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- EMDB-53939: Structure of complement C3 in an extended conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-53939
TitleStructure of complement C3 in an extended conformation
Map dataNone
Sample
  • Complex: Tertiary structure of inactive complement C3.
    • Protein or peptide: Complement C3
KeywordsInhibition Complement Structural Nanoparticle / IMMUNE SYSTEM
Function / homology
Function and homology information


C5L2 anaphylatoxin chemotactic receptor binding / 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 lipid storage / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment ...C5L2 anaphylatoxin chemotactic receptor binding / 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 lipid storage / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / complement activation, GZMK pathway / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of D-glucose transmembrane transport / complement activation / complement receptor mediated signaling pathway / complement activation, alternative pathway / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / fatty acid metabolic process / Regulation of Complement cascade / Peptide ligand-binding receptors / Post-translational protein phosphorylation / positive regulation of receptor-mediated endocytosis / positive regulation of protein phosphorylation / 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 / inflammatory response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / 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 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Complement C3/4/5, macroglobulin domain MG1 ...Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / : / Alpha-macro-globulin thiol-ester bond-forming region / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / 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 / 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 / Tissue inhibitor of metalloproteinases-like, OB-fold / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsWhittaker JJ / Eikrem D / Whittaker J / Seisenbaeva G / Nilsson-Ekdahl K / Nilsson B / Sandgren M / Kessler VG
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Swedish Research Council2022-03971_VR Sweden
CitationJournal: To Be Published
Title: Titanium Nanoparticles Strongly Bind to Complement C3 of the Alternative Pathway
Authors: Whittaker JJ / Eikrem D / Whittaker J / Seisenbaeva G / Nilsson-Ekdahl K / Nilsson B / Sandgren M / Kessler VG
History
DepositionJun 4, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53939.png

Downloads & links

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Map

FileDownload / File: emd_53939.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 200 pix.
= 259.2 Å		1.3 Å/pix.
x 200 pix.
= 259.2 Å		1.3 Å/pix.
x 200 pix.
= 259.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-1.2885914 - 1.5274757
Average (Standard dev.)-0.00030279742 (±0.029978642)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53939_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53939_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tertiary structure of inactive complement C3.

EntireName: Tertiary structure of inactive complement C3.
Components
  • Complex: Tertiary structure of inactive complement C3.
    • Protein or peptide: Complement C3

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Supramolecule #1: Tertiary structure of inactive complement C3.

SupramoleculeName: Tertiary structure of inactive complement C3. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Purified from human blood.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 185 KDa

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Macromolecule #1: Complement C3

MacromoleculeName: Complement C3 / type: protein_or_peptide / ID: 1
Details: N-terminal domain (Macroglobulin 1 domain) and Macroglobulin 2 domain a.a 1-195.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 187.370969 KDa
SequenceString: MGPTSGPSLL LLLLTHLPLA LGSPMYSIIT PNILRLESEE TMVLEAHDAQ GDVPVTVTVH DFPGKKLVLS SEKTVLTPAT NHMGNVTFT IPANREFKSE KGRNKFVTVQ ATFGTQVVEK VVLVSLQSGY LFIQTDKTIY TPGSTVLYRI FTVNHKLLPV G RTVMVNIE ...String:
MGPTSGPSLL LLLLTHLPLA LGSPMYSIIT PNILRLESEE TMVLEAHDAQ GDVPVTVTVH DFPGKKLVLS SEKTVLTPAT NHMGNVTFT IPANREFKSE KGRNKFVTVQ ATFGTQVVEK VVLVSLQSGY LFIQTDKTIY TPGSTVLYRI FTVNHKLLPV G RTVMVNIE NPEGIPVKQD SLSSQNQLGV LPLSWDIPEL VNMGQWKIRA YYENSPQQVF STEFEVKEYV LPSFEVIVEP TE KFYYIYN EKGLEVTITA RFLYGKKVEG TAFVIFGIQD GEQRISLPES LKRIPIEDGS GEVVLSRKVL LDGVQNPRAE DLV GKSLYV SATVILHSGS DMVQAERSGI PIVTSPYQIH FTKTPKYFKP GMPFDLMVFV TNPDGSPAYR VPVAVQGEDT VQSL TQGDG VAKLSINTHP SQKPLSITVR TKKQELSEAE QATRTMQALP YSTVGNSNNY LHLSVLRTEL RPGETLNVNF LLRMD RAHE AKIRYYTYLI MNKGRLLKAG RQVREPGQDL VVLPLSITTD FIPSFRLVAY YTLIGASGQR EVVADSVWVD VKDSCV GSL VVKSGQSEDR QPVPGQQMTL KIEGDHGARV VLVAVDKGVF VLNKKNKLTQ SKIWDVVEKA DIGCTPGSGK DYAGVFS DA GLTFTSSSGQ QTAQRAELQC PQPAARRRRS VQLTEKRMDK VGKYPKELRK CCEDGMRENP MRFSCQRRTR FISLGEAC K KVFLDCCNYI TELRRQHARA SHLGLARSNL DEDIIAEENI VSRSEFPESW LWNVEDLKEP PKNGISTKLM NIFLKDSIT TWEILAVSMS DKKGICVADP FEVTVMQDFF IDLRLPYSVV RNEQVEIRAV LYNYRQNQEL KVRVELLHNP AFCSLATTKR RHQQTVTIP PKSSLSVPYV IVPLKTGLQE VEVKAAVYHH FISDGVRKSL KVVPEGIRMN KTVAVRTLDP ERLGREGVQK E DIPPADLS DQVPDTESET RILLQGTPVA QMTEDAVDAE RLKHLIVTPS GCGEQNMIGM TPTVIAVHYL DETEQWEKFG LE KRQGALE LIKKGYTQQL AFRQPSSAFA AFVKRAPSTW LTAYVVKVFS LAVNLIAIDS QVLCGAVKWL ILEKQKPDGV FQE DAPVIH QEMIGGLRNN NEKDMALTAF VLISLQEAKD ICEEQVNSLP GSITKAGDFL EANYMNLQRS YTVAIAGYAL AQMG RLKGP LLNKFLTTAK DKNRWEDPGK QLYNVEATSY ALLALLQLKD FDFVPPVVRW LNEQRYYGGG YGSTQATFMV FQALA QYQK DAPDHQELNL DVSLQLPSRS SKITHRIHWE SASLLRSEET KENEGFTVTA EGKGQGTLSV VTMYHAKAKD QLTCNK FDL KVTIKPAPET EKRPQDAKNT MILEICTRYR GDQDATMSIL DISMMTGFAP DTDDLKQLAN GVDRYISKYE LDKAFSD RN TLIIYLDKVS HSEDDCLAFK VHQYFNVELI QPGAVKVYAY YNLEESCTRF YHPEKEDGKL NKLCRDELCR CAEENCFI Q KSDDKVTLEE RLDKACEPGV DYVYKTRLVK VQLSNDFDEY IMAIEQTIKS GSDEVQVGQQ RTFISPIKCR EALKLEEKK HYLMWGLSSD FWGEKPNLSY IIGKDTWVEH WPEEDECQDE ENQKQCQDLG AFTESMVVFG CPN

UniProtKB: Complement C3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 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).
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 500 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.04 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
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

MicroscopeTFS KRIOS
Details30 deg tilt for entire data collection.
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number real images: 17600 / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.8 µm / Calibrated defocus min: 1.0 µm / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 101194
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1 / Avg.num./class: 200000
FSC plot (resolution estimation)

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