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- PDB-9jxr: Cryo-EM structure of Drosophila melanogaster PXo-G604A -

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Basic information

Entry
Database: PDB / ID: 9jxr
TitleCryo-EM structure of Drosophila melanogaster PXo-G604A
ComponentsSolute carrier family 53 member 1
KeywordsTRANSPORT PROTEIN / phosphate channel
Function / homology
Function and homology information


regulation of cellular response to phosphate starvation / negative regulation of JUN kinase activity / phosphate transmembrane transporter activity / phosphate ion transport / intracellular phosphate ion homeostasis / cellular response to phosphate starvation / inositol hexakisphosphate binding / organelle membrane / negative regulation of cell population proliferation / plasma membrane
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 speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsWang, X. / Bai, Z. / Wallis, C. / Wang, H. / Han, Y. / Jin, R. / Lei, M. / Gu, C. / Jessen, H. / Shears, S. ...Wang, X. / Bai, Z. / Wallis, C. / Wang, H. / Han, Y. / Jin, R. / Lei, M. / Gu, C. / Jessen, H. / Shears, S. / Sun, Y. / Corry, B. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022ZD0207400 China
CitationJournal: Mol.Cell / Year: 2025
Title: Cryo-EM structure of human XPR1 in apo state
Authors: Wang, X. / Bai, Z. / Wallis, C. / Wang, H. / Han, Y. / Jin, R. / Lei, M. / Gu, C. / Jessen, H. / Shears, S. / Sun, Y. / Corry, B. / Zhang, Y.
History
DepositionOct 11, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Solute carrier family 53 member 1
B: Solute carrier family 53 member 1


Theoretical massNumber of molelcules
Total (without water)156,6252
Polymers156,6252
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Solute carrier family 53 member 1 / Inorganic phosphate-sensitive XPR1 homolog / Phosphate exporter PXo / Xenotropic and polytropic ...Inorganic phosphate-sensitive XPR1 homolog / Phosphate exporter PXo / Xenotropic and polytropic retrovirus receptor 1


Mass: 78312.453 Da / Num. of mol.: 2 / Mutation: G604A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: PXo, XPR1, CG10483 / Production host: Homo sapiens (human) / References: UniProt: Q9VRR2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of Drosophila melanogaster PXo-G604A
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 49.41 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58767 / Symmetry type: POINT

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