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- EMDB-63562: Acetyl-CoA-bound SLC33A1 in a cytoplasm-facing conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-63562
TitleAcetyl-CoA-bound SLC33A1 in a cytoplasm-facing conformation
Map data
Sample
  • Complex: SLC33A1 in complex with acetyl-CoA
    • Protein or peptide: Acetyl-coenzyme A transporter 1
  • Ligand: ACETYL COENZYME *A
KeywordsSLC33A1 / AT1 / Acetyl-CoA / TRANSPORT PROTEIN
Function / homology
Function and homology information


acetyl-CoA transmembrane transporter activity / acetyl-CoA transmembrane transport / Transport of vitamins, nucleosides, and related molecules / Defective SLC33A1 causes spastic paraplegia 42 (SPG42) / transmembrane transport / Golgi membrane / endoplasmic reticulum membrane / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Acetyl-coenzyme A transporter 1-like / Acetyl-coenzyme A transporter 1 / AmpG-like permease/Acetyl-coenzyme A transporter 1 / MFS transporter superfamily
Similarity search - Domain/homology
Acetyl-coenzyme A transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhou D / Zhang Z
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)32471252 China
CitationJournal: Cell Discov / Year: 2025
Title: Mechanistic insights into the acetyl-CoA recognition by SLC33A1.
Authors: Dong Zhou / Nanhao Chen / Shitang Huang / Chen Song / Zhe Zhang /
History
DepositionFeb 25, 2025-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63562.png

Downloads & links

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Map

FileDownload / File: emd_63562.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.7083718 - 2.3888872
Average (Standard dev.)0.00080292614 (±0.045510218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63562_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_63562_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 : SLC33A1 in complex with acetyl-CoA

EntireName: SLC33A1 in complex with acetyl-CoA
Components
  • Complex: SLC33A1 in complex with acetyl-CoA
    • Protein or peptide: Acetyl-coenzyme A transporter 1
  • Ligand: ACETYL COENZYME *A

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Supramolecule #1: SLC33A1 in complex with acetyl-CoA

SupramoleculeName: SLC33A1 in complex with acetyl-CoA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60 KDa

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Macromolecule #1: Acetyl-coenzyme A transporter 1

MacromoleculeName: Acetyl-coenzyme A transporter 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 62.131855 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSPTISHKDS SRQRRPGNFS HSLDMKSGPL PPGGWDDSHL DSAGREGDRE ALLGDTGTGD FLKAPQSFRA ELSSILLLLF LYVLQGIPL GLAGSIPLIL QSKNVSYTDQ AFFSFVFWPF SLKLLWAPLV DAVYVKNFGR RKSWLVPTQY ILGLFMIYLS T QVDRLLGN ...String:
MSPTISHKDS SRQRRPGNFS HSLDMKSGPL PPGGWDDSHL DSAGREGDRE ALLGDTGTGD FLKAPQSFRA ELSSILLLLF LYVLQGIPL GLAGSIPLIL QSKNVSYTDQ AFFSFVFWPF SLKLLWAPLV DAVYVKNFGR RKSWLVPTQY ILGLFMIYLS T QVDRLLGN TDDRTPDVIA LTVAFFLFEF LAATQDIAVD GWALTMLSRE NVGYASTCNS VGQTAGYFLG NVLFLALESA DF CNKYLRF QPQPRGIVTL SDFLFFWGTV FLITTTLVAL LKKENEVSVV KEETQGITDT YKLLFAIIKM PAVLTFCLLI LTA KIGFSA ADAVTGLKLV EEGVPKEHLA LLAVPMVPLQ IILPLIISKY TAGPQPLNTF YKAMPYRLLL GLEYALLVWW TPKV EHQGG FPIYYYIVVL LSYALHQVTV YSMYVSIMAF NAKVSDPLIG GTYMTLLNTV SNLGGNWPST VALWLVDPLT VKECV GASN QNCRTPDAVE LCKKLGGSCV TALDGYYVES IICVFIGFGW WFFLGPKFKK LQDEGSSSWK CKRNNLEGGS LEVLFQ

UniProtKB: Acetyl-coenzyme A transporter 1

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Macromolecule #2: ACETYL COENZYME *A

MacromoleculeName: ACETYL COENZYME *A / type: ligand / ID: 2 / Number of copies: 1 / Formula: ACO
Molecular weightTheoretical: 809.571 Da
Chemical component information

ChemComp-ACO:
ACETYL COENZYME *A

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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

Concentration10 mg/mL
BufferpH: 7.25
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 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: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 238758
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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