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- EMDB-16758: PHT1 in the outward facing conformation, bound to Sb27 -

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Basic information

Entry
Database: EMDB / ID: EMD-16758
TitlePHT1 in the outward facing conformation, bound to Sb27
Map dataMap sharpened in cryoSPARC. Used for final model refinement.
Sample
  • Complex: PHT1-Sb27
    • Complex: Solute carrier family 15 member 4
      • Protein or peptide: Solute carrier family 15 member 4
    • Complex: Sybody 27
      • Protein or peptide: Sybody 27
KeywordsPHT1 / Peptide transporter / Histidine transporter / Sybody 27 / SLE / SLC15A4 / MEMBRANE PROTEIN
Function / homology:
Function and homology information
Biological speciesHomo sapiens (human) / Escherichia coli (E. coli) / Gallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsCustodio T / Killer M / Loew C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2023
Title: Molecular basis of TASL recruitment by the peptide/histidine transporter 1, PHT1.
Authors: Tânia F Custódio / Maxime Killer / Dingquan Yu / Virginia Puente / Daniel P Teufel / Alexander Pautsch / Gisela Schnapp / Marc Grundl / Jan Kosinski / Christian Löw /
Abstract: PHT1 is a histidine /oligopeptide transporter with an essential role in Toll-like receptor innate immune responses. It can act as a receptor by recruiting the adaptor protein TASL which leads to type ...PHT1 is a histidine /oligopeptide transporter with an essential role in Toll-like receptor innate immune responses. It can act as a receptor by recruiting the adaptor protein TASL which leads to type I interferon production via IRF5. Persistent stimulation of this signalling pathway is known to be involved in the pathogenesis of systemic lupus erythematosus (SLE). Understanding how PHT1 recruits TASL at the molecular level, is therefore clinically important for the development of therapeutics against SLE and other autoimmune diseases. Here we present the Cryo-EM structure of PHT1 stabilized in the outward-open conformation. By combining biochemical and structural modeling techniques we propose a model of the PHT1-TASL complex, in which the first 16 N-terminal TASL residues fold into a helical structure that bind in the central cavity of the inward-open conformation of PHT1. This work provides critical insights into the molecular basis of PHT1/TASL mediated type I interferon production.
History
DepositionFeb 23, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16758.png

Downloads & links

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Map

FileDownload / File: emd_16758.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap sharpened in cryoSPARC. Used for final model refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.86931455 - 1.2928109
Average (Standard dev.)0.0010519194 (±0.027611876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16758_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Map post processed with DeepEMhancer. Tight Target model....

Fileemd_16758_additional_1.map
AnnotationMap post processed with DeepEMhancer. Tight Target model. Used for display and initial docking of sybody 27 only.
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened full map. Final Non Uniform Refinement in cryoSPARC.

Fileemd_16758_additional_2.map
AnnotationUnsharpened full map. Final Non Uniform Refinement in cryoSPARC.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_16758_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_16758_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : PHT1-Sb27

EntireName: PHT1-Sb27
Components
  • Complex: PHT1-Sb27
    • Complex: Solute carrier family 15 member 4
      • Protein or peptide: Solute carrier family 15 member 4
    • Complex: Sybody 27
      • Protein or peptide: Sybody 27

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Supramolecule #1: PHT1-Sb27

SupramoleculeName: PHT1-Sb27 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Solute carrier family 15 member 4

SupramoleculeName: Solute carrier family 15 member 4 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Sybody 27

SupramoleculeName: Sybody 27 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Solute carrier family 15 member 4

MacromoleculeName: Solute carrier family 15 member 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 63.566996 KDa
Recombinant expressionOrganism: Homo sapiens subsp. 'Denisova' (Denisova hominin)
SequenceString: MEEAEQSERS PLLGSGERGR AAIGAFHGRR LACAAVLLAE LLERVAFYGI TSNLVLFLNG PPYDWEGAQA SQALLLFMGI TYLVSPFGG WLADALLGKF GTILLSMALY LLGMLAFPVI AAPHTRQGLC GDIPLYPVEN CSSPATNATL APCSQVGTTR Y CAAATFVG ...String:
MEEAEQSERS PLLGSGERGR AAIGAFHGRR LACAAVLLAE LLERVAFYGI TSNLVLFLNG PPYDWEGAQA SQALLLFMGI TYLVSPFGG WLADALLGKF GTILLSMALY LLGMLAFPVI AAPHTRQGLC GDIPLYPVEN CSSPATNATL APCSQVGTTR Y CAAATFVG LVLVGLGVGS VKANITPFGA DQVKDRGPEA TRRFFNWFYW SINLGAILSL GGIAYIQQNV SFVIGYSIPA IC IGISFMV FLCGQSFFIT KPPDGSAFTD MFKILAYSCC SRKRHMEHST NSEGQGVLQQ PRKQSLFEMA KLSRGGPFRE DKV EDVKAL VKIIPVFLAL IPYWTVYFQM QTTYVLQSLH LKIPEIANDT NSVHTFPAAW LTMFDAVLIL ILIPLKDKLV DPVL KRNGL LPSSLKRIAV GMFFVMCSAF AAGILESNRL KIVKVKTINQ TIGNVTYHAA DMPIWWQIPQ YVLIGFSEIF ASIAG LEFA YSAAPKSMQS AIMGLFFFFS GIGSFVGSGL LALVSIKEIG WMSNHTDFGN INGCQLNYYF FLLAAIQGAT LLLFLI VSV KYDHQKSKMN DVAANGRI

UniProtKB: UNIPROTKB: F1NG54

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Macromolecule #2: Sybody 27

MacromoleculeName: Sybody 27 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.504001 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLVESGGG SVQAGGSLRL SCAASGDIET IWYLGWFRQA PGKEREGVAA LSTVTGSTYY ADSVKGRFTV SLDNAKNTVY LQMNSLKPE DTALYYCAAA YTGWMAPLWQ WVYSYWGQGT QVTVS

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 75.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1328233
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: experimental model
Output model

PDB-8cni:
PHT1 in the outward facing conformation, bound to Sb27

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