[English] 日本語
Yorodumi
- EMDB-61877: Cryo-EM structure of Drosophila melanogaster PXo-G604A -

+
Open data


ID or keywords:

Loading...

-
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: KIDINS220 and InsP8 safeguard the stepwise regulation of phosphate exporter XPR1.
Authors: Xiaojie Wang / Zhongjian Bai / Ciara Wallis / Huanchen Wang / Yaoyao Han / Ruitao Jin / Mingguang Lei / Tian Yang / Chunfang Gu / Henning Jessen / Stephen Shears / Yadong Sun / Ben Corry / Yixiao Zhang /
Abstract: XPR1 is emerging as the only known inorganic phosphate (Pi) exporter in humans, critical for Pi homeostasis, with its activity stimulated by inositol pyrophosphate InsP8 and regulated by neuronal ...XPR1 is emerging as the only known inorganic phosphate (Pi) exporter in humans, critical for Pi homeostasis, with its activity stimulated by inositol pyrophosphate InsP8 and regulated by neuronal scaffold protein KIDINS220. Our structural studies reveal that InsP8 specifically activates XPR1 in a stepwise manner, involving profound SYG1/PHO/XPR1 (SPX) domain movements. Each XPR1 subunit functions with four gating states, in which Pi permeates a constriction site via a "knock-kiss-kick" process. By contrast, KIDINS220 delicately stabilizes XPR1 in a closed conformation through multiple mechanisms, one of which involves trapping the XPR1 α1 helix-critical for InsP8 binding-within an interaction hub. InsP8 serves as a key to release KIDINS220's restraint, reinforcing a "key-to-locks" mechanism to safeguard the stepwise activation. Additionally, our study provides direct structural insights into XPR1-associated neuronal disorders and highlights the evolutionary conservation and divergence among XPR1 orthologs, offering a comprehensive understanding of Pi homeostasis across species.
History
DepositionOct 11, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61877.png

Downloads & links

-
Map

FileDownload / File: emd_61877.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 337.6 Å		1.06 Å/pix.
x 320 pix.
= 337.6 Å		1.06 Å/pix.
x 320 pix.
= 337.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
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 °

-
Supplemental data

-
Half map: #2

Fileemd_61877_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61877_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
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

+
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more