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- PDB-7pmw: HsPepT1 bound to Ala-Phe in the outward facing occluded conformation -

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Basic information

Entry
Database: PDB / ID: 7pmw
TitleHsPepT1 bound to Ala-Phe in the outward facing occluded conformation
Components
  • ALA-PHE
  • Solute carrier family 15 member 1
KeywordsMEMBRANE PROTEIN / HsPepT1 / PepT1 / Peptide transporter
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 / brush border / monoatomic ion transport / protein 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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsKiller, M. / Wald, J. / Pieprzyk, J. / Marlovits, T.C. / Loew, C.
Funding support1items
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: Solute carrier family 15 member 1
B: ALA-PHE


Theoretical massNumber of molelcules
Total (without water)79,1092
Polymers79,1092
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area620 Å2
ΔGint-3 kcal/mol
Surface area32210 Å2
MethodPISA

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Components

#1: Protein Solute carrier family 15 member 1 / Intestinal H(+)/peptide cotransporter / Oligopeptide transporter / small intestine isoform / ...Intestinal H(+)/peptide cotransporter / Oligopeptide transporter / small intestine isoform / Peptide transporter 1 / HsPepT1


Mass: 78872.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HsPepT1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SLC15A1, PEPT1 / Production host: Homo sapiens (human) / References: UniProt: P46059
#2: Protein/peptide ALA-PHE


Mass: 236.267 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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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

Component
IDNameTypeEntity IDParent-IDSource
1Human PepT1COMPLEX#10RECOMBINANT
2ALA-PHECOMPLEX#21RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: PROPANE / Humidity: 100 % / Chamber temperature: 278 K

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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 FIELDBright-field microscopy
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: cryoSPARC / Version: 3 / Category: final Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 107791 / Symmetry type: POINT

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