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- PDB-6fcz: Model of gC1q-Fc complex based on 7A EM map -

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Basic information

Entry
Database: PDB / ID: 6fcz
TitleModel of gC1q-Fc complex based on 7A EM map
Components
  • Complement C1q subcomponent subunit A
  • Complement C1q subcomponent subunit B
  • Complement C1q subcomponent subunit C
  • Immunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / Complement / antibody / complex / C1
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 / immunoglobulin complex / 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 / adaptive immune response / immune response / innate immune response / synapse / extracellular space / extracellular region / plasma membrane
Similarity search - Function
C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...C1q domain / C1q domain / C1q domain profile. / Complement component C1q domain. / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Complement C1q subcomponent subunit A / Complement C1q subcomponent subunit B / Complement C1q subcomponent subunit C / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å
AuthorsUgurlar, D. / Howes, S.C. / de Kreuk, B.J.K. / de Jong, R.N. / Beurskens, F.J. / Koster, A.J. / Parren, P.W.H.I. / Sharp, T.H. / Gros, P. / Koning, R.I.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific ResearchCW 714.013.002 Netherlands
CitationJournal: Science / Year: 2018
Title: Structures of C1-IgG1 provide insights into how danger pattern recognition activates complement.
Authors: Deniz Ugurlar / Stuart C Howes / Bart-Jan de Kreuk / Roman I Koning / Rob N de Jong / Frank J Beurskens / Janine Schuurman / Abraham J Koster / Thomas H Sharp / Paul W H I Parren / Piet Gros /
Abstract: Danger patterns on microbes or damaged host cells bind and activate C1, inducing innate immune responses and clearance through the complement cascade. How these patterns trigger complement initiation ...Danger patterns on microbes or damaged host cells bind and activate C1, inducing innate immune responses and clearance through the complement cascade. How these patterns trigger complement initiation remains elusive. Here, we present cryo-electron microscopy analyses of C1 bound to monoclonal antibodies in which we observed heterogeneous structures of single and clustered C1-immunoglobulin G1 (IgG1) hexamer complexes. Distinct C1q binding sites are observed on the two Fc-CH2 domains of each IgG molecule. These are consistent with known interactions and also reveal additional interactions, which are supported by functional IgG1-mutant analysis. Upon antibody binding, the C1q arms condense, inducing rearrangements of the C1rs proteases and tilting C1q's cone-shaped stalk. The data suggest that C1r may activate C1s within single, strained C1 complexes or between neighboring C1 complexes on surfaces.
History
DepositionDec 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type

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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
H: Immunoglobulin gamma-1 heavy chain
K: Immunoglobulin gamma-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)93,0685
Polymers93,0685
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area9570 Å2
ΔGint-50 kcal/mol
Surface area36920 Å2
MethodPISA

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Components

#1: Protein Complement C1q subcomponent subunit A


Mass: 14914.804 Da / Num. of mol.: 1 / Fragment: UNP residues 112-244 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02745
#2: Protein Complement C1q subcomponent subunit B


Mass: 14996.058 Da / Num. of mol.: 1 / Fragment: UNP Residues 119-250 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02746
#3: Protein Complement C1q subcomponent subunit C


Mass: 14302.143 Da / Num. of mol.: 1 / Fragment: UNP residues 117-245 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02747
#4: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 24427.619 Da / Num. of mol.: 2 / Fragment: UNP residues 234-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1C1-IgG1 complexCOMPLEX#1-#40MULTIPLE SOURCES
2Complement C1qCOMPLEX#1-#31NATURAL
3Immunoglobulin gamma-1COMPLEX#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 10 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79120 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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