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- EMDB-38623: transporter -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38623
Titletransporter
Map datatransporter
Sample
  • Complex: Complex with B
    • Protein or peptide: Solute carrier family 52, riboflavin transporter, member 3
  • Ligand: RIBOFLAVIN
Keywordstransporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


flavin adenine dinucleotide biosynthetic process / Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin transport / riboflavin transmembrane transporter activity / sensory perception of sound / cellular response to heat / nuclear membrane / apical plasma membrane / nucleus ...flavin adenine dinucleotide biosynthetic process / Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin transport / riboflavin transmembrane transporter activity / sensory perception of sound / cellular response to heat / nuclear membrane / apical plasma membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Solute carrier family 52, riboflavin transporter / Solute carrier family 52, riboflavin transporter
Similarity search - Domain/homology
Solute carrier family 52, riboflavin transporter, member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsJiang DH / Wang K
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971134 China
CitationJournal: To Be Published
Title: Structure of transporter
Authors: Jiang DH / Wang K
History
DepositionJan 9, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38623.png

Downloads & links

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Map

FileDownload / File: emd_38623.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtransporter
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.688
Minimum - Maximum-2.487219 - 4.3379264
Average (Standard dev.)-0.0010494151 (±0.06337792)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: transporter

Fileemd_38623_half_map_1.map
Annotationtransporter
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: transporter

Fileemd_38623_half_map_2.map
Annotationtransporter
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 with B

EntireName: Complex with B
Components
  • Complex: Complex with B
    • Protein or peptide: Solute carrier family 52, riboflavin transporter, member 3
  • Ligand: RIBOFLAVIN

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Supramolecule #1: Complex with B

SupramoleculeName: Complex with B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 52, riboflavin transporter, member 3

MacromoleculeName: Solute carrier family 52, riboflavin transporter, member 3
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.83175 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFLMHLLVC VFGMGSWVTI NGLWVELPLL VMELPEGWYL PSYLTVVIQL ANIGPLLVTL LHHFRPSCLS EVPIIFTLLG VGTVTCIIF AFLWNMTSWV LDGHHSIAFL VLTFFLALVD CTSSVTFLPF MSRLPTYYLT TFFVGEGLSG LLPALVALAQ G SGLTTCVN ...String:
MAFLMHLLVC VFGMGSWVTI NGLWVELPLL VMELPEGWYL PSYLTVVIQL ANIGPLLVTL LHHFRPSCLS EVPIIFTLLG VGTVTCIIF AFLWNMTSWV LDGHHSIAFL VLTFFLALVD CTSSVTFLPF MSRLPTYYLT TFFVGEGLSG LLPALVALAQ G SGLTTCVN VTEISDSVPS PVPTRETDIA QGVPRALVSA LPGMEAPLSH LESRYLPAHF SPLVFFLLLS IMMACCLVAF FV LQRQPRC WEASVEDLLN DQVTLHSIRP REENDLGPAG TVDSSQGQGY LEEKAAPCCP AHLAFIYTLV AFVNALTNGM LPS VQTYSC LSYGPVAYHL AATLSIVANP LASLVSMFLP NRSLLFLGVL SVLGTCFGGY NMAMAVMSPC PLLQGHWGGE VLIV ASWVL FSGCLSYVKV MLGVVLRDLS RSALLWCGAA VQLGSLLGAL LMFPLVNVLR LFSSADFCNL HCPA

UniProtKB: Solute carrier family 52, riboflavin transporter, member 3

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Macromolecule #2: RIBOFLAVIN

MacromoleculeName: RIBOFLAVIN / type: ligand / ID: 2 / Number of copies: 1 / Formula: RBF
Molecular weightTheoretical: 376.364 Da
Chemical component information

ChemComp-RBF:
RIBOFLAVIN

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99741
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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