[English] 日本語
Yorodumi
- EMDB-47207: Structure of the phosphate exporter XPR1/SLC53A1, high Pi and Ins... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47207
TitleStructure of the phosphate exporter XPR1/SLC53A1, high Pi and InsP6-bound
Map dataphosphate exporter XPR1/SLC53A1, high Pi and InsP6-bound
Sample
  • Organelle or cellular component: XPR1/SLC53A1
    • Protein or peptide: XPR1/SLC53A1
KeywordsInorganic phosphate exporter / TRANSPORT PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhu Q / Diver MM
Funding support United States, 1 items
OrganizationGrant numberCountry
The Robertson Foundation United States
CitationJournal: Nat Commun / Year: 2025
Title: Transport and InsP gating mechanisms of the human inorganic phosphate exporter XPR1.
Authors: Qinyu Zhu / Madeleine F Yaggi / Nikolaus Jork / Henning J Jessen / Melinda M Diver /
Abstract: Inorganic phosphate (Pi) has essential metabolic and structural roles in living organisms. The Pi exporter, XPR1/SLC53A1, is critical for cellular Pi homeostasis. When intercellular Pi is high, cells ...Inorganic phosphate (Pi) has essential metabolic and structural roles in living organisms. The Pi exporter, XPR1/SLC53A1, is critical for cellular Pi homeostasis. When intercellular Pi is high, cells accumulate inositol pyrophosphate (1,5-InsP), a signaling molecule required for XPR1 function. Inactivating XPR1 mutations lead to brain calcifications, causing neurological symptoms including movement disorders, psychosis, and dementia. Here, cryo-electron microscopy structures of dimeric XPR1 and functional characterization delineate the substrate translocation pathway and how InsP initiates Pi transport. Binding of InsP to XPR1, but not the related inositol polyphosphate InsP, rigidifies the intracellular SPX domains, with InsP bridging the dimers and SPX and transmembrane domains. Locked in this state, the C-terminal tail is sequestered, revealing the entrance to the transport pathway, thus explaining the obligate roles of the SPX domain and InsP. Together, these findings advance our understanding of XPR1 transport activity and expand opportunities for rationalizing disease mechanisms and therapeutic intervention.
History
DepositionOct 8, 2024-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 2, 2025-
Current statusApr 2, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47207.png

Downloads & links

-
Map

FileDownload / File: emd_47207.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationphosphate exporter XPR1/SLC53A1, high Pi and InsP6-bound
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 316.992 Å		0.83 Å/pix.
x 384 pix.
= 316.992 Å		0.83 Å/pix.
x 384 pix.
= 316.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8255 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.526174 - 0.76890194
Average (Standard dev.)-0.000050023777 (±0.011202103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.992 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A

Fileemd_47207_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_47207_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : XPR1/SLC53A1

EntireName: XPR1/SLC53A1
Components
  • Organelle or cellular component: XPR1/SLC53A1
    • Protein or peptide: XPR1/SLC53A1

-
Supramolecule #1: XPR1/SLC53A1

SupramoleculeName: XPR1/SLC53A1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: XPR1/SLC53A1

MacromoleculeName: XPR1/SLC53A1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MKFAEHLSAH ITPEWRKQYI QYEAFKDMLY SAQDQAPSVE VTDEDTVKRY FAKFEEKFFQ TCEKELAKIN TFYSEKLAEA QRRFATLQNE LQSSLDAQKE STGVTTLRQR RKPVFHLSHE ERVQHRNIKD LKLAFSEFYL SLILLQNYQN LNFTGFRKIL KKHDKILETS ...String:
MKFAEHLSAH ITPEWRKQYI QYEAFKDMLY SAQDQAPSVE VTDEDTVKRY FAKFEEKFFQ TCEKELAKIN TFYSEKLAEA QRRFATLQNE LQSSLDAQKE STGVTTLRQR RKPVFHLSHE ERVQHRNIKD LKLAFSEFYL SLILLQNYQN LNFTGFRKIL KKHDKILETS RGADWRVAHV EVAPFYTCKK INQLISETEA VVTNELEDGD RQKAMKRLRV PPLGAAQPAP AWTTFRVGLF CGIFIVLNIT LVLAAVFKLE TDRSIWPLIR IYRGGFLLIE FLFLLGINTY GWRQAGVNHV LIFELNPRSN LSHQHLFEIA GFLGILWCLS LLACFFAPIS VIPTYVYPLA LYGFMVFFLI NPTKTFYYKS RFWLLKLLFR VFTAPFHKVG FADFWLADQL NSLSVILMDL EYMICFYSLE LKWDESKGLL PNNSEESGIC HKYTYGVRAI VQCIPAWLRF IQCLRRYRDT KRAFPHLVNA GKYSTTFFMV TFAALYSTHK ERGHSDTMVF FYLWIVFYII SSCYTLIWDL KMDWGLFDKN AGENTFLREE IVYPQKAYYY CAIIEDVILR FAWTIQISIT STTLLPHSGD IIATVFAPLE VFRRFVWNFF RLENEHLNNC GEFRAVRDIS VAPLNADDQT LLEQMMDQDD GVRNRQKNRS WKYNQSISLR RPRLASQSKA RDTKVLIEDT DDEANT

-
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 (6k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100408
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