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- EMDB-53371: Cryo-EM structure of the inward-open choline-bound state of choli... -

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Basic information

Entry
Database: EMDB / ID: EMD-53371
TitleCryo-EM structure of the inward-open choline-bound state of choline/ethanolamine transporter FLVCR2
Map data
Sample
  • Organelle or cellular component: Choline/ethanolamine transporter FLVCR2 in DDM
    • Protein or peptide: Immunoglobulin G-binding protein A,Choline/ethanolamine transporter FLVCR2
  • Ligand: CHOLINE ION
KeywordsCholine transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


heme export / ethanolamine transmembrane transporter activity / choline transmembrane transporter activity / heme transmembrane transporter activity / choline transport / IgG binding / transport across blood-brain barrier / mitochondrial membrane / heme binding / endoplasmic reticulum membrane ...heme export / ethanolamine transmembrane transporter activity / choline transmembrane transporter activity / heme transmembrane transporter activity / choline transport / IgG binding / transport across blood-brain barrier / mitochondrial membrane / heme binding / endoplasmic reticulum membrane / extracellular region / membrane / plasma membrane
Similarity search - Function
: / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain ...: / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / Major facilitator superfamily / Major Facilitator Superfamily / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / MFS transporter superfamily
Similarity search - Domain/homology
Immunoglobulin G-binding protein A / Choline/ethanolamine transporter FLVCR2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsDriller JH / Nel L / Pedersen BP
Funding support Denmark, European Union, 4 items
OrganizationGrant numberCountry
LundbeckfondenR380-2021-1207 Denmark
H2020 Marie Curie Actions of the European Commission890822European Union
Danish Council for Independent Research0135-00032B Denmark
The Carlsberg FoundationCF19-0127 Denmark
CitationJournal: To Be Published
Title: Comparative and structural analysis of choline transport between eukaryotic choline transport protein families FLVCR and CTL
Authors: Nel L / Driller JH / Driller R / Frain KM / Pedersen BP
History
DepositionApr 10, 2025-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53371.png

Downloads & links

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Map

FileDownload / File: emd_53371.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 192 pix.
= 248.448 Å		1.29 Å/pix.
x 192 pix.
= 248.448 Å		1.29 Å/pix.
x 192 pix.
= 248.448 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.4201967 - 1.9380711
Average (Standard dev.)0.000015042657 (±0.032448832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 248.448 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53371_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_53371_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 : Choline/ethanolamine transporter FLVCR2 in DDM

EntireName: Choline/ethanolamine transporter FLVCR2 in DDM
Components
  • Organelle or cellular component: Choline/ethanolamine transporter FLVCR2 in DDM
    • Protein or peptide: Immunoglobulin G-binding protein A,Choline/ethanolamine transporter FLVCR2
  • Ligand: CHOLINE ION

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Supramolecule #1: Choline/ethanolamine transporter FLVCR2 in DDM

SupramoleculeName: Choline/ethanolamine transporter FLVCR2 in DDM / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Immunoglobulin G-binding protein A,Choline/ethanolamine transport...

MacromoleculeName: Immunoglobulin G-binding protein A,Choline/ethanolamine transporter FLVCR2
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.364492 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MGPMVNENKE QQNAFYEILS LPNLNEEQRN AFIQSLKDDP SQSANLLAEA KKLNEQQAAF YEILHLPNLN EEQRNAFIQS LKDDPSQSA NLLAEAKKLN EQQAAFYEIL HLPNLNEEQR NAFIQSLKDD PSQSANLLAE AKKLNELQKR RWAVVLVFSC Y SMCNSFQW ...String:
MGPMVNENKE QQNAFYEILS LPNLNEEQRN AFIQSLKDDP SQSANLLAEA KKLNEQQAAF YEILHLPNLN EEQRNAFIQS LKDDPSQSA NLLAEAKKLN EQQAAFYEIL HLPNLNEEQR NAFIQSLKDD PSQSANLLAE AKKLNELQKR RWAVVLVFSC Y SMCNSFQW IQYGSINNIF MHFYGVSAFA IDWLSMCYML TYIPLLLPVA WLLEKFGLRT IALTGSALNC LGAWVKLGSL KP HLFPVTV VGQLICSVAQ VFILGMPSRI ASVWFGANEV STACSVAVFG NQLGIAIGFL VPPVLVPNIE DRDELAYHIS IMF YIIGGV ATLLLILVII VFKEKPKYPP SRAQSLSYAL TSPDASYLGS IARLFKNLNF VLLVITYGLN AGAFYALSTL LNRM VIWHY PGEEVNAGRI GLTIVIAGML GAVISGIWLD RSKTYKETTL VVYIMTLVGM VVYTFTLNLG HLWVVFITAG TMGFF MTGY LPLGFEFAVE LTYPESEGIS SGLLNISAQV FGIIFTISQG QIIDNYGTKP GNIFLCVFLT LGAALTAFIK ADLRRQ KAN KETLENKLQE EEEESNTSKV PTAVSEDHLG LVPR

UniProtKB: Immunoglobulin G-binding protein A, Choline/ethanolamine transporter FLVCR2

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Macromolecule #2: CHOLINE ION

MacromoleculeName: CHOLINE ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: CHT
Molecular weightTheoretical: 104.171 Da
Chemical component information

ChemComp-CHT:
CHOLINE ION

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 271101
Initial angle assignmentType: RANDOM ASSIGNMENT / Details: Ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: Non-uniform refinement
FSC plot (resolution estimation)

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