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- EMDB-18338: Cryo-EM structure of the outward-facing heme-bound FLVCR2 -

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Basic information

Entry
Database: EMDB / ID: EMD-18338
TitleCryo-EM structure of the outward-facing heme-bound FLVCR2
Map data
Sample
  • Complex: FLVCR monomer
    • Protein or peptide: Heme transporter FLVCR2
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
KeywordsMFS / choline transport / human 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 / transport across blood-brain barrier / mitochondrial membrane / heme binding / endoplasmic reticulum membrane / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWeng T-H / Wu D / Safarian S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: To Be Published
Title: Cryo-EM structure of the outward-facing heme-bound FLVCR2
Authors: Weng T-H / Wu D / Safarian S
History
DepositionAug 28, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18338.png

Downloads & links

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Map

FileDownload / File: emd_18338.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 200 pix.
= 167.4 Å		0.84 Å/pix.
x 200 pix.
= 167.4 Å		0.84 Å/pix.
x 200 pix.
= 167.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.8043256 - 3.347334
Average (Standard dev.)0.0038609214 (±0.1071208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 167.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18338_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_18338_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 : FLVCR monomer

EntireName: FLVCR monomer
Components
  • Complex: FLVCR monomer
    • Protein or peptide: Heme transporter FLVCR2
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: FLVCR monomer

SupramoleculeName: FLVCR monomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58 KDa

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Macromolecule #1: Heme transporter FLVCR2

MacromoleculeName: Heme transporter FLVCR2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.277094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVNEGPNQEE SDDTPVPESA LQADPSVSVH PSVSVHPSVS INPSVSVHPS SSAHPSALAQ PSGLAHPSSS GPEDLSVIKV SRRRWAVVL VFSCYSMCNS FQWIQYGSIN NIFMHFYGVS AFAIDWLSMC YMLTYIPLLL PVAWLLEKFG LRTIALTGSA L NCLGAWVK ...String:
MVNEGPNQEE SDDTPVPESA LQADPSVSVH PSVSVHPSVS INPSVSVHPS SSAHPSALAQ PSGLAHPSSS GPEDLSVIKV SRRRWAVVL VFSCYSMCNS FQWIQYGSIN NIFMHFYGVS AFAIDWLSMC YMLTYIPLLL PVAWLLEKFG LRTIALTGSA L NCLGAWVK LGSLKPHLFP VTVVGQLICS VAQVFILGMP SRIASVWFGA NEVSTACSVA VFGNQLGIAI GFLVPPVLVP NI EDRDELA YHISIMFYII GGVATLLLIL VIIVFKEKPK YPPSRAQSLS YALTSPDASY LGSIARLFKN LNFVLLVITY GLN AGAFYA LSTLLNRMVI WHYPGEEVNA GRIGLTIVIA GMLGAVISGI WLDRSKTYKE TTLVVYIMTL VGMVVYTFTL NLGH LWVVF ITAGTMGFFM TGYLPLGFEF AVELTYPESE GISSGLLNIS AQVFGIIFTI SQGQIIDNYG TKPGNIFLCV FLTLG AALT AFIKADLRRQ KANKETLENK LQEEEEESNT SKVPTAVSED HLDYKDDDDK

UniProtKB: Choline/ethanolamine transporter FLVCR2

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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

Concentration1.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
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: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5419952
Startup modelType of model: OTHER / Details: Ab initio reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 51266
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3-f1


Chain - Chain ID: A / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8qcz:
Cryo-EM structure of the outward-facing heme-bound FLVCR2

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