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- EMDB-17328: Homogeneously refined Cryo-EM map centred on MG7 of C3* -

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Basic information

Entry
Database: EMDB / ID: EMD-17328
TitleHomogeneously refined Cryo-EM map centred on MG7 of C3*
Map dataFull map from homogeneous refinement centred on MG7
Sample
  • Complex: Complement factor C3* intermediate
    • Protein or peptide: Complement factor C3
KeywordsComplement cascade / complement factor C3 / thioester protein / IMMUNE SYSTEM
Function / homology
Function and homology information


oviduct epithelium development / 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 / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage ...oviduct epithelium development / 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 / complement-mediated synapse pruning / Alternative complement activation / positive regulation of G protein-coupled receptor signaling pathway / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / neuron remodeling / endopeptidase inhibitor activity / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / fatty acid metabolic process / complement activation, classical pathway / Regulation of Complement cascade / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / 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 / azurophil granule lumen / G alpha (i) signalling events / secretory granule lumen / blood microparticle / inflammatory response / positive regulation of protein phosphorylation / immune response / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : ...: / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / 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 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.4 Å
AuthorsJoergensen MH / Andersen GR
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: To Be Published
Title: Cryo-EM analysis of complement C3 reveals a reversible opening of the macroglobulin-ring
Authors: Joergensen MH / Andersen GR
History
DepositionMay 9, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17328.png

Downloads & links

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Map

FileDownload / File: emd_17328.map.gz / Format: CCP4 / Size: 14.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map from homogeneous refinement centred on MG7
Voxel sizeX=Y=Z: 1.92441 Å
Density
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum-0.24012472 - 0.8431951
Average (Standard dev.)-0.0046170256 (±0.028980989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions156156156
Spacing156156156
CellA=B=C: 300.208 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map (B) from homogeneous refinement centred on MG7

Fileemd_17328_half_map_1.map
AnnotationHalf-map (B) from homogeneous refinement centred on MG7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map (A) from homogeneous refinement centred on MG7

Fileemd_17328_half_map_2.map
AnnotationHalf-map (A) from homogeneous refinement centred on MG7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complement factor C3* intermediate

EntireName: Complement factor C3* intermediate
Components
  • Complex: Complement factor C3* intermediate
    • Protein or peptide: Complement factor C3

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Supramolecule #1: Complement factor C3* intermediate

SupramoleculeName: Complement factor C3* intermediate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Activated to C3* by nucleophilic reaction with methylamine
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Complement factor C3

MacromoleculeName: Complement factor C3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: SPMYSIITPN ILRLESEETM VLEAHDAQGD VPVTVTVH D FPGKKLVLSS EKTVLTPATN HMGNVTFTIP ANREFKSEKG RNKFVTVQAT FGTQVVEKV VLVSLQSGYL FIQTDKTIYT PGSTVLYRIF TVNHKLLPVG RTVMVNIENP EGIPVKQDSL SSQNQLGVL ...String:
SPMYSIITPN ILRLESEETM VLEAHDAQGD VPVTVTVH D FPGKKLVLSS EKTVLTPATN HMGNVTFTIP ANREFKSEKG RNKFVTVQAT FGTQVVEKV VLVSLQSGYL FIQTDKTIYT PGSTVLYRIF TVNHKLLPVG RTVMVNIENP EGIPVKQDSL SSQNQLGVL PLSWDIPELV NMGQWKIRAY YENSPQQVFS TEFEVKEYVL PSFEVIVEPT E KFYYIYNE KGLEVTITAR FLYGKKVEGT AFVIFGIQDG EQRISLPESL KRIPIEDGSG EV VLSRKVL LDGVQNPRAE DLVGKSLYVS ATVILHSGSD MVQAERSGIP IVTSPYQIHF TKT PKYFKP GMPFDLMVFV TNPDGSPAYR VPVAVQGEDT VQSLTQGDGV AKLSINTHPS QKPL SITVR TKKQELSEAE QATRTMQALP YSTVGNSNNY LHLSVLRTEL RPGETLNVNF LLRMD RAHE AKIRYYTYLI MNKGRLLKAG RQVREPGQDL VVLPLSITTD FIPSFRLVAY YTLIGA SGQ REVVADSVWV DVKDSCVGSL VVKSGQSEDR QPVPGQQMTL KIEGDHGARV VLVAVDK GV FVLNKKNKLT QSKIWDVVEK ADIGCTPGSG KDYAGVFSDA GLTFTSSSGQ QTAQRAEL Q CPQPAARRRR SVQLTEKRMD KVGKYPKELR KCCEDGMREN PMRFSCQRRT RFISLGEAC KKVFLDCCNY ITELRRQHAR ASHLGLARSN LDEDIIAEEN IVSRSEFPES WLWNVEDLKE PPKNGISTK LMNIFLKDSI TTWEILAVSM SDKKGICVAD PFEVTVMQDF FIDLRLPYSV V RNEQVEIR AVLYNYRQNQ ELKVRVELLH NPAFCSLATT KRRHQQTVTI PPKSSLSVPY VI VPLKTGL QEVEVKAAVY HHFISDGVRK SLKVVPEGIR MNKTVAVRTL DPERLGREGV QKE DIPPAD LSDQVPDTES ETRILLQGTP VAQMTEDAVD AERLKHLIVT PSGCGEQNMI GMTP TVIAV HYLDETEQWE KFGLEKRQGA LELIKKGYTQ QLAFRQPSSA FAAFVKRAPS TWLTA YVVK VFSLAVNLIA IDSQVLCGAV KWLILEKQKP DGVFQEDAPV IHQEMIGGLR NNNEKD MAL TAFVLISLQE AKDICEEQVN SLPGSITKAG DFLEANYMNL QRSYTVAIAG YALAQMG RL KGPLLNKFLT TAKDKNRWED PGKQLYNVEA TSYALLALLQ LKDFDFVPPV VRWLNEQR Y YGGGYGSTQA TFMVFQALAQ YQKDAPDHQE LNLDVSLQLP SRSSKITHRI HWESASLLR SEETKENEGF TVTAEGKGQG TLSVVTMYHA KAKDQLTCNK FDLKVTIKPA PETEKRPQDA KNTMILEIC TRYRGDQDAT MSILDISMMT GFAPDTDDLK QLANGVDRYI SKYELDKAFS D RNTLIIYL DKVSHSEDDC LAFKVHQYFN VELIQPGAVK VYAYYNLEES CTRFYHPEKE DG KLNKLCR DELCRCAEEN CFIQKSDDKV TLEERLDKAC EPGVDYVYKT RLVKVQLSND FDE YIMAIE QTIKSGSDEV QVGQQRTFIS PIKCREALKL EEKKHYLMWG LSSDFWGEKP NLSY IIGKD TWVEHWPEED ECQDEENQKQ CQDLGAFTES MVVFGCPN

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

Concentration0.2 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4SMES
150.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsVast majority of C3* with negligible amounts of native C3 and C3MA

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8263 / Average exposure time: 1.4 sec. / Average electron dose: 59.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.4 µm / Calibrated defocus min: 0.7000000000000001 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 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

Particle selectionNumber selected: 2156605
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56532
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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