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- EMDB-17327: Combined map of C3* (composite structure) -

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Basic information

Entry
Database: EMDB / ID: EMD-17327
TitleCombined map of C3* (composite structure)
Map dataCombined map of C3* based on a focused map on the MG-ring, a focused map on TE-CUB and a consensus map 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


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 / complement-mediated synapse pruning / Alternative complement activation / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment ...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 / complement-mediated synapse pruning / Alternative complement activation / Activation of C3 and C5 / positive regulation of phagocytosis, engulfment / positive regulation of lipid storage / positive regulation of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / positive regulation of type IIa hypersensitivity / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement activation / complement activation, alternative pathway / endopeptidase inhibitor activity / neuron remodeling / amyloid-beta clearance / B cell activation / positive regulation of vascular endothelial growth factor production / complement activation, classical pathway / Purinergic signaling in leishmaniasis infection / Peptide ligand-binding receptors / Regulation of Complement cascade / fatty acid metabolic process / Post-translational protein phosphorylation / response to bacterium / positive regulation of receptor-mediated endocytosis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of angiogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / positive regulation of protein phosphorylation / G alpha (i) signalling events / secretory granule lumen / blood microparticle / immune response / G protein-coupled receptor signaling pathway / inflammatory response / receptor ligand activity / 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 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. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain ...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. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Anaphylatoxin, complement system domain / : / Anaphylatoxin domain signature. / Alpha-macro-globulin thiol-ester bond-forming region / 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 / Netrin domain / NTR domain profile. / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / 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: 8.1 Å
AuthorsJoergensen MH / Andersen GR
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Cryo-EM analysis of complement C3 reveals a reversible major opening of the macroglobulin ring.
Authors: Trine Amalie Fogh Gadeberg / Martin Høgholm Jørgensen / Heidi Gytz Olesen / Josefine Lorentzen / Seandean Lykke Harwood / Ana Viana Almeida / Marlene Uglebjerg Fruergaard / Rasmus Kjeldsen ...Authors: Trine Amalie Fogh Gadeberg / Martin Høgholm Jørgensen / Heidi Gytz Olesen / Josefine Lorentzen / Seandean Lykke Harwood / Ana Viana Almeida / Marlene Uglebjerg Fruergaard / Rasmus Kjeldsen Jensen / Philipp Kanis / Henrik Pedersen / Emil Tranchant / Steen Vang Petersen / Ida Buch Thøgersen / Birthe Brandt Kragelund / Joseph Anthony Lyons / Jan Johannes Enghild / Gregers Rom Andersen /
Abstract: The C3 protein is the central molecule within the complement system and undergoes proteolytic activation to C3b in the presence of pathogens. Pattern-independent activation of C3 also occurs via ...The C3 protein is the central molecule within the complement system and undergoes proteolytic activation to C3b in the presence of pathogens. Pattern-independent activation of C3 also occurs via hydrolysis, resulting in C3(HO), but the structural details of C3 hydrolysis remain elusive. Here we show that the conformation of the C3(HO) analog, C3MA, is indistinguishable from C3b. In contrast, the reaction intermediate C3* adopts a conformation dramatically different from both C3 and C3MA. In C3*, unlocking of the macroglobulin (MG) 3 domain creates a large opening in the MG ring through which the anaphylatoxin (ANA) domain translocates through a transient opening. C3MA formation is inhibited by an MG3-specific nanobody and prevented by linking the ANA domain to the C3 β-chain. Our study reveals an unexpected dynamic behavior of C3 and forms the basis for elucidation of the in vivo contribution of C3 hydrolysis and for controlling complement upon intravascular hemolysis and surface-contact-induced activation.
History
DepositionMay 9, 2023-
Header (metadata) releaseApr 24, 2024-
Map releaseApr 24, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17327.png

Downloads & links

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Map

FileDownload / File: emd_17327.map.gz / Format: CCP4 / Size: 6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined map of C3* based on a focused map on the MG-ring, a focused map on TE-CUB and a consensus map centred on MG7.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.59 Å/pix.
x 116 pix.
= 300.44 Å		2.59 Å/pix.
x 116 pix.
= 300.44 Å		2.59 Å/pix.
x 116 pix.
= 300.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.59 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.96
Minimum - Maximum-22.639531999999999 - 51.437309999999997
Average (Standard dev.)0.0044996557 (±0.9845199)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions116116116
Spacing116116116
CellA=B=C: 300.44 Å
α=β=γ: 90.0 °

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Supplemental data

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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: 8.1 Å / Resolution method: OTHER / Number images used: 56532
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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