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- EMDB-51524: Maps from particle subsets of methylamine treated human complemen... -

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Basic information

Entry
Database: EMDB / ID: EMD-51524
TitleMaps from particle subsets of methylamine treated human complement C3 showing three distinct ANA positions
Map dataC3MA map showing ANA position #2
Sample
  • Complex: methylamine treated complement C3 in complex with a nanobody enabling dimer formation
    • Complex: nanobody hC3Nb1 with mutation
    • Complex: complement C3
KeywordsComplement / nanobody / IMMUNE SYSTEM
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsJoergensen MH / Andersen GR
Funding support Denmark, 3 items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
Novo Nordisk FoundationNNF18OC0052105 Denmark
Danish Council for Independent Research4181-00137B 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
DepositionSep 13, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51524.png

Downloads & links

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Map

FileDownload / File: emd_51524.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC3MA map showing ANA position #2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 480 pix.
= 310.56 Å		0.65 Å/pix.
x 480 pix.
= 310.56 Å		0.65 Å/pix.
x 480 pix.
= 310.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.08336025 - 0.20146246
Average (Standard dev.)0.00024344432 (±0.00858295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 310.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: C3MA map showing ANA position #1

Fileemd_51524_additional_1.map
AnnotationC3MA map showing ANA position #1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C3MA map showing ANA position #1 half B

Fileemd_51524_additional_2.map
AnnotationC3MA map showing ANA position #1 half B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C3MA map showing ANA position #1 half A

Fileemd_51524_additional_3.map
AnnotationC3MA map showing ANA position #1 half A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C3MA map showing ANA position #3 half A

Fileemd_51524_additional_4.map
AnnotationC3MA map showing ANA position #3 half A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C3MA map showing ANA position #3

Fileemd_51524_additional_5.map
AnnotationC3MA map showing ANA position #3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C3MA map showing ANA position #3 half B

Fileemd_51524_additional_6.map
AnnotationC3MA map showing ANA position #3 half B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: C3MA map showing ANA position #2 half B

Fileemd_51524_half_map_1.map
AnnotationC3MA map showing ANA position #2 half B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: C3MA map showing ANA position #2 half A

Fileemd_51524_half_map_2.map
AnnotationC3MA map showing ANA position #2 half A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : methylamine treated complement C3 in complex with a nanobody enab...

EntireName: methylamine treated complement C3 in complex with a nanobody enabling dimer formation
Components
  • Complex: methylamine treated complement C3 in complex with a nanobody enabling dimer formation
    • Complex: nanobody hC3Nb1 with mutation
    • Complex: complement C3

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Supramolecule #1: methylamine treated complement C3 in complex with a nanobody enab...

SupramoleculeName: methylamine treated complement C3 in complex with a nanobody enabling dimer formation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 185 KDa

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Supramolecule #2: nanobody hC3Nb1 with mutation

SupramoleculeName: nanobody hC3Nb1 with mutation / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Lama glama (llama)

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Supramolecule #3: complement C3

SupramoleculeName: complement C3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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

Concentration1.0 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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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 BIOQUANTUM (6k x 4k) / Average electron dose: 59.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.438 µm / Nominal defocus min: 0.17 µm / Nominal magnification: 130000
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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 16159
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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