic information

Entry
Database: PDB / ID: 2wnu
TitleComplex between c1q globular heads and heparan sulfate
Components(COMPLEMENT C1Q SUBCOMPONENT SUBUNIT ...) x 3
KeywordsIMMUNE SYSTEM / COLLAGEN / 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 / extrinsic component of postsynaptic membrane / negative regulation of macrophage differentiation / synapse pruning / extrinsic component of presynaptic membrane / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer ...complement component C1 complex / complement component C1q complex / extrinsic component of postsynaptic membrane / negative regulation of macrophage differentiation / synapse pruning / extrinsic component of presynaptic membrane / negative regulation of granulocyte differentiation / vertebrate eye-specific patterning / complement-mediated synapse pruning / collagen trimer / complement activation / Classical antibody-mediated complement activation / Initial triggering of complement / neuron remodeling / complement activation, classical pathway / Regulation of Complement cascade / astrocyte activation / microglial cell activation / synapse organization / cell-cell signaling / amyloid-beta binding / : / blood microparticle / postsynapse / immune response / innate immune response / synapse / glutamatergic 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 ...: / 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: 2.3 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
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 / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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)90,7048
Polymers89,8886
Non-polymers8172
Water3,171176
1
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)45,5394
Polymers44,9443
Non-polymers5951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-39.1 kcal/mol
Surface area15970 Å2
MethodPISA
2
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)45,1654
Polymers44,9443
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-37.8 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.090, 48.160, 87.730
Angle α, β, γ (deg.)92.86, 92.20, 113.64
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGSERSERAA92 - 2223 - 133
21ARGARGSERSERDD92 - 2223 - 133
12THRTHRASPASPBB92 - 2232 - 133
22THRTHRASPASPEE92 - 2232 - 133
13LYSLYSASPASPCC89 - 2173 - 131
23LYSLYSASPASPFF89 - 2173 - 131

NCS ensembles :
ID
1
2
3

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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, 2 molecules

#4: Polysaccharide 2-O-sulfo-beta-L-altropyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 595.486 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NSO/3=O/3=O_6*OSO/3=O/3=O][a2111A-1b_1-5_2*OSO/3=O/3=O]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNSO36SO3]{[(4+1)][a-L-4-deoxy-IdopA2SO3]{}}LINUCSPDB-CARE
#5: 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


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 , 1 types, 176 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.71 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 29046 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 1.97 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 10.66
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 1.97 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 3.8 / % possible all: 88.1

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Processing

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

1pk6


Resolution: 2.3→19.65 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.86 / SU B: 8.281 / SU ML: 0.203 / Cross valid method: THROUGHOUT / ESU R: 0.965 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25558 1451 5 %RANDOM
Rwork0.19779 ---
obs0.20064 27550 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.552 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.12 Å20.13 Å2
2---0.78 Å20.49 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 50 176 6442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226500
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.161.9468835
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4255790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.79323.654312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.543151035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1041541
X-RAY DIFFRACTIONr_chiral_restr0.0770.2972
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025003
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22815
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24234
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2372
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.581.54034
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01626400
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.06832778
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.6764.52435
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A524tight positional0.030.05
12D524tight positional0.030.05
21B520tight positional0.030.05
22E520tight positional0.030.05
31C520tight positional0.030.05
32F520tight positional0.030.05
11A516loose positional0.225
12D516loose positional0.225
21B509loose positional0.395
22E509loose positional0.395
31C507loose positional0.125
32F507loose positional0.125
11A524tight thermal0.060.5
12D524tight thermal0.060.5
21B520tight thermal0.050.5
22E520tight thermal0.050.5
31C520tight thermal0.060.5
32F520tight thermal0.060.5
11A516loose thermal0.7310
12D516loose thermal0.7310
21B509loose thermal0.8210
22E509loose thermal0.8210
31C507loose thermal0.6410
32F507loose thermal0.6410
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 100 -
Rwork0.244 1884 -
obs--100 %

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