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- PDB-9qu4: Cryo-EM structure of the inward-open choline-bound state of choli... -

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Basic information

Entry
Database: PDB / ID: 9qu4
TitleCryo-EM structure of the inward-open choline-bound state of choline/ethanolamine transporter FLVCR2
ComponentsImmunoglobulin G-binding protein A,Choline/ethanolamine transporter FLVCR2
KeywordsMEMBRANE PROTEIN / Choline transporter
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
CHOLINE ION / Immunoglobulin G-binding protein A / Choline/ethanolamine transporter FLVCR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsDriller, J.H. / Nel, L. / Pedersen, B.P.
Funding support Denmark, European Union, 4items
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, J.H. / Driller, R. / Frain, K.M. / Pedersen, B.P.
History
DepositionApr 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 11, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin G-binding protein A,Choline/ethanolamine transporter FLVCR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4692
Polymers66,3641
Non-polymers1041
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody Immunoglobulin G-binding protein A,Choline/ethanolamine transporter FLVCR2 / IgG-binding protein A / Staphylococcal protein A / SpA / Calcium-chelate transporter / CCT / Feline ...IgG-binding protein A / Staphylococcal protein A / SpA / Calcium-chelate transporter / CCT / Feline leukemia virus subgroup C receptor-related protein 2 / Heme transporter FLVCR2


Mass: 66364.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: spa, FLVCR2, C14orf58 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P38507, UniProt: Q9UPI3
#2: Chemical ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Choline/ethanolamine transporter FLVCR2 in DDM / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 59.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 271101 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 64.37 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033216
ELECTRON MICROSCOPYf_angle_d0.49284380
ELECTRON MICROSCOPYf_chiral_restr0.0366517
ELECTRON MICROSCOPYf_plane_restr0.0033529
ELECTRON MICROSCOPYf_dihedral_angle_d4.9882434

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