[English] 日本語
Yorodumi
- EMDB-43684: Cryo-EM structure of FLVCR2 in the outward-facing state with chol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43684
TitleCryo-EM structure of FLVCR2 in the outward-facing state with choline bound
Map dataFLVCR2 in the outward-facing state in complex with choline and Fab FLV23
Sample
  • Complex: FLVCR2 in the outward-facing state complexed with choline and Fab FLV23
    • Protein or peptide: Feline leukemia virus subgroup C cellular receptor 2
    • Protein or peptide: Fab FLV23 heavy chain
    • Protein or peptide: Fab FLV23 light chain
  • Ligand: CHOLINE ION
KeywordsCholine transporter / blood-brain barrier / membrane protein / MFS fold / TRANSPORT PROTEIN
Function / homology
Function and homology information


endothelial tip cell fate specification / ethanolamine transmembrane transporter activity / choline transmembrane transporter activity / heme transmembrane transporter activity / choline transport / sprouting angiogenesis / transport across blood-brain barrier / mitochondrial membrane / brain development / gene expression ...endothelial tip cell fate specification / ethanolamine transmembrane transporter activity / choline transmembrane transporter activity / heme transmembrane transporter activity / choline transport / sprouting angiogenesis / transport across blood-brain barrier / mitochondrial membrane / brain development / gene expression / in utero embryonic development / heme binding / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
: / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Choline/ethanolamine transporter FLVCR2
Similarity search - Component
Biological speciesMus musculus (house mouse) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsCater RJ / Mancia F
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS129105-01 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL166866-01 United States
CitationJournal: Nature / Year: 2024
Title: Structural and molecular basis of choline uptake into the brain by FLVCR2.
Authors: Rosemary J Cater / Dibyanti Mukherjee / Eva Gil-Iturbe / Satchal K Erramilli / Ting Chen / Katie Koo / Nicolás Santander / Andrew Reckers / Brian Kloss / Tomasz Gawda / Brendon C Choy / ...Authors: Rosemary J Cater / Dibyanti Mukherjee / Eva Gil-Iturbe / Satchal K Erramilli / Ting Chen / Katie Koo / Nicolás Santander / Andrew Reckers / Brian Kloss / Tomasz Gawda / Brendon C Choy / Zhening Zhang / Aditya Katewa / Amara Larpthaveesarp / Eric J Huang / Scott W J Mooney / Oliver B Clarke / Sook Wah Yee / Kathleen M Giacomini / Anthony A Kossiakoff / Matthias Quick / Thomas Arnold / Filippo Mancia /
Abstract: Choline is an essential nutrient that the human body needs in vast quantities for cell membrane synthesis, epigenetic modification and neurotransmission. The brain has a particularly high demand for ...Choline is an essential nutrient that the human body needs in vast quantities for cell membrane synthesis, epigenetic modification and neurotransmission. The brain has a particularly high demand for choline, but how it enters the brain remains unknown. The major facilitator superfamily transporter FLVCR1 (also known as MFSD7B or SLC49A1) was recently determined to be a choline transporter but is not highly expressed at the blood-brain barrier, whereas the related protein FLVCR2 (also known as MFSD7C or SLC49A2) is expressed in endothelial cells at the blood-brain barrier. Previous studies have shown that mutations in human Flvcr2 cause cerebral vascular abnormalities, hydrocephalus and embryonic lethality, but the physiological role of FLVCR2 is unknown. Here we demonstrate both in vivo and in vitro that FLVCR2 is a BBB choline transporter and is responsible for the majority of choline uptake into the brain. We also determine the structures of choline-bound FLVCR2 in both inward-facing and outward-facing states using cryo-electron microscopy. These results reveal how the brain obtains choline and provide molecular-level insights into how FLVCR2 binds choline in an aromatic cage and mediates its uptake. Our work could provide a novel framework for the targeted delivery of therapeutic agents into the brain.
History
DepositionFeb 12, 2024-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43684.png

Downloads & links

-
Map

FileDownload / File: emd_43684.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFLVCR2 in the outward-facing state in complex with choline and Fab FLV23
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 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: 0.245
Minimum - Maximum-1.80969 - 2.1254811
Average (Standard dev.)-0.00033968608 (±0.032298487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: FLVCR2 in the outward-facing state in complex with...

