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- EMDB-38622: transporter -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38622
Titletransporter
Map data
Sample
  • Complex: complex with A
    • Protein or peptide: Solute carrier family 52, riboflavin transporter, member 2
  • Ligand: RIBOFLAVIN
Keywordstransporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


4-hydroxybutyrate receptor activity / Vitamin B2 (riboflavin) metabolism / riboflavin metabolic process / riboflavin transport / riboflavin transmembrane transporter activity / virus receptor activity / plasma membrane
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 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) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38622.png

Downloads & links

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Map

FileDownload / File: emd_38622.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.)
0.85 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: 1.58
Minimum - Maximum-6.162407 - 9.388358
Average (Standard dev.)-0.0016482223 (±0.13864674)
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: #1

Fileemd_38622_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_38622_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 with A

EntireName: complex with A
Components
  • Complex: complex with A
    • Protein or peptide: Solute carrier family 52, riboflavin transporter, member 2
  • Ligand: RIBOFLAVIN

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Supramolecule #1: complex with A

SupramoleculeName: complex with A / 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 2

MacromoleculeName: Solute carrier family 52, riboflavin transporter, member 2
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.803797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAAPTPARPV LTHLLVALFG MGSWAAVNGI WVELPVVVKE LPEGWSLPSY VSVLVALGNL GLLVVTLWRR LAPGKDEQVP IRVVQVLGM VGTALLASLW HHVAPVAGQL HSVAFLALAF VLALACCASN VTFLPFLSHL PPRFLRSFFL GQGLSALLPC V LALVQGVG ...String:
MAAPTPARPV LTHLLVALFG MGSWAAVNGI WVELPVVVKE LPEGWSLPSY VSVLVALGNL GLLVVTLWRR LAPGKDEQVP IRVVQVLGM VGTALLASLW HHVAPVAGQL HSVAFLALAF VLALACCASN VTFLPFLSHL PPRFLRSFFL GQGLSALLPC V LALVQGVG RLECPPAPIN GTPGPPLDFL ERFPASTFFW ALTALLVASA AAFQGLLLLL PPPPSVPTGE LGSGLQVGAP GA EEEVEES SPLQEPPSQA AGTTPGPDPK AYQLLSARSA CLLGLLAATN ALTNGVLPAV QSFSCLPYGR LAYHLAVVLG SAA NPLACF LAMGVLCRSL AGLGGLSLLG VFCGGYLMAL AVLSPCPPLV GTSAGVVLVV LSWVLCLGVF SYVKVAASSL LHGG GRPAL LAAGVAIQVG SLLGAVAMFP PTSIYHVFHS RKDCADPCDS

UniProtKB: Solute carrier family 52, riboflavin transporter, member 2

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Macromolecule #2: RIBOFLAVIN

MacromoleculeName: RIBOFLAVIN / type: ligand / ID: 2 / Number of copies: 2 / 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: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143636
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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