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- EMDB-61871: Cryo-EM structure of human XPR1-R570L -

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Basic information

Entry
Database: EMDB / ID: EMD-61871
TitleCryo-EM structure of human XPR1-R570L
Map data
Sample
  • Complex: Homodimer of XPR1 mutant (R570L)
    • Protein or peptide: Solute carrier family 53 member 1
Keywordsphosphate channel / phosphate exporter / PFBC / TRANSPORT PROTEIN
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)
Methodsingle 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, 1 items
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, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: PDBc / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_61871.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.055 Å
Density
Contour LevelBy AUTHOR: 0.707
Minimum - Maximum-3.875009 - 5.0559983
Average (Standard dev.)0.0040169163 (±0.090595275)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 274.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Homodimer of XPR1 mutant (R570L)

EntireName: Homodimer of XPR1 mutant (R570L)
Components
  • Complex: Homodimer of XPR1 mutant (R570L)
    • Protein or peptide: Solute carrier family 53 member 1

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Supramolecule #1: Homodimer of XPR1 mutant (R570L)

SupramoleculeName: Homodimer of XPR1 mutant (R570L) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 46.504273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PAWTTFRVGL FCGIFIVLNI TLVLAAVFKL ETDRSIWPLI RIYRGGFLLI EFLFLLGINT YGWRQAGVNH VLIFELNPRS NLSHQHLFE IAGFLGILWC LSLLACFFAP ISVIPTYVYP LALYGFMVFF LINPTKTFYY KSRFWLLKLL FRVFTAPFHK V GFADFWLA ...String:
PAWTTFRVGL FCGIFIVLNI TLVLAAVFKL ETDRSIWPLI RIYRGGFLLI EFLFLLGINT YGWRQAGVNH VLIFELNPRS NLSHQHLFE IAGFLGILWC LSLLACFFAP ISVIPTYVYP LALYGFMVFF LINPTKTFYY KSRFWLLKLL FRVFTAPFHK V GFADFWLA DQLNSLSVIL MDLEYMICFY SLELKWDESK GLLPNNSEES GICHKYTYGV RAIVQCIPAW LRFIQCLRRY RD TKRAFPH LVNAGKYSTT FFMVTFAALY STHKERGHSD TMVFFYLWIV FYIISSCYTL IWDLKMDWGL FDKNAGENTF LRE EIVYPQ KAYYYCAIIE DVILLFAWTI QISITSTTLL PHSGDIIATV FAPLEVFRRF VWNFFRLENE HLNNCGEFRA

UniProtKB: Solute carrier family 53 member 1

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 49.41 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 229444
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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