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- EMDB-52578: Cryo-EM structure of human SLC35B1 with ADP -

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Basic information

Entry
Database: EMDB / ID: EMD-52578
TitleCryo-EM structure of human SLC35B1 with ADP
Map data
Sample
  • Complex: Complex of human SLC35B1 with Fv-MBP and ADP
    • Protein or peptide: Solute carrier family 35 member B1
    • Protein or peptide: Maltodextrin-binding protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
KeywordsATP:ADP exchanger / AXER / ADP / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


UDP-galactose transmembrane transporter activity / UDP-glucose transmembrane transporter activity / UDP-galactose transmembrane transport / ATP:ADP antiporter activity / cell envelope / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing ...UDP-galactose transmembrane transporter activity / UDP-glucose transmembrane transporter activity / UDP-galactose transmembrane transport / ATP:ADP antiporter activity / cell envelope / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / periplasmic space / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / nucleoplasm / metal ion binding
Similarity search - Function
UAA transporter / UAA transporter family / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Maltodextrin-binding protein / Solute carrier family 35 member B1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsGulati A / Ahn D / Suades A / Drew D
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Nature / Year: 2025
Title: Stepwise ATP translocation into the endoplasmic reticulum by human SLC35B1.
Authors: Ashutosh Gulati / Do-Hwan Ahn / Albert Suades / Yurie Hult / Gernot Wolf / So Iwata / Giulio Superti-Furga / Norimichi Nomura / David Drew /
Abstract: ATP generated in the mitochondria is exported by an ADP/ATP carrier of the SLC25 family. The endoplasmic reticulum (ER) cannot synthesize ATP but must import cytoplasmic ATP to energize protein ...ATP generated in the mitochondria is exported by an ADP/ATP carrier of the SLC25 family. The endoplasmic reticulum (ER) cannot synthesize ATP but must import cytoplasmic ATP to energize protein folding, quality control and trafficking. It was recently proposed that a member of the nucleotide sugar transporter family, termed SLC35B1 (also known as AXER), is not a nucleotide sugar transporter but a long-sought-after ER importer of ATP. Here we report that human SLC35B1 does not bind nucleotide sugars but indeed executes strict ATP/ADP exchange with uptake kinetics consistent with the import of ATP into crude ER microsomes. A CRISPR-Cas9 cell-line knockout demonstrated that SLC35B1 clusters with the most essential SLC transporters for cell growth, consistent with its proposed physiological function. We have further determined seven cryogenic electron microscopy structures of human SLC35B1 in complex with an Fv fragment and either bound to an ATP analogue or ADP in all major conformations of the transport cycle. We observed that nucleotides were vertically repositioned up to approximately 6.5 Å during translocation while retaining key interactions with a flexible substrate-binding site. We conclude that SLC35B1 operates by a stepwise ATP translocation mechanism, which is a previously undescribed model for substrate translocation by an SLC transporter.
History
DepositionJan 17, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52578.png

Downloads & links

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Map

FileDownload / File: emd_52578.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 240 pix.
= 259.992 Å		1.08 Å/pix.
x 240 pix.
= 259.992 Å		1.08 Å/pix.
x 240 pix.
= 259.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.3054334 - 0.7304839
Average (Standard dev.)0.0009219375 (±0.016042167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 259.992 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52578_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52578_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52578_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of human SLC35B1 with Fv-MBP and ADP

EntireName: Complex of human SLC35B1 with Fv-MBP and ADP
Components
  • Complex: Complex of human SLC35B1 with Fv-MBP and ADP
    • Protein or peptide: Solute carrier family 35 member B1
    • Protein or peptide: Maltodextrin-binding protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

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Supramolecule #1: Complex of human SLC35B1 with Fv-MBP and ADP

SupramoleculeName: Complex of human SLC35B1 with Fv-MBP and ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 35 member B1

MacromoleculeName: Solute carrier family 35 member B1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.624293 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MASSSSLVPD RLRLPLCFLG VFVCYFYYGI LQEKITRGKY GEGAKQETFT FALTLVFIQC VINAVFAKIL IQFFDTARVD HTRSWLYAA CSISYLGAMV SSNSALQFVN YPTQVLGKSC KPIPVMLLGV TLLKKKYPLA KYLCVLLIVA GVALFMYKPK K VVGIEEHT ...String:
MASSSSLVPD RLRLPLCFLG VFVCYFYYGI LQEKITRGKY GEGAKQETFT FALTLVFIQC VINAVFAKIL IQFFDTARVD HTRSWLYAA CSISYLGAMV SSNSALQFVN YPTQVLGKSC KPIPVMLLGV TLLKKKYPLA KYLCVLLIVA GVALFMYKPK K VVGIEEHT VGYGELLLLL SLTLDGLTGV SQDHMRAHYQ TGSNHMMLNI NLWSTLLLGM GILFTGELWE FLSFAERYPA II YNILLFG LTSALGQSFI FMTVVYFGPL TCSIITTTRK FFTILASVIL FANPISPMQW VGTVLVFLGL GLDAKFGKGA KKT SHGENL YFQ

UniProtKB: Solute carrier family 35 member B1

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Macromolecule #2: Maltodextrin-binding protein

MacromoleculeName: Maltodextrin-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 67.695742 KDa
Recombinant expressionOrganism: Brevibacillus choshinensis (bacteria)
SequenceString: DIVMTQSPAS LTVSLGQSVT ISCRASENVE YYGTSLMQWY QQKPGQPPKF LIYGASNIES GVPARFSGSG SGTDFSLNIH PVEEDDIAM YFCQQSRKVP YTFGSGTKLE IKGSGKIEEG KLVIWINGDK GYNGLAEVGK KFEKDTGIKV TVEHPDKLEE K FPQVAATG ...String:
DIVMTQSPAS LTVSLGQSVT ISCRASENVE YYGTSLMQWY QQKPGQPPKF LIYGASNIES GVPARFSGSG SGTDFSLNIH PVEEDDIAM YFCQQSRKVP YTFGSGTKLE IKGSGKIEEG KLVIWINGDK GYNGLAEVGK KFEKDTGIKV TVEHPDKLEE K FPQVAATG DGPDIIFWAH DRFGGYAQSG LLAEITPDKA FQDKLYPFTW DAVRYNGKLI AYPIAVEALS LIYNKDLLPN PP KTWEEIP ALDKELKAKG KSALMFNLQE PYFTWPLIAA DGGYAFKYEN GKYDIKDVGV DNAGAKAGLT FLVDLIKNKH MNA DTDYSI AEAAFNKGET AMTINGPWAW SNIDTSKVNY GVTVLPTFKG QPSKPFVGVL SAGINAASPN KELAKEFLEN YLLT DEGLE AVNKDKPLGA VALKSYEEEL VKDPRIAATM ENAQKGEIMP NIPQMSAFWY AVRTAVINAA SGRQTVDEAL KDAQT NALG SGEVQLQESG PGLVKPSQSL SLTCSVTGYS ITSDYYWNWI RQFPGNKLEW MAYIRYDGTS DYNPSLKNRI SITRDT SKN QFFLKLNSVA TEDTATYYCA RAYYYDGINF DYWGQGTTLT VSSENLYFQ

UniProtKB: Maltodextrin-binding protein

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 4 / Number of copies: 1 / Formula: PEV
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

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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: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.94 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.4 µm
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 reconstructionResolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 323707
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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