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- EMDB-24922: Cryo-EM structure of a mammalian peptide transporter (PepT1/slc15... -

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Basic information

Entry
Database: EMDB / ID: EMD-24922
TitleCryo-EM structure of a mammalian peptide transporter (PepT1/slc15a1) in nanodisc
Map dataCryo-EM map of horse PepT1 in nanodisc
Sample
  • Complex: PepT1 in MSP1D1 nanodisc
    • Protein or peptide: Solute carrier family 15 member 1
KeywordsPepT1 / SLC15 / ECD / transporter / nanodisc / TRANSPORT PROTEIN
Function / homology
Function and homology information


proton-dependent oligopeptide secondary active transmembrane transporter activity / tripeptide transmembrane transporter activity / dipeptide import across plasma membrane / peptide:proton symporter activity / dipeptide transmembrane transporter activity / brush border / protein transport / apical plasma 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 speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsShen J / Zhou M
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK122784 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM145416 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL086392 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098878 United States
Cancer Prevention and Research Institute of Texas (CPRIT)R1223 United States
National Science Foundation (NSF, United States)DMR-1420541 United States
CitationJournal: Structure / Year: 2022
Title: Extracellular domain of PepT1 interacts with TM1 to facilitate substrate transport.
Authors: Jiemin Shen / Miaohui Hu / Xiao Fan / Zhenning Ren / Corinne Portioli / Xiuwen Yan / Mingqiang Rong / Ming Zhou /
Abstract: Mammalian peptide transporters, PepT1 and PepT2, mediate uptake of small peptides and are essential for their absorption. PepT also mediates absorption of many drugs and prodrugs to enhance their ...Mammalian peptide transporters, PepT1 and PepT2, mediate uptake of small peptides and are essential for their absorption. PepT also mediates absorption of many drugs and prodrugs to enhance their bioavailability. PepT has twelve transmembrane (TM) helices that fold into an N-terminal domain (NTD, TM1-6) and a C-terminal domain (CTD, TM7-12) and has a large extracellular domain (ECD) between TM9-10. It is well recognized that peptide transport requires movements of the NTD and CTD, but the role of the ECD in PepT1 remains unclear. Here we report the structure of horse PepT1 encircled in lipid nanodiscs and captured in the inward-open apo conformation. The structure shows that the ECD bridges the NTD and CTD by interacting with TM1. Deletion of ECD or mutations to the ECD-TM1 interface impairs the transport activity. These results demonstrate an important role of ECD in PepT1 and enhance our understanding of the transport mechanism in PepT1.
History
DepositionSep 19, 2021-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24922.png

Downloads & links

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Map

FileDownload / File: emd_24922.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of horse PepT1 in nanodisc
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 200 pix.
= 222.8 Å		1.11 Å/pix.
x 200 pix.
= 222.8 Å		1.11 Å/pix.
x 200 pix.
= 222.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.114 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-2.6736183 - 2.9949765
Average (Standard dev.)-0.0025204455 (±0.056625314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 222.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : PepT1 in MSP1D1 nanodisc

EntireName: PepT1 in MSP1D1 nanodisc
Components
  • Complex: PepT1 in MSP1D1 nanodisc
    • Protein or peptide: Solute carrier family 15 member 1

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Supramolecule #1: PepT1 in MSP1D1 nanodisc

SupramoleculeName: PepT1 in MSP1D1 nanodisc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Equus caballus (horse)

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Equus caballus (horse)
Molecular weightTheoretical: 78.723992 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGMSRSQSCF GYPLSIFFIV VNEFCERFSY YGMRALLILY FTLFIGWDDN LSTAIYHTFV ALCYLTPILG ALIADSWLGK FKTIVSLSI VYTIGQVVLA VSSINDLTDG NRDGTPDSLP VHVALSMIGL ALIAFGTGGI KPCVSAFGGD QFEEGQEKQR N RFFSIFYL ...String:
MGMSRSQSCF GYPLSIFFIV VNEFCERFSY YGMRALLILY FTLFIGWDDN LSTAIYHTFV ALCYLTPILG ALIADSWLGK FKTIVSLSI VYTIGQVVLA VSSINDLTDG NRDGTPDSLP VHVALSMIGL ALIAFGTGGI KPCVSAFGGD QFEEGQEKQR N RFFSIFYL AINAGSLLST IITPILRVQQ CGIHSKQACY PLAFGVPAAL MAVSLIVFVI GSRMYKKFQP QGNIMAKVAK CI GFAITNR IRHRSNKFPK REHWLDWAKE KYDERLISQI KMVTRVMFLY IPLPMFWALF DQQGSRWTLQ ATTMNGQIGV IEI QPDQMQ TVNAILIVIM VPIMDAVVYP LIAKCGLNFT SLKKMTVGMF LASMAFVAAA IVQVEIDKTL PVFPNGHEVQ VKVL NIGNN SMNISFPGET MAVNQMSQTG DFMTFDVDKL SINISSTGSP VTPVTHNFEQ GHRHTILVWA PNHYRVIKDG LDRKP EKGQ NGIRFVNAFD KSFDVTMDGT VYVNVTSHSA SEYQFFPSGK KSFTINSTEI SQQCERNFTS PRLGFGSAYT YVMGRK ADG CPELSVFGDI PPNTVNMALQ IPQYFLLTCG EVVFSVTGLE FSYSQAPSNM KSVLQAGWLL TVAVGNIIVL IVAGAGQ FS KQWAEYILFA ALLLVVCVIF GIMAQFYTYV NPAEVEAKFD DDEKKKNPEK ENPYYTLDSV SQTRM

UniProtKB: Solute carrier family 15 member 1

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.9000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 315767
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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