9W1B | pdb_00009w1b

Cryo-EM structure of a Fungal XPR1 with InsP6

PDB DOI: https://doi.org/10.2210/pdb9W1B/pdb
EM Map EMD-65525: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Schizosaccharomyces pombe 972h-
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-07-25 Released: 2026-03-18
Deposition Author(s): Shen, H.Z., Yang, H., Wang, Y.C.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural insights into the gating mechanism of a fission yeast phosphate exporter SpXpr1

Shen, H.Z., Yang, H., Wang, Y.C.

To be published.

Macromolecule Content

Total Structure Weight: 184.1 kDa
Atom Count: 10,194
Modeled Residue Count: 1,144
Deposited Residue Count: 1,414
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SYG1 homolog	A, B [auth E]	707	Schizosaccharomyces pombe 972h-	Mutation(s): 0 Gene Names: SPCC1827.07c, SPCP1E11.01c
UniProt
Find proteins for Q9UU86 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9UU86 Go to UniProtKB: Q9UU86
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UU86
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
POV Query on POV Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain CA [auth E] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain P [auth A] SDF format, chain S [auth E] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain Z [auth E] SDF format, chain C [auth A] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain C [auth A] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain C [auth A]	AA [auth E] BA [auth E] C [auth A] CA [auth E] D [auth A] AA [auth E], BA [auth E], C [auth A], CA [auth E], D [auth A], E [auth A], F [auth A], H [auth A], I [auth A], J [auth A], K [auth A], P [auth A], S [auth E], U [auth E], V [auth E], W [auth E], X [auth E], Z [auth E]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C₄₂ H₈₂ N O₈ P WTJKGGKOPKCXLL-PFDVCBLKSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain C [auth A] Focus chain CA [auth E] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth A] Focus chain S [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain C [auth A] Focus chain CA [auth E] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth A] Focus chain S [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Focus chain Z [auth E]
8PE Query on 8PE Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain Y [auth E] MOL2 format, chain G [auth A] MOL2 format, chain Y [auth E] mmCIF format, chain G [auth A] mmCIF format, chain Y [auth E]	G [auth A], Y [auth E]	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate C₃₇ H₇₄ N O₈ P RFJQNULIDFTTLL-PGUFJCEWSA-N		Interactions Focus chain G [auth A] Focus chain Y [auth E] Interactions & Density Focus chain G [auth A] Focus chain Y [auth E]
IHP (Subject of Investigation/LOI) Query on IHP Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth E] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth E] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth E]	L [auth A], Q [auth A], R [auth A], T [auth E]	INOSITOL HEXAKISPHOSPHATE C₆ H₁₈ O₂₄ P₆ IMQLKJBTEOYOSI-GPIVLXJGSA-N		Interactions Focus chain L [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth E] Interactions & Density Focus chain L [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth E]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	DA [auth E] EA [auth E] FA [auth E] M [auth A] N [auth A] DA [auth E], EA [auth E], FA [auth E], M [auth A], N [auth A], O [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]