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

Validation slider image for 9W1B

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 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 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 P [auth A] SDF format, chain D [auth A] 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 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 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 P [auth A] MOL2 format, chain D [auth A] 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 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 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 P [auth A] mmCIF format, chain D [auth A] 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 N [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [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]

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-03-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2024YFA0916903

Revision History (Full details and data files)

Version 1.0: 2026-03-18
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.