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- EMDB-61877: Cryo-EM structure of Drosophila melanogaster PXo-G604A -

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Basic information

Entry
Database: EMDB / ID: EMD-61877
TitleCryo-EM structure of Drosophila melanogaster PXo-G604A
Map data
Sample
  • Complex: Cryo-EM structure of Drosophila melanogaster PXo-G604A
    • Protein or peptide: Solute carrier family 53 member 1
Keywordsphosphate channel / TRANSPORT PROTEIN
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)
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_61877.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.055 Å
Density
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-2.4831247 - 4.793653
Average (Standard dev.)-0.0001311947 (±0.070925966)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 337.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of Drosophila melanogaster PXo-G604A

EntireName: Cryo-EM structure of Drosophila melanogaster PXo-G604A
Components
  • Complex: Cryo-EM structure of Drosophila melanogaster PXo-G604A
    • Protein or peptide: Solute carrier family 53 member 1

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Supramolecule #1: Cryo-EM structure of Drosophila melanogaster PXo-G604A

SupramoleculeName: Cryo-EM structure of Drosophila melanogaster PXo-G604A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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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: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 78.312453 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKFAEHLTAH ITPEWRKQYI NYEEMKAMLY AAIEQSPSAE LVEREMVTRY FAKFDEEFFH YCDKELAKIN TFYSEKMAEA TRKYGSLRS ELTEALEMGH PKKLPAWKRR TPLGKKNVPA RKIQDLKLAF SEFYLGLILL QNYQNLNFTG FRKILKKHDK L LSVDYGAR ...String:
MKFAEHLTAH ITPEWRKQYI NYEEMKAMLY AAIEQSPSAE LVEREMVTRY FAKFDEEFFH YCDKELAKIN TFYSEKMAEA TRKYGSLRS ELTEALEMGH PKKLPAWKRR TPLGKKNVPA RKIQDLKLAF SEFYLGLILL QNYQNLNFTG FRKILKKHDK L LSVDYGAR WRTDHVEAAH FYTNKDIDRL IQETEQAVTQ DIEGGDRQRA MKRLRVPPLG EQQSPWTTFK VGLFSGAFVV LF ITVVIAA MFYGFGENWR AGMRMFRAPF LIIECLFLWG VNVYGWRSSG VNHVLIFELD PRNHLSEQNI MEVASVFGVI WAC CVLSYI FCDPLGIPQY AAPLCLYTLM AAFLLNPTKT FHHEARFWAI RILIRVIMAP FCFVNFADFW LADQLNSMVP AFLD IPFLI CFFGRSPTWH KAGKAASHCV EYVSLLHPIV AIMPAYFRFA QCIRRYRDTK ESFPHLVNAA KYATSFFVVI FAHKY HTTT DTYPLSKENP WFYCWITAAI FSSCYAYTWD IKMDWGLFDS KAGDNRFLRE EIVYSSTWFY YFGIIEDLIL RFSWTL SMS LIEAGYIEGD VMMTILSPLE VFRRFIWNYF RLENEHLNNV AKFRAVRDIS VAPMDCSDQT TILRMMDETD GVLNRRR GK AAGGKSATKK NKQEQRLLLQ GESIEDLCS

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 / In silico model: AF-Q9UBH6-F1 / Details: AlphaFold predicted
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58767
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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