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- PDB-9jxg: Cryo-EM structure of apo human XPR1, class 3, with symmetrically ... -

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Basic information

Entry
Database: PDB / ID: 9jxg
TitleCryo-EM structure of apo human XPR1, class 3, with symmetrically dimerized SPX domains
ComponentsSolute carrier family 53 member 1
KeywordsTRANSPORT PROTEIN / phosphate channel / phosphate exporter / PFBC
Function / homology
Function and homology information


phosphate transmembrane transporter activity / phosphate ion transport / intracellular phosphate ion homeostasis / phosphate ion transmembrane transport / cellular response to phosphate starvation / inositol hexakisphosphate binding / efflux transmembrane transporter activity / response to virus / virus receptor activity / 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 speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.75 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)163,2702
Polymers163,2702
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Solute carrier family 53 member 1 / Phosphate exporter SLC53A1 / Protein SYG1 homolog / Xenotropic and polytropic murine leukemia virus ...Phosphate exporter SLC53A1 / Protein SYG1 homolog / Xenotropic and polytropic murine leukemia virus receptor X3 / X-receptor / Xenotropic and polytropic retrovirus receptor 1


Mass: 81634.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPR1, SLC53A1, SYG1, X3 / Production host: Homo sapiens (human) / References: UniProt: Q9UBH6
Has protein modificationN

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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: Homodimer of XPR1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
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

EM software
IDNameCategory
1Gautomatchparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103528 / Symmetry type: POINT
RefinementHighest resolution: 3.75 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0139952
ELECTRON MICROSCOPYf_angle_d1.03413479
ELECTRON MICROSCOPYf_dihedral_angle_d5.261272
ELECTRON MICROSCOPYf_chiral_restr0.0371463
ELECTRON MICROSCOPYf_plane_restr0.0051674

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