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- PDB-9rbo: A cryo-EM structure of native C3 protein in a compact conformation. -

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Basic information

Entry
Database: PDB / ID: 9rbo
TitleA cryo-EM structure of native C3 protein in a compact conformation.
Components
  • (Complement C3 beta chain) x 2
  • Acylation stimulating protein
  • Complement C3b alpha' chain
KeywordsIMMUNE SYSTEM / Inhibition Complement Structural Nanoparticle
Function / homology
Function and homology information


C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / Alternative complement activation / complement-mediated synapse pruning / positive regulation of type IIa hypersensitivity / Activation of C3 and C5 ...C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / Alternative complement activation / complement-mediated synapse pruning / positive regulation of type IIa hypersensitivity / Activation of C3 and C5 / positive regulation of lipid storage / complement activation, GZMK pathway / positive regulation of phagocytosis, engulfment / positive regulation of G protein-coupled receptor signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement receptor mediated signaling pathway / complement activation, alternative pathway / complement activation / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / complement activation, classical pathway / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Regulation of Complement cascade / Peptide ligand-binding receptors / response to bacterium / Post-translational protein phosphorylation / fatty acid metabolic process / positive regulation of protein phosphorylation / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / azurophil granule lumen / secretory granule lumen / blood microparticle / G alpha (i) signalling events / immune response / endoplasmic reticulum lumen / G protein-coupled receptor signaling pathway / inflammatory response / receptor ligand activity / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain ...Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWhittaker, J.J. / Eikrem, D. / Seisenbaeva, G. / Nilsson-Ekdahl, K. / Nilsson, B. / Sandgren, M. / Kessler, V.G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2022-03971_VR Sweden
CitationJournal: To Be Published
Title: Titania Nanoparticles Regulate Innate Immunity
Authors: Whittaker, J.J. / Eikrem, D. / Seisenbaeva, G. / Nilsson-Ekdahl, K. / Nilsson, B. / Sandgren, M. / Kessler, V.G.
History
DepositionMay 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Complement C3 beta chain
B: Complement C3 beta chain
C: Acylation stimulating protein
D: Complement C3b alpha' chain


Theoretical massNumber of molelcules
Total (without water)165,3364
Polymers165,3364
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Complement C3 beta chain


Mass: 22051.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: N-terminal domain (Macroglobulin 1 domain) and Macroglobulin 2 domain a.a. 10-205.
Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#2: Protein Complement C3 beta chain


Mass: 34775.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Macroglobulin 4, 5, 6b domains and the LNK region a.a. 328 - 643.
Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#3: Protein/peptide Acylation stimulating protein / ASP / C3adesArg


Mass: 5892.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: C3a domain a.a. 662 - 712. / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#4: Protein Complement C3b alpha' chain


Mass: 102616.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Macroglobulin ring domain 6a, 7, 8 and CUB, TED, anchor, C345 (N-terminal domain) a.a. 740-1641.
Source: (natural) Homo sapiens (human) / References: UniProt: P01024
Has protein modificationY

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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

ComponentName: Tertiary structure of inactive complement C3. / Type: COMPLEX / Details: Purified from human blood. / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.185 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Details: Protein purified using VB++ at physiological pH. Before vitrification, protein buffer was exchanged to pure filtered water and low NaCl concentration (15 mM).
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K
Details: Vitrification performed at 95% relative humidity in a 4 degree environment. 3uL of protein in pure, filtered water was plunge frozen on a grid in liquid ethane.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: 30 deg tilt for entire data collection.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 1800 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 51 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 17600
Image scansWidth: 4000 / Height: 4000 / Movie frames/image: 60

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 200000 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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