8XV2 | pdb_00008xv2

Thiamine-bound human SLC19A3

PDB DOI: https://doi.org/10.2210/pdb8XV2/pdb
EM Map EMD-38691: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Escherichia coli, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2024-01-14 Released: 2024-03-27
Deposition Author(s): Dang, Y., Wang, G.P., Zhang, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8XV2

This is version 1.2 of the entry. See complete history.

Literature

Substrate and drug recognition mechanisms of SLC19A3.

Dang, Y., Zhang, T., Pidathala, S., Wang, G., Wang, Y., Chen, N., Song, C., Lee, C.H., Zhang, Z.

(2024) Cell Res 34: 458-461

PubMed: 38503960 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-024-00951-2
Primary Citation Related Structures:
8XV2, 8XV5, 8XV9

Organizational Affiliation

State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

Macromolecule Content

Total Structure Weight: 68.18 kDa
Atom Count: 3,128
Modeled Residue Count: 388
Deposited Residue Count: 607
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,Thiamine transporter 2	A	607	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: cybC, SLC19A3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Find proteins for Q9BZV2 (Homo sapiens) Explore Q9BZV2 Go to UniProtKB: Q9BZV2
PHAROS: Q9BZV2 GTEx: ENSG00000135917
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P0ABE7 Q9BZV2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VIB (Subject of Investigation/LOI) Query on VIB 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]	3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM C₁₂ H₁₇ N₄ O S JZRWCGZRTZMZEH-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.12_2829:

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171201
Ministry of Science and Technology (MoST, China)	China	2021YFA1302300

Revision History (Full details and data files)

Version 1.0: 2024-03-27
Type: Initial release
Version 1.1: 2024-04-03
Changes: Database references
Version 1.2: 2024-06-12
Changes: Database references

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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.