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- EMDB-68586: Cryo-EM consensus map of Bovine lactoferrin in TBS buffer -

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Basic information

Entry
Database: EMDB / ID: EMD-68586
TitleCryo-EM consensus map of Bovine lactoferrin in TBS buffer
Map data
Sample
  • Complex: Lactoferrin
KeywordsIron binding / Glycoprotein / Bilobed structure / Antimicrobial / Transferrin family / ANTIBIOTIC
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.97 Å
AuthorsWada M / Yamazaki K / Wada Y / Ohga K / Ishii Y / Nakagawa A / Yoshikawa H / Okuno S / Nojima T / Ochi H ...Wada M / Yamazaki K / Wada Y / Ohga K / Ishii Y / Nakagawa A / Yoshikawa H / Okuno S / Nojima T / Ochi H / Hirose M / Kato T / Katoh T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Generation of Conformational Energy Landscape from Lactoferrin cryo-EM images with Mitigated Preferred Orientations by cryoTWIN
Authors: Wada M / Yamazaki K / Wada Y / Ohga K / Ishii Y / Nakagawa A / Yoshikawa H / Okuno S / Nojima T / Ochi H / Hirose M / Kato T / Katoh T
History
DepositionJan 19, 2026-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_68586.png

Downloads & links

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Map

FileDownload / File: emd_68586.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 224 pix.
= 151.2 Å		0.68 Å/pix.
x 224 pix.
= 151.2 Å		0.68 Å/pix.
x 224 pix.
= 151.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0404
Minimum - Maximum-0.06048053 - 0.17150812
Average (Standard dev.)0.00066510326 (±0.007194234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 151.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68586_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68586_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 : Lactoferrin

EntireName: Lactoferrin
Components
  • Complex: Lactoferrin

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Supramolecule #1: Lactoferrin

SupramoleculeName: Lactoferrin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (domestic cattle)

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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

Concentration0.95 mg/mL
BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 5762 pixel / Number grids imaged: 1 / Number real images: 3127 / Average electron dose: 1.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.318 µm / Calibrated defocus min: 0.2295 µm / Calibrated magnification: 74074 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0608 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
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: 2697777
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: SGD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 556748
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
Final 3D classificationNumber classes: 61 / Avg.num./class: 9127 / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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