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- EMDB-51551: Cryo-EM structure of human SLC35B1 in inward facing conformation -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51551
TitleCryo-EM structure of human SLC35B1 in inward facing conformation
Map data
Sample
  • Complex: Complex of human SLC35B1 with Fv-MBP
    • Protein or peptide: Solute carrier family 35 member B1
    • Protein or peptide: Fv-MBP
KeywordsATP:ADP exchanger / AXER / AMP-PNP / 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 / Golgi membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / nucleoplasm
Similarity search - Function
UAA transporter / UAA transporter family
Similarity search - Domain/homology
Solute carrier family 35 member B1
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsGulati A / Ahn D / Suades A / Drew D
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: Structure and step-wise nucleotide translocation of the human ATP/ADP exchanger SLC35B1
Authors: Gulati A / Ahn D / Suades A / Chatzikyriakidou Y / Wolf G / Iwata S / Nomura N / Drew D
History
DepositionSep 16, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51551.png

Downloads & links

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Map

FileDownload / File: emd_51551.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 320 pix.
= 292.384 Å		0.91 Å/pix.
x 320 pix.
= 292.384 Å		0.91 Å/pix.
x 320 pix.
= 292.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9137 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.6010349 - 0.9884334
Average (Standard dev.)0.0003329811 (±0.010626061)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 292.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51551_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51551_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51551_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 : Complex of human SLC35B1 with Fv-MBP

EntireName: Complex of human SLC35B1 with Fv-MBP
Components
  • Complex: Complex of human SLC35B1 with Fv-MBP
    • Protein or peptide: Solute carrier family 35 member B1
    • Protein or peptide: Fv-MBP

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

SupramoleculeName: Complex of human SLC35B1 with Fv-MBP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: Fv-MBP

MacromoleculeName: Fv-MBP / 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

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.1 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: 0.6 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: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 180530
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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