8XSN | pdb_00008xsn

transporter

PDB DOI: https://doi.org/10.2210/pdb8XSN/pdb
EM Map EMD-38623: EMDB EMDataResource

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

Deposited: 2024-01-09 Released: 2025-07-16
Deposition Author(s): Jiang, D.H., Wang, K.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8XSN

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

Literature

Structure of transporter

Jiang, D.H., Wang, K.

To be published.

Macromolecule Content

Total Structure Weight: 51.21 kDa
Atom Count: 2,703
Modeled Residue Count: 357
Deposited Residue Count: 469
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 52, riboflavin transporter, member 3	A	469	Homo sapiens	Mutation(s): 0 Gene Names: SLC52A3, C20orf54, RFT2, RFVT3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQ40 (Homo sapiens) Explore Q9NQ40 Go to UniProtKB: Q9NQ40
PHAROS: Q9NQ40 GTEx: ENSG00000101276
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NQ40
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RBF (Subject of Investigation/LOI) Query on RBF Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RIBOFLAVIN C₁₇ H₂₀ N₄ O₆ AUNGANRZJHBGPY-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.29 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31971134

Revision History (Full details and data files)

Version 1.0: 2025-07-16
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.