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- PDB-6z6v: Globular head of C1q in complex with the nanobody C1qNb75 -

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Basic information

Entry
Database: PDB / ID: 6z6v
TitleGlobular head of C1q in complex with the nanobody C1qNb75
Components
  • (Complement C1q subcomponent subunit ...) x 3
  • Nanobody C1q75
KeywordsIMMUNE SYSTEM / complement / antibody / nanobody / 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 / 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)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsLaursen, N.S. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
CitationJournal: Front Immunol / Year: 2020
Title: Functional and Structural Characterization of a Potent C1q Inhibitor Targeting the Classical Pathway of the Complement System.
Authors: Laursen, N.S. / Pedersen, D.V. / Gytz, H. / Zarantonello, A. / Bernth Jensen, J.M. / Hansen, A.G. / Thiel, S. / Andersen, G.R.
History
DepositionMay 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 16, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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
G: Nanobody C1q75
H: Nanobody C1q75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,35310
Polymers121,9118
Non-polymers4422
Water5,981332
1
A: Complement C1q subcomponent subunit A
B: Complement C1q subcomponent subunit B
C: Complement C1q subcomponent subunit C
G: Nanobody C1q75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1775
Polymers60,9554
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-43 kcal/mol
Surface area20320 Å2
MethodPISA
2
D: Complement C1q subcomponent subunit A
E: Complement C1q subcomponent subunit B
F: Complement C1q subcomponent subunit C
H: Nanobody C1q75
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1775
Polymers60,9554
Non-polymers2211
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7580 Å2
ΔGint-41 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.816, 119.744, 131.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROSERSER(chain 'A' and (resid 91 through 222 or resid 1001))AA91 - 2224 - 135
121NAGNAGNAGNAG(chain 'A' and (resid 91 through 222 or resid 1001))AI1001
231PROPROSERSER(chain 'D' and resid 91 through 1001)DD91 - 2224 - 135
241NAGNAGNAGNAG(chain 'D' and resid 91 through 1001)DJ1001
152THRTHRMETMETchain 'B'BB92 - 2241 - 133
262THRTHRMETMETchain 'E'EE92 - 2241 - 133
173GLNGLNPHEPHEchain 'C'CC88 - 2155 - 132
283GLNGLNPHEPHE(chain 'F' and resid 88 through 215)FF88 - 2155 - 132
194GLNGLNGLYGLY(chain 'G' and (resid 4 through 17 or resid 19 through 125))GG4 - 163 - 15
1104LEULEUSERSER(chain 'G' and (resid 4 through 17 or resid 19 through 125))GG19 - 12518 - 124
2114GLNGLNGLYGLY(chain 'H' and (resid 4 through 17 or resid 19 through 125))HH4 - 163 - 15
2124LEULEUSERSER(chain 'H' and (resid 4 through 17 or resid 19 through 125))HH19 - 12518 - 124

NCS ensembles :
ID
1
2
3
4

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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: 15230.149 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1QA / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P02745
#2: Protein Complement C1q subcomponent subunit B


Mass: 16156.327 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1QB / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P02746
#3: Protein Complement C1q subcomponent subunit C


Mass: 15176.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1QC, C1QG / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P02747

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Antibody / Sugars / Non-polymers , 3 types, 336 molecules GH

#4: Antibody Nanobody C1q75


Mass: 14392.776 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#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.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BIS-Tris pH 5.5, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.19→65.9 Å / Num. obs: 48574 / % possible obs: 94.69 % / Redundancy: 12.7 % / Biso Wilson estimate: 38.53 Å2 / CC1/2: 0.999 / Rsym value: 0.117 / Net I/σ(I): 15.7
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 6.1 % / Num. unique obs: 2516 / CC1/2: 0.63 / % possible all: 50

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HZF

5hzf


Resolution: 2.19→65.89 Å / SU ML: 0.2795 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.1586
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 2000 4.12 %
Rwork0.1778 46561 -
obs0.1798 48561 94.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.78 Å2
Refinement stepCycle: LAST / Resolution: 2.19→65.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8141 0 0 332 8473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01048340
X-RAY DIFFRACTIONf_angle_d1.392611307
X-RAY DIFFRACTIONf_chiral_restr0.07641225
X-RAY DIFFRACTIONf_plane_restr0.00791474
X-RAY DIFFRACTIONf_dihedral_angle_d27.63493179
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.3613560.2791300X-RAY DIFFRACTION37.72
2.24-2.30.30831320.24863076X-RAY DIFFRACTION88.72
2.3-2.370.34231460.23653416X-RAY DIFFRACTION98.83
2.37-2.450.32981500.21953475X-RAY DIFFRACTION99.92
2.45-2.540.28661480.21133454X-RAY DIFFRACTION99.97
2.54-2.640.23211490.20843468X-RAY DIFFRACTION99.81
2.64-2.760.28451500.20363477X-RAY DIFFRACTION99.89
2.76-2.90.22571500.19663483X-RAY DIFFRACTION100
2.9-3.080.2761500.18983526X-RAY DIFFRACTION100
3.08-3.320.26221510.18663488X-RAY DIFFRACTION100
3.32-3.660.20271510.16953539X-RAY DIFFRACTION99.89
3.66-4.190.191520.15233532X-RAY DIFFRACTION99.92
4.19-5.270.17411540.13453578X-RAY DIFFRACTION100
5.27-65.890.20311610.1773749X-RAY DIFFRACTION99.8
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)
11.31974770855-0.08463729365940.0741133447831.41117178651-0.1406967156251.91549182587-0.01760052089340.0524796571765-0.123671354355-0.0690222676829-0.0173452702988-0.07206174450220.124560515419-0.02371242740720.03343275904560.226844294209-0.01564220722180.02142560715230.2460389926550.02572754419570.27677675682729.538840552235.20999935155.25845075684
21.10838779344-0.007086701846760.02432161489121.496879683220.2459636107941.63932589915-0.02688396861570.0539943482215-0.0411557487527-0.09396743258870.0351177530114-0.0170172656311-0.0304025697756-0.0870530926296-0.004293478604330.264947699282-0.0416331094560.004296783961810.3231607350130.00542812975350.239685476166-0.8341143634498.3325628735838.4775036489
34.011025587341.096173105160.1390950643633.235857443561.476160932475.029960687930.316110043575-0.6763905381270.09840809685350.304857528217-0.3920875323640.1767851379210.225885174-0.8037939142970.07617933650650.313645976503-0.03553862879040.008119077547670.5524922881880.01478220233980.28849991600433.755288244847.074171263239.4331183209
45.24602951848-0.158938446378-0.4687002983077.309747687131.067346867473.00310305330.0440133769064-0.1147270084460.3285118138680.304273952997-0.0790589216162-0.343200817269-0.536413576351-0.1320323979620.01773396835670.4228019434970.0606408139804-0.0457213284710.3092064618540.04823021982670.2912078193253.7931577430641.111319189653.3274664091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B or chain C
2X-RAY DIFFRACTION2chain D or chain E or chain F
3X-RAY DIFFRACTION3chain G
4X-RAY DIFFRACTION4chain H

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