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- EMDB-51529: Cryo-EM structure of human SLC35B1 with AMP-PNP -

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Basic information

Entry
Database: EMDB / ID: EMD-51529
TitleCryo-EM structure of human SLC35B1 with AMP-PNP
Map data
Sample
  • Complex: Complex of human SLC35B1 with AMP-PNP
    • Protein or peptide: Solute carrier family 35 member B1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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 / Superti-Furga G / Nomura N / Drew D
History
DepositionSep 13, 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_51529.png

Downloads & links

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Map

FileDownload / File: emd_51529.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.)
1.11 Å/pix.
x 240 pix.
= 265.8 Å		1.11 Å/pix.
x 240 pix.
= 265.8 Å		1.11 Å/pix.
x 240 pix.
= 265.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1075 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-1.2029046 - 1.984333
Average (Standard dev.)0.00049023854 (±0.014333389)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 265.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51529_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51529_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_51529_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 AMP-PNP

EntireName: Complex of human SLC35B1 with AMP-PNP
Components
  • Complex: Complex of human SLC35B1 with AMP-PNP
    • Protein or peptide: Solute carrier family 35 member B1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: Complex of human SLC35B1 with AMP-PNP

SupramoleculeName: Complex of human SLC35B1 with AMP-PNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*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: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114510
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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