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- EMDB-51538: Cryo-EM structure of human SLC35B1-E33A variant with ADP in inwar... -

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Basic information

Entry
Database: EMDB / ID: EMD-51538
TitleCryo-EM structure of human SLC35B1-E33A variant with ADP in inward facing conformation
Map data
Sample
  • Complex: Complex of human SLC35B1-E33A variant with Fv-MBP in inward facing conformation
    • Protein or peptide: SLC35B1-E33A inward facing conformation
    • Protein or peptide: Maltodextrin-binding protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsATP:ADP exchanger / AXER / ER membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


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 / metal ion binding
Similarity search - Function
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
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 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_51538.png

Downloads & links

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Map

FileDownload / File: emd_51538.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 259.2 Å		0.65 Å/pix.
x 400 pix.
= 259.2 Å		0.65 Å/pix.
x 400 pix.
= 259.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.062598675 - 0.15188634
Average (Standard dev.)0.00029532833 (±0.0036603191)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51538_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51538_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_51538_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-E33A variant with Fv-MBP in inward facin...

EntireName: Complex of human SLC35B1-E33A variant with Fv-MBP in inward facing conformation
Components
  • Complex: Complex of human SLC35B1-E33A variant with Fv-MBP in inward facing conformation
    • Protein or peptide: SLC35B1-E33A inward facing conformation
    • Protein or peptide: Maltodextrin-binding protein
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of human SLC35B1-E33A variant with Fv-MBP in inward facin...

SupramoleculeName: Complex of human SLC35B1-E33A variant with Fv-MBP in inward facing conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: SLC35B1-E33A inward facing conformation

MacromoleculeName: SLC35B1-E33A inward facing conformation / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.566258 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MASSSSLVPD RLRLPLCFLG VFVCYFYYGI LQAKITRGKY GEGAKQETFT FALTLVFIQC VINAVFAKIL IQFFDTARVD HTRSWLYAA CSISYLGAMV SSNSALQFVN YPTQVLGKSC KPIPVMLLGV TLLKKKYPLA KYLCVLLIVA GVALFMYKPK K VVGIEEHT ...String:
MASSSSLVPD RLRLPLCFLG VFVCYFYYGI LQAKITRGKY 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

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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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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: 61.1 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: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74221
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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