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- PDB-8xv5: Pyridoxamine-bound human SLC19A3 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8xv5
TitlePyridoxamine-bound human SLC19A3
ComponentsSoluble cytochrome b562,Thiamine transporter 2
KeywordsTRANSPORT PROTEIN / SLC19A3 / pyridoxamine
Function / homology
Function and homology information


pyridoxine transport / thiamine-containing compound metabolic process / Vitamin B1 (thiamin) metabolism / thiamine transmembrane transport / thiamine transmembrane transporter activity / thiamine transport / thiamine diphosphate biosynthetic process / electron transport chain / transmembrane transport / periplasmic space ...pyridoxine transport / thiamine-containing compound metabolic process / Vitamin B1 (thiamin) metabolism / thiamine transmembrane transport / thiamine transmembrane transporter activity / thiamine transport / thiamine diphosphate biosynthetic process / electron transport chain / transmembrane transport / periplasmic space / electron transfer activity / iron ion binding / heme binding / membrane / plasma membrane
Similarity search - Function
Thiamine transporter 2 / Reduced folate carrier / Reduced folate carrier / Cytochrome b562 / Cytochrome b562 / MFS transporter superfamily / Cytochrome c/b562
Similarity search - Domain/homology
Chem-PXM / Soluble cytochrome b562 / Thiamine transporter 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDang, Y. / Wang, G.P. / Zhang, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171201 China
Ministry of Science and Technology (MoST, China)2021YFA1302300 China
CitationJournal: Cell Res / Year: 2024
Title: Substrate and drug recognition mechanisms of SLC19A3.
Authors: Yu Dang / Tianyi Zhang / Shabareesh Pidathala / Guopeng Wang / Yijie Wang / Nanhao Chen / Chen Song / Chia-Hsueh Lee / Zhe Zhang /
History
DepositionJan 14, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble cytochrome b562,Thiamine transporter 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0782
Polymers67,9101
Non-polymers1681
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Soluble cytochrome b562,Thiamine transporter 2 / Cytochrome b-562 / ThTr-2 / ThTr2 / Solute carrier family 19 member 3


Mass: 67910.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: cybC, SLC19A3 / Production host: Homo sapiens (human) / References: UniProt: P0ABE7, UniProt: Q9BZV2
#2: Chemical ChemComp-PXM / 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL / PYRIDOXAMINE


Mass: 168.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: human SLC19A3 in complex with pyridoxamine / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.06 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.12_2829: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 246167 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0053218
ELECTRON MICROSCOPYf_angle_d0.8774396
ELECTRON MICROSCOPYf_dihedral_angle_d6.3931819
ELECTRON MICROSCOPYf_chiral_restr0.053502
ELECTRON MICROSCOPYf_plane_restr0.008527

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