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- EMDB-53900: A cryo-EM structure of native C3 protein in a compact conformation. -

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Basic information

Entry
Database: EMDB / ID: EMD-53900
TitleA cryo-EM structure of native C3 protein in a compact conformation.
Map data
Sample
  • Complex: Tertiary structure of inactive complement C3.
    • Protein or peptide: Complement C3 beta chain
    • Protein or peptide: Complement C3 beta chain
    • Protein or peptide: Acylation stimulating protein
    • Protein or peptide: Complement C3b alpha' chain
KeywordsInhibition Complement Structural Nanoparticle / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsWhittaker JJ / Eikrem D / 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: Titania Nanoparticles Regulate Innate Immunity
Authors: Whittaker JJ / Eikrem D / Seisenbaeva G / Nilsson-Ekdahl K / Nilsson B / Sandgren M / Kessler VG
History
DepositionMay 27, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53900.png

Downloads & links

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Map

FileDownload / File: emd_53900.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 400 pix.
= 259.2 Å		0.65 Å/pix.
x 400 pix.
= 259.2 Å		0.65 Å/pix.
x 400 pix.
= 259.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.34730774 - 0.9232462
Average (Standard dev.)0.0001838501 (±0.021007646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53900_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53900_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_53900_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 beta chain
    • Protein or peptide: Complement C3 beta chain
    • Protein or peptide: Acylation stimulating protein
    • Protein or peptide: Complement C3b alpha' chain

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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 beta chain

MacromoleculeName: Complement C3 beta chain / type: protein_or_peptide / ID: 1
Details: N-terminal domain (Macroglobulin 1 domain) and Macroglobulin 2 domain a.a. 10-205.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.051092 KDa
SequenceString: NILRLESEET MVLEAHDAQG DVPVTVTVHD FPGKKLVLSS EKTVLTPATN HMGNVTFTIP ANREFKSEKG RNKFVTVQAT FGTQVVEKV VLVSLQSGYL FIQTDKTIYT PGSTVLYRIF TVNHKLLPVG RTVMVNIENP EGIPVKQDSL SSQNQLGVLP L SWDIPELV ...String:
NILRLESEET MVLEAHDAQG DVPVTVTVHD FPGKKLVLSS EKTVLTPATN HMGNVTFTIP ANREFKSEKG RNKFVTVQAT FGTQVVEKV VLVSLQSGYL FIQTDKTIYT PGSTVLYRIF TVNHKLLPVG RTVMVNIENP EGIPVKQDSL SSQNQLGVLP L SWDIPELV NMGQWKIRAY YENSPQQVFS TEFEVKEY

UniProtKB: Complement C3

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Macromolecule #2: Complement C3 beta chain

MacromoleculeName: Complement C3 beta chain / type: protein_or_peptide / ID: 2
Details: Macroglobulin 4, 5, 6b domains and the LNK region a.a. 328 - 643.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.77557 KDa
SequenceString: TSPYQIHFTK TPKYFKPGMP FDLMVFVTNP DGSPAYRVPV AVQGEDTVQS LTQGDGVAKL SINTHPSQKP LSITVRTKKQ ELSEAEQAT RTMQALPYST VGNSNNYLHL SVLRTELRPG ETLNVNFLLR MDRAHEAKIR YYTYLIMNKG RLLKAGRQVR E PGQDLVVL ...String:
TSPYQIHFTK TPKYFKPGMP FDLMVFVTNP DGSPAYRVPV AVQGEDTVQS LTQGDGVAKL SINTHPSQKP LSITVRTKKQ ELSEAEQAT RTMQALPYST VGNSNNYLHL SVLRTELRPG ETLNVNFLLR MDRAHEAKIR YYTYLIMNKG RLLKAGRQVR E PGQDLVVL PLSITTDFIP SFRLVAYYTL IGASGQREVV ADSVWVDVKD SCVGSLVVKS GQSEDRQPVP GQQMTLKIEG DH GARVVLV AVDKGVFVLN KKNKLTQSKI WDVVEKADIG CTPGSGKDYA GVFSDAGLTF TSSSGQQTAQ RAELQCPQP

UniProtKB: Complement C3

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Macromolecule #3: Acylation stimulating protein

MacromoleculeName: Acylation stimulating protein / type: protein_or_peptide / ID: 3 / Details: C3a domain a.a. 662 - 712. / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.892944 KDa
SequenceString:
YPKELRKCCE DGMRENPMRF SCQRRTRFIS LGEACKKVFL DCCNYITEL

UniProtKB: Complement C3

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Macromolecule #4: Complement C3b alpha' chain

MacromoleculeName: Complement C3b alpha' chain / type: protein_or_peptide / ID: 4
Details: Macroglobulin ring domain 6a, 7, 8 and CUB, TED, anchor, C345 (N-terminal domain) a.a. 740-1641.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.616656 KDa
SequenceString: VSRSEFPESW LWNVEDLKEP PKNGISTKLM NIFLKDSITT WEILAVSMSD KKGICVADPF EVTVMQDFFI DLRLPYSVVR NEQVEIRAV LYNYRQNQEL KVRVELLHNP AFCSLATTKR RHQQTVTIPP KSSLSVPYVI VPLKTGLQEV EVKAAVYHHF I SDGVRKSL ...String:
VSRSEFPESW LWNVEDLKEP PKNGISTKLM NIFLKDSITT WEILAVSMSD KKGICVADPF EVTVMQDFFI DLRLPYSVVR NEQVEIRAV LYNYRQNQEL KVRVELLHNP AFCSLATTKR RHQQTVTIPP KSSLSVPYVI VPLKTGLQEV EVKAAVYHHF I SDGVRKSL KVVPEGIRMN KTVAVRTLDP ERLGREGVQK EDIPPADLSD QVPDTESETR ILLQGTPVAQ MTEDAVDAER LK HLIVTPS GCGEQNMIGM TPTVIAVHYL DETEQWEKFG LEKRQGALEL IKKGYTQQLA FRQPSSAFAA FVKRAPSTWL TAY VVKVFS LAVNLIAIDS QVLCGAVKWL ILEKQKPDGV FQEDAPVIHQ EMIGGLRNNN EKDMALTAFV LISLQEAKDI CEEQ VNSLP GSITKAGDFL EANYMNLQRS YTVAIAGYAL AQMGRLKGPL LNKFLTTAKD KNRWEDPGKQ LYNVEATSYA LLALL QLKD FDFVPPVVRW LNEQRYYGGG YGSTQATFMV FQALAQYQKD APDHQELNLD VSLQLPSRSS KITHRIHWES ASLLRS EET KENEGFTVTA EGKGQGTLSV VTMYHAKAKD QLTCNKFDLK VTIKPAPETE KRPQDAKNTM ILEICTRYRG DQDATMS IL DISMMTGFAP DTDDLKQLAN GVDRYISKYE LDKAFSDRNT LIIYLDKVSH SEDDCLAFKV HQYFNVELIQ PGAVKVYA Y YNLEESCTRF YHPEKEDGKL NKLCRDELCR CAEENCFIQK SDDKVTLEER LDKACEPGVD YVYKTRLVKV QLSNDFDEY IMAIEQTIKS GSDEVQVGQQ RTFISPIKCR EALKLEEKKH YLMWGLSSDF WGEKPNLSYI IGKDTWVEHW PEEDECQDEE NQKQCQDLG 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 correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 200000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 1 / Avg.num./class: 200000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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