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- EMDB-13543: HsPepT1 bound to Ala-Phe in the outward facing open conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-13543
TitleHsPepT1 bound to Ala-Phe in the outward facing open conformation
Map datapost processed map in Phenix used for refinement
Sample
  • Complex: Human PepT1
    • Complex: ALA-PHE
      • Protein or peptide: ALA-PHE
    • Protein or peptide: Solute carrier family 15 member 1
KeywordsHsPepT1 / PepT1 / Peptide transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


proton-dependent oligopeptide secondary active transmembrane transporter activity / tripeptide import across plasma membrane / Proton/oligopeptide cotransporters / tripeptide transmembrane transporter activity / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / peptide transport / brush border / monoatomic ion transport ...proton-dependent oligopeptide secondary active transmembrane transporter activity / tripeptide import across plasma membrane / Proton/oligopeptide cotransporters / tripeptide transmembrane transporter activity / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / peptide transport / brush border / monoatomic ion transport / protein transport / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
Oligopeptide transporter / PTR2 family proton/oligopeptide symporters signature 1. / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKiller M / Wald J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2021
Title: Structural snapshots of human PepT1 and PepT2 reveal mechanistic insights into substrate and drug transport across epithelial membranes.
Authors: Maxime Killer / Jiri Wald / Joanna Pieprzyk / Thomas C Marlovits / Christian Löw /
Abstract: The uptake of peptides in mammals plays a crucial role in nutrition and inflammatory diseases. This process is mediated by promiscuous transporters of the solute carrier family 15, which form part of ...The uptake of peptides in mammals plays a crucial role in nutrition and inflammatory diseases. This process is mediated by promiscuous transporters of the solute carrier family 15, which form part of the major facilitator superfamily. Besides the uptake of short peptides, peptide transporter 1 (PepT1) is a highly abundant drug transporter in the intestine and represents a major route for oral drug delivery. PepT2 also allows renal drug reabsorption from ultrafiltration and brain-to-blood efflux of neurotoxic compounds. Here, we present cryogenic electron microscopy (cryo-EM) structures of human PepT1 and PepT2 captured in four different states throughout the transport cycle. The structures reveal the architecture of human peptide transporters and provide mechanistic insights into substrate recognition and conformational transitions during transport. This may support future drug design efforts to increase the bioavailability of different drugs in the human body.
History
DepositionSep 3, 2021-
Header (metadata) releaseOct 20, 2021-
Map releaseOct 20, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pmx
  • Surface level: 6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13543.png

Downloads & links

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Map

FileDownload / File: emd_13543.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost processed map in Phenix used for refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.67 Å/pix.
x 300 pix.
= 201. Å		0.67 Å/pix.
x 300 pix.
= 201. Å		0.67 Å/pix.
x 300 pix.
= 201. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-15.952111 - 30.78388
Average (Standard dev.)0.000000000003542 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 201.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.670.670.67
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z201.000201.000201.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-15.95230.7840.000

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Supplemental data

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Mask #1

Fileemd_13543_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: post processed map in deepEMhancer used for illustration...

Fileemd_13543_additional_1.map
Annotationpost processed map in deepEMhancer used for illustration only (tightTarget model)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_13543_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_13543_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 PepT1

EntireName: Human PepT1
Components
  • Complex: Human PepT1
    • Complex: ALA-PHE
      • Protein or peptide: ALA-PHE
    • Protein or peptide: Solute carrier family 15 member 1

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Supramolecule #1: Human PepT1

SupramoleculeName: Human PepT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: ALA-PHE

SupramoleculeName: ALA-PHE / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Solute carrier family 15 member 1

MacromoleculeName: Solute carrier family 15 member 1 / type: protein_or_peptide / ID: 1 / Details: HsPepT1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 78.872422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGMSKSHSFF GYPLSIFFIV VNEFCERFSY YGMRAILILY FTNFISWDDN LSTAIYHTFV ALCYLTPILG ALIADSWLGK FKTIVSLSI VYTIGQAVTS VSSINDLTDH NHDGTPDSLP VHVVLSLIGL ALIALGTGGI KPCVSAFGGD QFEEGQEKQR N RFFSIFYL ...String:
MGMSKSHSFF GYPLSIFFIV VNEFCERFSY YGMRAILILY FTNFISWDDN LSTAIYHTFV ALCYLTPILG ALIADSWLGK FKTIVSLSI VYTIGQAVTS VSSINDLTDH NHDGTPDSLP VHVVLSLIGL ALIALGTGGI KPCVSAFGGD QFEEGQEKQR N RFFSIFYL AINAGSLLST IITPMLRVQQ CGIHSKQACY PLAFGVPAAL MAVALIVFVL GSGMYKKFKP QGNIMGKVAK CI GFAIKNR FRHRSKAFPK REHWLDWAKE KYDERLISQI KMVTRVMFLY IPLPMFWALF DQQGSRWTLQ ATTMSGKIGA LEI QPDQMQ TVNAILIVIM VPIFDAVLYP LIAKCGFNFT SLKKMAVGMV LASMAFVVAA IVQVEIDKTL PVFPKGNEVQ IKVL NIGNN TMNISLPGEM VTLGPMSQTN AFMTFDVNKL TRINISSPGS PVTAVTDDFK QGQRHTLLVW APNHYQVVKD GLNQK PEKG ENGIRFVNTF NELITITMSG KVYANISSYN ASTYQFFPSG IKGFTISSTE IPPQCQPNFN TFYLEFGSAY TYIVQR KND SCPEVKVFED ISANTVNMAL QIPQYFLLTC GEVVFSVTGL EFSYSQAPSN MKSVLQAGWL LTVAVGNIIV LIVAGAG QF SKQWAEYILF AALLLVVCVI FAIMARFYTY INPAEIEAQF DEDEKKNRLE KSNPYFMSGA NSQKQM

UniProtKB: Solute carrier family 15 member 1

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Macromolecule #2: ALA-PHE

MacromoleculeName: ALA-PHE / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 236.267 Da
SequenceString:
AF

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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

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: PROPANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 466042
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3)
FSC plot (resolution estimation)

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