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- EMDB-50405: EM Map of KCC3b (SLC12A6b) in Complex with Nanobody Binder BN001T-N -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-50405
TitleEM Map of KCC3b (SLC12A6b) in Complex with Nanobody Binder BN001T-N
Map data
Sample
  • Complex: Heterooligomeric Complex of KCC3 (Isoform B) and Nanobody BN001T-N
    • Complex: Homodimeric complex of KCC3 (Isoform B), SLC12A6
    • Complex: Nanobody BN001T-N
KeywordsComplex / SLC12A6 / KCC3 / Nanobody / Transporter / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsChi G / Bohstedt T / Stefanic S / Castro-Hartmann P / Qian P / Burgess-Brown N / Sader K / Duerr KL / Sauer DB
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)777372European Union
CitationJournal: To Be Published
Title: EM Map of KCC3b (SLC12A6b) in Complex with Nanobody Binder BN001T-N
Authors: Chi G / Bohstedt T / Stefanic S / Castro-Hartmann P / Qian P / Burgess-Brown N / Sader K / Duerr KL / Sauer DB
History
DepositionMay 23, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50405.png

Downloads & links

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Map

FileDownload / File: emd_50405.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 500 pix.
= 325. Å		0.65 Å/pix.
x 500 pix.
= 325. Å		0.65 Å/pix.
x 500 pix.
= 325. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.44609496 - 0.9215937
Average (Standard dev.)-0.0031212682 (±0.033371676)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 325.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50405_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50405_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_50405_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 : Heterooligomeric Complex of KCC3 (Isoform B) and Nanobody BN001T-N

EntireName: Heterooligomeric Complex of KCC3 (Isoform B) and Nanobody BN001T-N
Components
  • Complex: Heterooligomeric Complex of KCC3 (Isoform B) and Nanobody BN001T-N
    • Complex: Homodimeric complex of KCC3 (Isoform B), SLC12A6
    • Complex: Nanobody BN001T-N

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Supramolecule #1: Heterooligomeric Complex of KCC3 (Isoform B) and Nanobody BN001T-N

SupramoleculeName: Heterooligomeric Complex of KCC3 (Isoform B) and Nanobody BN001T-N
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Homodimeric complex of KCC3 (Isoform B), SLC12A6

SupramoleculeName: Homodimeric complex of KCC3 (Isoform B), SLC12A6 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Nanobody BN001T-N

SupramoleculeName: Nanobody BN001T-N / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Lama glama (llama)

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 1587 / Average electron dose: 41.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: OTHER
Details: GS-FSC curve indicates 3.8 A with 0.143 cutoff, however actual resolution is only ~6 A upon manual inspection.
Number images used: 182315
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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