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- EMDB-38065: Cryo-EM structures of human XPR1 in closed states -

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Basic information

Entry
Database: EMDB / ID: EMD-38065
TitleCryo-EM structures of human XPR1 in closed states
Map datamain map
Sample
  • Complex: transport
    • Protein or peptide: Solute carrier family 53 member 1
  • Ligand: PHOSPHATE ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL
  • Ligand: water
Keywordstransport / TRANSPORT PROTEIN
Function / homology
Function and homology information


: / phosphate ion transport / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding / phosphate ion transmembrane transport / cellular response to phosphate starvation / efflux transmembrane transporter activity / response to virus / trans-Golgi network / virus receptor activity ...: / phosphate ion transport / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding / phosphate ion transmembrane transport / cellular response to phosphate starvation / efflux transmembrane transporter activity / response to virus / trans-Golgi network / virus receptor activity / Golgi apparatus / plasma membrane / cytoplasm
Similarity search - Function
EXS, C-terminal / EXS family / EXS domain profile. / SPX domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
Solute carrier family 53 member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 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: STRUCTURE OF TRANSPORT
Authors: Jiang DH / Yan R
History
DepositionNov 16, 2023-
Header (metadata) releaseJul 3, 2024-
Map releaseJul 3, 2024-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38065.png

Downloads & links

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Map

FileDownload / File: emd_38065.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: 0.63
Minimum - Maximum-4.850767 - 6.7983255
Average (Standard dev.)-0.0002759139 (±0.14032522)
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

Fileemd_38065_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_38065_half_map_2.map
Annotationhalf 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 : transport

EntireName: transport
Components
  • Complex: transport
    • Protein or peptide: Solute carrier family 53 member 1
  • Ligand: PHOSPHATE ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: CHOLESTEROL
  • Ligand: water

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Supramolecule #1: transport

SupramoleculeName: transport / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 53 member 1

MacromoleculeName: Solute carrier family 53 member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.831422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: APAWTTFRVG LFCGIFIVLN ITLVLAAVFK LETDRSIWPL IRIYRGGFLL IEFLFLLGIN TYGWRQAGVN HVLIFELNPR SNLSHQHLF EIAGFLGILW CLSLLACFFA PISVIPTYVY PLALYGFMVF FLINPTKTFY YKSRFWLLKL LFRVFTAPFH K VGFADFWL ...String:
APAWTTFRVG LFCGIFIVLN ITLVLAAVFK LETDRSIWPL IRIYRGGFLL IEFLFLLGIN TYGWRQAGVN HVLIFELNPR SNLSHQHLF EIAGFLGILW CLSLLACFFA PISVIPTYVY PLALYGFMVF FLINPTKTFY YKSRFWLLKL LFRVFTAPFH K VGFADFWL ADQLNSLSVI LMDLEYMICF YSLELKWDES KGLLPNNSEE SGICHKYTYG VRAIVQCIPA WLRFIQCLRR YR DTKRAFP HLVNAGKYST TFFMVTFAAL YSTHKERGHS DTMVFFYLWI VFYIISSCYT LIWDLKMDWG LFDKNAGENT FLR EEIVYP QKAYYYCAII EDVILRFAWT IQISITSTTL LPHSGDIIAT VFAPLEVFRR FVWNFFRLEN EHLNNCGEFR AVRD ISVAP LNADDQTLLE QMMDQDDGVR NRQKNRSWKY NQSISLRRPR LASQSKARDT KVLIEDTDDE ANT

UniProtKB: Solute carrier family 53 member 1

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Macromolecule #2: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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: 18 / 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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Macromolecule #4: CHOLESTEROL

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

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 14 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

MicroscopeFEI TITAN 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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 253874
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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