9J98 | pdb_00009j98

Open structure of human XPR1

• PDB DOI: https://doi.org/10.2210/pdb9J98/pdb
• EM Map EMD-61255: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens, Aequorea victoria
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2024-08-22 Released: 2025-03-12 
• Deposition Author(s): Wang, Y., Wang, Y., Yang, H., Shen, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of phosphate export by human XPR1.

Wang, Y., Wang, Y., Yang, H., Li, A., Ma, D., Shen, H.

(2025) Cell Res 35: 313-316

• PubMed: 40016597 
• DOI: https://doi.org/10.1038/s41422-025-01081-z
• Primary Citation of Related Structures:  
  9J97, 9J98

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Organizational Affiliation: 
• Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
Zhejiang Key Laboratory of Structural Biology, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China. [e-mail].
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China. [e-mail].
Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 226.8 kDa 
• Atom Count: 6,752 
• Modeled Residue Count: 794 
• Deposited Residue Count: 1,938 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 53 member 1,Green fluorescent protein	A, B	969	Homo sapiens, Aequorea victoria This entity is chimeric	Mutation(s): 0  Gene Names: XPR1, SLC53A1, SYG1, X3, GFP Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBH6 (Homo sapiens) Explore Q9UBH6  Go to UniProtKB:  Q9UBH6
PHAROS:  Q9UBH6 GTEx:  ENSG00000143324

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8PE	C [auth A], E [auth B]	(2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate C37 H74 N O8 P RFJQNULIDFTTLL-PGUFJCEWSA-N
CLR	D [auth A], F [auth B]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Wang, Y., Wang, Y., Yang, H., Shen, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release
  
• Version 1.1: 2025-04-16
  Changes: Data collection, Database references
• Version 1.2: 2025-07-16
  Changes: Data collection