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- EMDB-37768: CryoEM structure of the human SLC4A4 sodium-coupled acid-base tra... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-37768
TitleCryoEM structure of the human SLC4A4 sodium-coupled acid-base transporter NBCe1 from Biortus
Map data
Sample
  • Organelle or cellular component: Human SLC4A4 sodium-coupled acid-base transporter NBCe1
KeywordsHuman SLC4A4 sodium-coupled acid-base transporter NBCe1 / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHu J / Hu Y
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CryoEM structure of the human SLC4A4 sodium-coupled acid-base transporter NBCe1 from Biortus
Authors: Hu J / Hu Y
History
DepositionOct 13, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37768.png

Downloads & links

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Map

FileDownload / File: emd_37768.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 327.6 Å		0.82 Å/pix.
x 400 pix.
= 327.6 Å		0.82 Å/pix.
x 400 pix.
= 327.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.819 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.15138416 - 0.63316214
Average (Standard dev.)0.00032889057 (±0.024917837)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 327.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37768_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

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Half map: #2

Fileemd_37768_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37768_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 : Human SLC4A4 sodium-coupled acid-base transporter NBCe1

EntireName: Human SLC4A4 sodium-coupled acid-base transporter NBCe1
Components
  • Organelle or cellular component: Human SLC4A4 sodium-coupled acid-base transporter NBCe1

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Supramolecule #1: Human SLC4A4 sodium-coupled acid-base transporter NBCe1

SupramoleculeName: Human SLC4A4 sodium-coupled acid-base transporter NBCe1
type: organelle_or_cellular_component / ID: 1 / Parent: 0
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

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 169914
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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