[English] 日本語
Yorodumi
- EMDB-65520: Cryo-EM structure of a Fungal XPR1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65520
TitleCryo-EM structure of a Fungal XPR1
Map data
Sample
  • Complex: SpXPR1
    • Protein or peptide: Protein SYG1 homolog
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
  • Ligand: PHOSPHATE ION
Keywordsphosphate exporter / dimer / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


phosphate ion export across plasma membrane / phosphate transmembrane transporter activity / phosphate ion transport / cellular response to phosphate starvation / inositol hexakisphosphate binding / plasma membrane
Similarity search - Function
EXS, C-terminal / EXS family / EXS domain profile. / SPX domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
Phosphate exporter spx2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsShen HZ / Yang H / Wang YC
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2024YFA0916903 China
CitationJournal: To Be Published
Title: Structural insights into the gating mechanism of a fission yeast phosphate exporter SpXpr1
Authors: Shen HZ / Yang H / Wang YC
History
DepositionJul 24, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_65520.png

Downloads & links

-
Map

FileDownload / File: emd_65520.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å		1.09 Å/pix.
x 360 pix.
= 391.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.739
Minimum - Maximum-3.3325377 - 5.450619
Average (Standard dev.)-0.001138054 (±0.07741191)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 391.32 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_65520_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65520_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SpXPR1

EntireName: SpXPR1
Components
  • Complex: SpXPR1
    • Protein or peptide: Protein SYG1 homolog
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
  • Ligand: PHOSPHATE ION

-
Supramolecule #1: SpXPR1

SupramoleculeName: SpXPR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)

-
Macromolecule #1: Protein SYG1 homolog

MacromoleculeName: Protein SYG1 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972
Molecular weightTheoretical: 82.913281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKG GSGSGGSGSG SSGSTGKFGK VIEGQSVAEW ASAYFDYKKG KKIIAGIAKN PSEGLYGTSG ILGETPEEAI VKRGQIHRF HPLFQEFLDQ QANKVEEFFE NLVSDARERM DLISDQVDIY EKLRAFKKGT LESGSVVLIQ KQHSKLRQRL D SILNFSRL ...String:
MDYKDDDDKG GSGSGGSGSG SSGSTGKFGK VIEGQSVAEW ASAYFDYKKG KKIIAGIAKN PSEGLYGTSG ILGETPEEAI VKRGQIHRF HPLFQEFLDQ QANKVEEFFE NLVSDARERM DLISDQVDIY EKLRAFKKGT LESGSVVLIQ KQHSKLRQRL D SILNFSRL QPAYHIPARK SVPTDAYTPM VSYRKLKSKL KTTLLDFYDY LKLVSQYQHL NQQAFRKIVK KYDKTLHTDL QG FWVDYMS RYTFTDFSIT TNWQLHVEDI YARLFTNHNK KLALEHLKSF RQKEHFSANS MRFGLLFGAG LPLAIEAACY YNA TEQSSY LLQIWGGFFL VIFAFVLFDL DCYVWEKTRV NYMLIFEFNQ RKSLNWRQHL EIVGAVFFIF SLFFFLCMRN FFPG FTIYF PALFLGVVGT FLIAPVIVPY WRMRRYLIIQ LIRVFLSGLS TVHFQDFFFA DQMVSLTYAC GNISLFFCLY KRLWR QPQL CNSSHSPLLG FFTTLPGILR VFQCFRRYSD SLKSFPHLVN ALKYIFNILA QMFLSLWRIH PGLKYRVLYT IFAGVN SLF SYTWDILMDW NLLVRKDGRW QFREHRILKQ LWPYIIAMIL NFIVRSSFIF YCIFPNHIQH SSGISFFVTL AEIMRRC MW NILRVEHEEI YNRENLRAAR ELKPLDFVKP HSDVFVSHQI SSDKNYTDDE DSMDDQTDVD EAQFS

UniProtKB: Phosphate exporter spx2

-
Macromolecule #2: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 18 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

-
Macromolecule #3: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradeca...

MacromoleculeName: (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate
type: ligand / ID: 3 / Number of copies: 2 / Formula: 8PE
Molecular weightTheoretical: 691.959 Da
Chemical component information

ChemComp-8PE:
(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / phospholipid*YM

-
Macromolecule #4: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

-
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 210108
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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