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- EMDB-38692: Pyridoxamine-bound human SLC19A3 -

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Basic information

Entry
Database: EMDB / ID: EMD-38692
TitlePyridoxamine-bound human SLC19A3
Map data
Sample
  • Complex: human SLC19A3 in complex with pyridoxamine
    • Protein or peptide: Soluble cytochrome b562,Thiamine transporter 2
  • Ligand: 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL
KeywordsSLC19A3 / pyridoxamine / TRANSPORT PROTEIN
Function / homology
Function and homology information


pyridoxine transport / thiamine-containing compound metabolic process / Vitamin B1 (thiamin) metabolism / thiamine transmembrane transport / thiamine transport / thiamine transmembrane transporter activity / thiamine diphosphate biosynthetic process / transmembrane transport / electron transfer activity / periplasmic space ...pyridoxine transport / thiamine-containing compound metabolic process / Vitamin B1 (thiamin) metabolism / thiamine transmembrane transport / thiamine transport / thiamine transmembrane transporter activity / thiamine diphosphate biosynthetic process / transmembrane transport / electron transfer activity / periplasmic space / iron ion binding / heme binding / membrane / plasma membrane
Similarity search - Function
Thiamine transporter 2 / Reduced folate carrier / Reduced folate carrier / MFS transporter superfamily / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562
Similarity search - Domain/homology
Soluble cytochrome b562 / Thiamine transporter 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDang Y / Wang GP / Zhang Z
Funding support China, 2 items
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, 2024-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38692.png

Downloads & links

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Map

FileDownload / File: emd_38692.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.03303615 - 2.489759
Average (Standard dev.)0.0007832815 (±0.016213685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38692_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38692_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human SLC19A3 in complex with pyridoxamine

EntireName: human SLC19A3 in complex with pyridoxamine
Components
  • Complex: human SLC19A3 in complex with pyridoxamine
    • Protein or peptide: Soluble cytochrome b562,Thiamine transporter 2
  • Ligand: 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL

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Supramolecule #1: human SLC19A3 in complex with pyridoxamine

SupramoleculeName: human SLC19A3 in complex with pyridoxamine / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60 KDa

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Macromolecule #1: Soluble cytochrome b562,Thiamine transporter 2

MacromoleculeName: Soluble cytochrome b562,Thiamine transporter 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.910008 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LEVLFQGPSR ATADLEDNWE TLNDNLKVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDIL VGQIDDALK LANEGKVKEA QAAAEQLKTT RNAYIQKYLS WIYPTVILCL FGFFSMMRPS EPFLIPYLSG PDKNLTSAEI T NEIFPVWT ...String:
LEVLFQGPSR ATADLEDNWE TLNDNLKVIE KADNAAQVKD ALTKMRAAAL DAQKATPPKL EDKSPDSPEM KDFRHGFDIL VGQIDDALK LANEGKVKEA QAAAEQLKTT RNAYIQKYLS WIYPTVILCL FGFFSMMRPS EPFLIPYLSG PDKNLTSAEI T NEIFPVWT YSYLVLLLPV FVLTDYVRYK PVIILQGISF IITWLLLLFG QGVKTMQVVE FFYGMVTAAE VAYYAYIYSV VS PEHYQRV SGYCRSVTLA AYTAGSVLAQ LLVSLANMSY FYLNVISLAS VSVAFLFSLF LPMPKKSMFF HAKPSREIKK SSS VNPVLE ETHEGEAPGC EEQKPTSEIL STSGKLNKGQ LNSLKPSNVT VDVFVQWFQD LKECYSSKRL FYWSLWWAFA TAGF NQVLN YVQILWDYKA PSQDSSIYNG AVEAIATFGG AVAAFAVGYV KVNWDLLGEL ALVVFSVVNA GSLFLMHYTA NIWAC YAGY LIFKSSYMLL ITIAVFQIAV NLNVERYALV FGINTFIALV IQTIMTVIVV DQRGLNLPVS IQFLVYGSYF AVIAGI FLM RSMYITYSTK SQKDVQSPAP SENPDVSHPE EESNIIMSTK LSNS

UniProtKB: Soluble cytochrome b562, Thiamine transporter 2

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Macromolecule #2: 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL

MacromoleculeName: 4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL
type: ligand / ID: 2 / Number of copies: 1 / Formula: PXM
Molecular weightTheoretical: 168.193 Da
Chemical component information

ChemComp-PXM:
4-(AMINOMETHYL)-5-(HYDROXYMETHYL)-2-METHYLPYRIDIN-3-OL / Pyridoxamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 246167

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