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  PDBTMMemProtMDmpstruc


• 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)

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Experimental Data Snapshot

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

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 
• DOI: https://doi.org/10.1038/s41422-024-00951-2
• Primary Citation of Related Structures:  
  8XV2, 8XV5, 8XV9

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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.
School of Life Sciences, Peking University, Beijing, China.
Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Cryo-EM Platform, School of Life Sciences, Peking University, Beijing, China.
Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA. [e-mail].
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. [e-mail].
School of Life Sciences, Peking University, Beijing, China. [e-mail].
Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

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

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
UniProt Groups	P0ABE7Q9BZV2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VIB (Subject of Investigation/LOI)	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

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

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Dang, Y., Wang, G.P., Zhang, Z.

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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  

• 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