Fileemd_43684_half_map_1.map
AnnotationFLVCR2 in the outward-facing state in complex with choline and Fab FLV23 half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: FLVCR2 in the outward-facing state in complex with...

Fileemd_43684_half_map_2.map
AnnotationFLVCR2 in the outward-facing state in complex with choline and Fab FLV23 half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : FLVCR2 in the outward-facing state complexed with choline and Fab...

EntireName: FLVCR2 in the outward-facing state complexed with choline and Fab FLV23
Components
  • Complex: FLVCR2 in the outward-facing state complexed with choline and Fab FLV23
    • Protein or peptide: Feline leukemia virus subgroup C cellular receptor 2
    • Protein or peptide: Fab FLV23 heavy chain
    • Protein or peptide: Fab FLV23 light chain
  • Ligand: CHOLINE ION

-
Supramolecule #1: FLVCR2 in the outward-facing state complexed with choline and Fab...

SupramoleculeName: FLVCR2 in the outward-facing state complexed with choline and Fab FLV23
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 110 KDa

-
Macromolecule #1: Feline leukemia virus subgroup C cellular receptor 2

MacromoleculeName: Feline leukemia virus subgroup C cellular receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 60.103266 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVNESLNQEE SNDRPAPESE FQMDTSYSTQ PSGSIHPSVS GHPSVSGHPS VSGHPSVSIH PSVSIDPSVS VRPSSSALPS TLAQPSGLT HHSSLVREDS VIKVSKRRWV VVLVFSCYSL CNAFQWIQYG SINNIFMNFY GVSAFAIDWL SMCYMLTYIP L LLPVAWML ...String:
MVNESLNQEE SNDRPAPESE FQMDTSYSTQ PSGSIHPSVS GHPSVSGHPS VSGHPSVSIH PSVSIDPSVS VRPSSSALPS TLAQPSGLT HHSSLVREDS VIKVSKRRWV VVLVFSCYSL CNAFQWIQYG SINNIFMNFY GVSAFAIDWL SMCYMLTYIP L LLPVAWML EKFGLRTIAI TGSALNCLGA WVKLGSLEPH LFPVTMVGQV ICSVAQVFIL GMPSRIASVW FGADEVSTAC SV AVFGNQL GIAIGFLVPP VLVPNIKDPE KLAYHISIMF YIIGGVATFL FILVIIVFKE KPKHPPSRAQ SLSYALATTD ASY LSSIVR LFKNLNFVLL VITYGLNAGA FYALSTLLNR MVILHFPGEE VNAGRIGLTI VIAGMFGAMI SGIWLDKSKT YKET TLVVY IMTLVGMVVY TFTLNLNHLW VVFITAGTLG FFMTGYLPLG FEFAVELTYP ESEGVSSGLL NVSAQVFGIV FTISQ GQII DNHGTMFGNI FLCVFLALGS ALTAFIKSDL RRQRANKDAP ETKVQEEEEE EEGSNTSKVP VVSEAHL

UniProtKB: Choline/ethanolamine transporter FLVCR2

-
Macromolecule #2: Fab FLV23 heavy chain

MacromoleculeName: Fab FLV23 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 25.772633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NLSSYSIHWV RQAPGKGLEW VASISSYYGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSSRYEFFY SNSWWYWPAM DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NLSSYSIHWV RQAPGKGLEW VASISSYYGS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSSRYEFFY SNSWWYWPAM DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HT

-
Macromolecule #3: Fab FLV23 light chain

MacromoleculeName: Fab FLV23 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 23.357916 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSYVNPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSYVNPITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

-
Macromolecule #4: CHOLINE ION

MacromoleculeName: CHOLINE ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CHT
Molecular weightTheoretical: 104.171 Da
Chemical component information

ChemComp-CHT:
CHOLINE ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 433845
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more