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- EMDB-61869: Cryo-EM structure of human XPR1-R459C -

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Basic information

Entry
Database: EMDB / ID: EMD-61869
TitleCryo-EM structure of human XPR1-R459C
Map data
Sample
  • Complex: Homodimer of XPR1-R459C
    • 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: 3.12 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_61869.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: 0.523
Minimum - Maximum-2.0590246 - 3.4283073
Average (Standard dev.)0.0042093187 (±0.07245705)
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-R459C

EntireName: Homodimer of XPR1-R459C
Components
  • Complex: Homodimer of XPR1-R459C
    • Protein or peptide: Solute carrier family 53 member 1

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Supramolecule #1: Homodimer of XPR1-R459C

SupramoleculeName: Homodimer of XPR1-R459C / 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: 74.189711 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KFAEHLSAHI TPEWRKQYIQ YEAFKDMLYS AQDQAPSVEV TDEDTVKRYF AKFEEKFFQT CEKELAKINT FYSEKLAEAQ RRFATLQNE LQSSLDAQKE STGVTTLRQR RKPVFHLSHE ERVQHRNIKD LKLAFSEFYL SLILLQNYQN LNFTGFRKIL K KHDKILET ...String:
KFAEHLSAHI TPEWRKQYIQ YEAFKDMLYS AQDQAPSVEV TDEDTVKRYF AKFEEKFFQT CEKELAKINT FYSEKLAEAQ RRFATLQNE LQSSLDAQKE STGVTTLRQR RKPVFHLSHE ERVQHRNIKD LKLAFSEFYL SLILLQNYQN LNFTGFRKIL K KHDKILET SRGADWRVAH VEVAPFYTCK KINQLISETE AVVTNELEDG DRQKAMKRLR VPPLGAAQPA PAWTTFRVGL FC GIFIVLN ITLVLAAVFK LETDRSIWPL IRIYRGGFLL IEFLFLLGIN TYGWRQAGVN HVLIFELNPR SNLSHQHLFE IAG FLGILW CLSLLACFFA PISVIPTYVY PLALYGFMVF FLINPTKTFY YKSRFWLLKL LFRVFTAPFH KVGFADFWLA DQLN SLSVI LMDLEYMICF YSLELKWDES KGLLPNNSEE SGICHKYTYG VRAIVQCIPA WLCFIQCLRR YRDTKRAFPH LVNAG KYST TFFMVTFAAL YSTHKERGHS DTMVFFYLWI VFYIISSCYT LIWDLKMDWG LFDKNAGENT FLREEIVYPQ KAYYYC AII EDVILRFAWT IQISITSTTL LPHSGDIIAT VFAPLEVFRR FVWNFFRLEN EHLNNCGEFR AVRDISVAPL

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: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 159655
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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