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- EMDB-60664: Structure and iron-transporting mechanism of BOCT1 -

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Basic information

Entry
Database: EMDB / ID: EMD-60664
TitleStructure and iron-transporting mechanism of BOCT1
Map data
Sample
  • Cell: mBOCT1
    • Protein or peptide: Solute carrier family 22 (organic cation transporter), member 17
  • Ligand: FE (II) ION
KeywordsSLC / MFS / 11 TMs / Iron-transporting / PROTEIN TRANSPORT
Function / homology
Function and homology information


transmembrane transporter activity / membrane
Similarity search - Function
Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 22 member 17
Similarity search - Component
Biological speciesMus spicilegus (steppe mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsChen J / Chen L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130048 and 92157301 China
CitationJournal: to be published
Title: Structure and iron-transporting mechanism of BOCT1
Authors: Chen J / Chen L
History
DepositionJun 29, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60664.png

Downloads & links

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Map

FileDownload / File: emd_60664.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å		1.08 Å/pix.
x 256 pix.
= 277.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.57
Minimum - Maximum-3.597755 - 4.858121
Average (Standard dev.)0.00094774173 (±0.075522535)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 277.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60664_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_60664_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 : mBOCT1

EntireName: mBOCT1
Components
  • Cell: mBOCT1
    • Protein or peptide: Solute carrier family 22 (organic cation transporter), member 17
  • Ligand: FE (II) ION

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Supramolecule #1: mBOCT1

SupramoleculeName: mBOCT1 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus spicilegus (steppe mouse)

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Macromolecule #1: Solute carrier family 22 (organic cation transporter), member 17

MacromoleculeName: Solute carrier family 22 (organic cation transporter), member 17
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus spicilegus (steppe mouse)
Molecular weightTheoretical: 55.716895 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASDPIFTLA PPLHCHYGAL PPNASGWEQP PNSSGVSVAG AALAASAASG VVTSTDPSCS GFAPPDFNHC LKDWDYNGLP VLTTNAIGQ WDLVCDLGWQ VILEQILFIL GFASGYLFLG YPADRFGRRG IVLLTLGLVG PCGVGGAAAG SSTGIMALRF L LGFLLAGV ...String:
MASDPIFTLA PPLHCHYGAL PPNASGWEQP PNSSGVSVAG AALAASAASG VVTSTDPSCS GFAPPDFNHC LKDWDYNGLP VLTTNAIGQ WDLVCDLGWQ VILEQILFIL GFASGYLFLG YPADRFGRRG IVLLTLGLVG PCGVGGAAAG SSTGIMALRF L LGFLLAGV DLGVYLMRLE LCDPTQRLRV ALAGELVGVG GHFLFLGLAL VSKDWRFLQR MITAPCILFL FYGWPGLFLE SA RWLIVKR QIEEAQSVLR ILAERNRPHG QMLGEEAQEA LQELENTCPL PATSTFSFAS LLNYRNIWKN LLILGFTNFI AHA IRHCYQ PVGGGGSPSD FYLCSLLASG TAALACVFLG VTVDRFGRRG ILLLSMTLTG IASLVLLGLW DYLNDAAITT FSVL GLFSS QASAILSTLL ASEIIPTTVR GRGLGLIMAL GALGGLSCPA QRLHMGHGAF LQHVVLAACA LLCILSIMLL PETKR KLLP EVLRDGELCR RPSLLRQPPP NRCDHVPLLA TPNPAL

UniProtKB: Solute carrier family 22 member 17

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Macromolecule #2: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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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

Concentration5 mg/mL
BufferpH: 8.2 / Component - Concentration: 5.6 mg/mL / Component - Formula: NaCl / Component - Name: Sodium Chloride / Details: 0.001% MNG 20 mM Hepes
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 2.5 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsSpherical aberration corrector: Yes
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.53 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 63000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 63000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2579209
CTF correctionSoftware - Name: cryoSPARC (ver. V4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4) / Number images used: 171512
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. V4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. V4)
Final 3D classificationNumber classes: 3 / Avg.num./class: 130000 / Software - Name: cryoSPARC (ver. V4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9il4:
Structure and iron-transporting mechanism of BOCT1

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