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- EMDB-56650: Sulfate transporter SLC26A11 in nanodiscs with nanobody Nb11, loc... -

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Basic information

Entry
Database: EMDB / ID: EMD-56650
TitleSulfate transporter SLC26A11 in nanodiscs with nanobody Nb11, local refinement
Map datasharpend, filtered
Sample
  • Complex: SLC26A11 with nanobody Nb11 reconstituted into MSP1-E3D1 nanodiscs together with soyPC
    • Protein or peptide: human solute carrier family 26 member 11 (SLC26A11)
    • Protein or peptide: nanobody Nb11
Keywordssulfate transporter / chloride channel / lysosome / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / Vicugna pacos (alpaca)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHove T / Rasmussen T / Kuhn B / Geertsma ER / Bottcher B
Funding support Germany, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)359471283 Germany
German Research Foundation (DFG)456578072 Germany
German Research Foundation (DFG)525040890 Germany
German Research Foundation (DFG)FOR5046 GE 2841/3-1 Germany
German Research Foundation (DFG)FOR5046 GE 2841/2-1 Germany
CitationJournal: to be published
Title: Mechanism for (un)coupled transport in the human lysosomal sulfate transporter SLC26A11
Authors: Kuhn B / Geertsma ER / Kovermann P / Bungert-Plumke S / Fahlke C / Haddad BG / Machtens JP / Rasmussen T / Bottcher B
History
DepositionFeb 9, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56650.png

Downloads & links

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Map

FileDownload / File: emd_56650.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpend, filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 425.4 Å		1.06 Å/pix.
x 400 pix.
= 425.4 Å		1.06 Å/pix.
x 400 pix.
= 425.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.12923887 - 0.23094764
Average (Standard dev.)-0.0000516106 (±0.0044399155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 425.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_56650_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_56650_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SLC26A11 with nanobody Nb11 reconstituted into MSP1-E3D1 nanodisc...

EntireName: SLC26A11 with nanobody Nb11 reconstituted into MSP1-E3D1 nanodiscs together with soyPC
Components
  • Complex: SLC26A11 with nanobody Nb11 reconstituted into MSP1-E3D1 nanodiscs together with soyPC
    • Protein or peptide: human solute carrier family 26 member 11 (SLC26A11)
    • Protein or peptide: nanobody Nb11

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Supramolecule #1: SLC26A11 with nanobody Nb11 reconstituted into MSP1-E3D1 nanodisc...

SupramoleculeName: SLC26A11 with nanobody Nb11 reconstituted into MSP1-E3D1 nanodiscs together with soyPC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Macromolecule #1: human solute carrier family 26 member 11 (SLC26A11)

MacromoleculeName: human solute carrier family 26 member 11 (SLC26A11) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPSSVTALGQ ARSSGPGMAP SACCCSPAAL QRRLPILAWL PSYSLQWLKM DFVAGLSVGL TAIPQALAYA EVAGLPPQYG LYSAFMGCFV YFFLGTSRDV TLGPTAIMSL LVSFYTFHEP AYAVLLAFLS GCIQLAMGVL RLGFLLDFIS YPVIKGFTSA AAVTIGFGQI ...String:
MPSSVTALGQ ARSSGPGMAP SACCCSPAAL QRRLPILAWL PSYSLQWLKM DFVAGLSVGL TAIPQALAYA EVAGLPPQYG LYSAFMGCFV YFFLGTSRDV TLGPTAIMSL LVSFYTFHEP AYAVLLAFLS GCIQLAMGVL RLGFLLDFIS YPVIKGFTSA AAVTIGFGQI KNLLGLQNIP RPFFLQVYHT FLRIAETRVG DAVLGLVCML LLLVLKLMRD HVPPVHPEMP PGVRLSRGLV WAATTARNAL VVSFAALVAY SFEVTGYQPF ILTGETAEGL PPVRIPPFSV TTANGTISFT EMVQDMGAGL AVVPLMGLLE SIAVAKAFAS QNNYRIDANQ ELLAIGLTNM LGSLVSSYPV TGSFGRTAVN AQSGVCTPAG GLVTGVLVLL SLDYLTSLFY YIPKSALAAV IIMAVAPLFD TKIFRTLWRV KRLDLLPLCV TFLLCFWEVQ YGILAGALVS LLMLLHSAAR PETKVSEGPV LVLQPASGLS FPAMEALREE ILSRALEVSP PRCLVLECTH VCSIDYTVVL GLGELLQDFQ KQGVALAFVG LQVPVLRVLL SADLKGFQYF STLEEAEKHL RQE

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Macromolecule #2: nanobody Nb11

MacromoleculeName: nanobody Nb11 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSSSQLQLVE SGGGLVQPGG SLRLSCLASG RMFSDIYMGW YRQAPGKQRE LVARITGGGS INYADSVKGR FTISREYGKN TVYLQMNSLK PEDTAVYYCN ARYYGSDYWG KGTRVTVSAG RAGEQKLISE EDLNSAVDHH HHHH

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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 mg/mL
BufferpH: 7.25 / Component - Concentration: 20.0 mM / Component - Formula: C8H18N2O4S / Component - Name: HEPES
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.4 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: +20 blot force, 5 sec blot time.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 2552 / Average exposure time: 75.0 sec. / Average electron dose: 79.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
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: 1325543
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0)
Details: asymmetric local refinement after symmetry expansion
Number images used: 48803
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
FSC plot (resolution estimation)

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