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- PDB-8p6a: cryo-EM structure of human SLC15A4 in outward-open state -

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Basic information

Entry
Database: PDB / ID: 8p6a
Titlecryo-EM structure of human SLC15A4 in outward-open state
ComponentsSolute carrier family 15 member 4
KeywordsMEMBRANE PROTEIN / transporter / lysosome
Function / homology
Function and homology information


L-histidine transmembrane transporter activity / histidine transport / mast cell homeostasis / L-histidine transmembrane export from vacuole / peptidoglycan transmembrane transporter activity / peptidoglycan transport / Proton/oligopeptide cotransporters / positive regulation of toll-like receptor 8 signaling pathway / regulation of isotype switching to IgG isotypes / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway ...L-histidine transmembrane transporter activity / histidine transport / mast cell homeostasis / L-histidine transmembrane export from vacuole / peptidoglycan transmembrane transporter activity / peptidoglycan transport / Proton/oligopeptide cotransporters / positive regulation of toll-like receptor 8 signaling pathway / regulation of isotype switching to IgG isotypes / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / dipeptide import across plasma membrane / positive regulation of toll-like receptor 7 signaling pathway / peptide:proton symporter activity / dipeptide transmembrane transporter activity / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / endolysosome membrane / positive regulation of innate immune response / specific granule membrane / monoatomic ion transport / protein transport / early endosome membrane / lysosomal membrane / innate immune response / Neutrophil degranulation / membrane / plasma membrane
Similarity search - Function
PTR2 family proton/oligopeptide symporters signature 2. / PTR2 family proton/oligopeptide symporter, conserved site / Proton-dependent oligopeptide transporter family / POT family / MFS transporter superfamily
Similarity search - Domain/homology
Solute carrier family 15 member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsParker, J.L. / Kato, T. / Newstead, S.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust215519/Z/19/Z United Kingdom
Wellcome Trust219531/Z/19/Z United Kingdom
CitationJournal: To be published
Title: cryo-EM structure of human SLC15A4 PHT1 in outward-open state
Authors: Parker, J.L. / Kato, T. / Newstead, S.
History
DepositionMay 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 15 member 4


Theoretical massNumber of molelcules
Total (without water)63,3271
Polymers63,3271
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Solute carrier family 15 member 4 / Peptide transporter 4 / Peptide/histidine transporter 1 / hPHT1


Mass: 63327.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC15A4, PHT1, PTR4, FP12591 / Production host: Homo sapiens (human) / References: UniProt: Q8N697

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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: SLC15A4 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 44.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
2EPUimage acquisition
7UCSF Chimeramodel fitting
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 694787 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 80.81 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0033420
ELECTRON MICROSCOPYf_angle_d0.64984648
ELECTRON MICROSCOPYf_chiral_restr0.041544
ELECTRON MICROSCOPYf_plane_restr0.0032567
ELECTRON MICROSCOPYf_dihedral_angle_d3.657457

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