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- EMDB-64185: transporter -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-64185
Titletransporter
Map datamain map
Sample
  • Complex: inward state
    • Protein or peptide: Protein NRT1/ PTR FAMILY 2.10
  • Ligand: CHOLESTEROL
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
Keywordsinward / TRANSPORT PROTEIN
Function / homology
Function and homology information


glucosinolate:proton symporter activity / phloem glucosinolate loading / glucosinolate transport / Golgi trans cisterna / plasmodesma / transmembrane transporter activity / transmembrane transport / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
Proton-dependent oligopeptide transporter family / POT family / MFS transporter superfamily
Similarity search - Domain/homology
Protein NRT1/ PTR FAMILY 2.10
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsJiang DH / Yan R
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: transporter
Authors: Jiang DH / Yan R
History
DepositionApr 15, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64185.png

Downloads & links

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Map

FileDownload / File: emd_64185.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.228
Minimum - Maximum-1.0084443 - 1.5415431
Average (Standard dev.)-0.0007699873 (±0.031090239)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_64185_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_64185_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : inward state

EntireName: inward state
Components
  • Complex: inward state
    • Protein or peptide: Protein NRT1/ PTR FAMILY 2.10
  • Ligand: CHOLESTEROL
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

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Supramolecule #1: inward state

SupramoleculeName: inward state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Protein NRT1/ PTR FAMILY 2.10

MacromoleculeName: Protein NRT1/ PTR FAMILY 2.10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 71.105164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKSRVILNHR DRRDKNHNNN NTNHYTQVDT MERKPLEVEP STTTTNTDVV DSFEEEQRKI VYRGWKVMPF IIGNETFEKL GIIGTLSNL LVYLTSVFNL KSYTAATIIN AFSGTINFGT FIAAFLCDTY FGRYKTLSVA VIACFLGSFV ILLTAAIPSL H PVACGNKI ...String:
MKSRVILNHR DRRDKNHNNN NTNHYTQVDT MERKPLEVEP STTTTNTDVV DSFEEEQRKI VYRGWKVMPF IIGNETFEKL GIIGTLSNL LVYLTSVFNL KSYTAATIIN AFSGTINFGT FIAAFLCDTY FGRYKTLSVA VIACFLGSFV ILLTAAIPSL H PVACGNKI SCEGPSVGQI LFLLMGLGFL VVGAGGIRPC NLAFGADQFN PKSESGKKGI NSFFNWYFFT FTFAQIISLT AV VYIQSNV SWTIGLIIPV ALMFLACVIF FAGDRLYVKV KASGSPLAGI ARVIAAAIKK RGLKPVKQPW VNLYNHIPSN YAN TTLKYT DQFRFLDKAA IMTPEEKLNS DGTASDPWKL CTLQQVEEVK CIVRVIPIWF ASTIYYLAIT IQMTYPVFQA LQSD RRLGS GGFRIPAATY VVFLMTGMTV FIIFYDRVLV PSLRRVTGLE TGISLLQRIG AGFTFAIMSL LVSGFIEERR RNFAL TKPT LGMAPRTGEI SSMSALWLIP QLTLAGIAEA FAAIGQMEFY YKQFPENMKS FAGSIFYVGA GVSSYLASFL ISTVHR TTA HSPSGNWLAE DLNKAKLDYF YFMLTGLMVV NMAYFLLMAR WYRYKGGNDE DITEIETNEE ETKQQQLQDK NSV

UniProtKB: Protein NRT1/ PTR FAMILY 2.10

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Macromolecule #2: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 4 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 10 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72964
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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