8JF0

Human sodium-dependent vitamin C transporter 1 in an intermediate state

PDB DOI: https://doi.org/10.2210/pdb8JF0/pdb
EM Map EMD-36205: EMDB EMDataResource

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

Deposited: 2023-05-16 Released: 2024-05-22
Deposition Author(s): Kobayashi, T.A., Kusakizako, T., Nureki, O.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 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

Cryo-EM structures of human sodium-dependent vitamin C transporter 1

Kobayashi, T.A., Kusakizako, T., Nureki, O.

To be published.

Macromolecule Content

Total Structure Weight: 64.86 kDa
Atom Count: 3,289
Modelled Residue Count: 436
Deposited Residue Count: 598
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 23 member 1	A	598	Homo sapiens	Mutation(s): 0 Gene Names: SLC23A1, SVCT1, YSPL3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHI7 (Homo sapiens) Explore Q9UHI7 Go to UniProtKB: Q9UHI7
PHAROS: Q9UHI7 GTEx: ENSG00000170482
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UHI7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1.1
MODEL REFINEMENT	Servalcat	0.2.115

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-05-22

Deposition Author(s):

Kobayashi, T.A.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History (Full details and data files)

Version 1.0: 2024-05-22
Type: Initial release

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 R01GM133198.