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- EMDB-19000: Cryo-EM structure of coagulation factor beta-XIIa in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-19000
TitleCryo-EM structure of coagulation factor beta-XIIa in complex with the garadacimab Fab fragment (asymmetric dimer)
Map dataLocal resolution filtered map
Sample
  • Complex: Ternary complex of coagulation factor beta-XIIa with garadacimab Fab fragment and anti-LC-lambda VHH
KeywordsComplex / coagulation / trypsin-like serine protease / hereditary angioedema (HAE) / BLOOD CLOTTING
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDrulyte I
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for inhibition of beta-FXIIa by garadacimab
Authors: Drulyte I / Ghai R / Ow SY / Kapp EA / Quek AJ / Panousis C / Wilson MJ / Nash AD / Pelzing M
History
DepositionNov 29, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19000.png

Downloads & links

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Map

FileDownload / File: emd_19000.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal resolution filtered map
Voxel sizeX=Y=Z: 1.095 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.9212264 - 1.1401873
Average (Standard dev.)0.0009757301 (±0.018317135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 306.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19000_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_19000_msk_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_19000_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_19000_additional_2.map
AnnotationSharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_19000_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_19000_half_map_2.map
AnnotationHalf map 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 : Ternary complex of coagulation factor beta-XIIa with garadacimab ...

EntireName: Ternary complex of coagulation factor beta-XIIa with garadacimab Fab fragment and anti-LC-lambda VHH
Components
  • Complex: Ternary complex of coagulation factor beta-XIIa with garadacimab Fab fragment and anti-LC-lambda VHH

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Supramolecule #1: Ternary complex of coagulation factor beta-XIIa with garadacimab ...

SupramoleculeName: Ternary complex of coagulation factor beta-XIIa with garadacimab Fab fragment and anti-LC-lambda VHH
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 174 KDa

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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

Concentration2 mg/mL
BufferpH: 5.5 / Details: 10 mM Na Acetate, 100 mM NaCl pH 5.5
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsImmediately before blotting and plunge freezing, fluorinated octyl maltoside (FOM) was added to the sample to the final concentration of 0.005%-0.01% (w/v)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Details: Electron source E-CFEG (cold-FEG), energy filter Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 4000 / Average electron dose: 50.0 e/Å2 / Details: 2000 with 0.005% FOM and 2000 with 0.01% FOM
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: 1.25 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
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: 271636
Details: Particles were picked from each of the datasets independently using a blob picker using 50-170 A diameter. 124767 particles were picked from the 0.005% FOM dataset and 146869 particles from ...Details: Particles were picked from each of the datasets independently using a blob picker using 50-170 A diameter. 124767 particles were picked from the 0.005% FOM dataset and 146869 particles from the 0.01% FOM dataset.
Startup modelType of model: INSILICO MODEL / In silico model: Ab Initio
Details: Ab Initio reconstruction was performed in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Details: Non-uniform refinement in cryoSPARC was used / Number images used: 17108
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Non-uniform refinement in cryoSPARC was used
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: Non-uniform refinement in cryoSPARC was used
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC
Details: CryoSPARC 3D Variability Analysis was used to determine the final particle stack for this reconstruction
FSC plot (resolution estimation)

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