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- PDB-9bir: Cryo-EM structure of the mammalian peptide transporter PepT2 boun... -

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Basic information

Entry
Database: PDB / ID: 9bir
TitleCryo-EM structure of the mammalian peptide transporter PepT2 bound to cefadroxil
Components
  • Solute carrier family 15 member 2
  • nanobody
KeywordsMEMBRANE PROTEIN / protein-coupled peptide transporter / peptide transport / antibiotics
Function / homology
Function and homology information


high-affinity oligopeptide transmembrane transporter activity / Proton/oligopeptide cotransporters / tripeptide import across plasma membrane / peptidoglycan transport / tripeptide transmembrane transporter activity / dipeptide transport / metanephric proximal tubule development / dipeptide import across plasma membrane / oligopeptide transport / peptide:proton symporter activity ...high-affinity oligopeptide transmembrane transporter activity / Proton/oligopeptide cotransporters / tripeptide import across plasma membrane / peptidoglycan transport / tripeptide transmembrane transporter activity / dipeptide transport / metanephric proximal tubule development / dipeptide import across plasma membrane / oligopeptide transport / peptide:proton symporter activity / dipeptide transmembrane transporter activity / antibacterial innate immune response / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / xenobiotic transport / renal absorption / phagocytic vesicle membrane / 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 / Alpha/beta knot methyltransferases / MFS transporter superfamily
Similarity search - Domain/homology
: / Solute carrier family 15 member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsParker, J.L. / Deme, J.C. / Lea, S.M. / Newstead, S.
Funding support United Kingdom, United States, 4items
OrganizationGrant numberCountry
Wellcome Trust215519 United Kingdom
Wellcome Trust219531 United Kingdom
Wellcome Trust218514 United Kingdom
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: To Be Published
Title: Structural basis for antibiotic transport and inhibition in the mammalian proton-coupled peptide transporter, PepT2
Authors: Parker, J.L. / Deme, J.C. / Lichtinger, S.M. / Kuteyi, G. / Biggin, P.C. / Lea, S.M. / Newstead, S.
History
DepositionApr 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Solute carrier family 15 member 2
B: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3353
Polymers96,9722
Non-polymers3631
Water00
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 2


Mass: 82477.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc15a2 / Production host: Homo sapiens (human) / References: UniProt: Q63424
#2: Antibody nanobody


Mass: 14494.183 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lama glama (llama)
#3: Chemical ChemComp-A1APP / Cefadroxil / (1S,2R,3R,6R,7R)-7-{[(2R)-2-amino-2-(4-hydroxyphenyl)acetyl]amino}-3-methyl-8-oxo-5-thia-1-azabicyclo[4.2.0]octane-2-carboxylic acid


Mass: 363.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3O5S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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
1Complex of the mammalian peptide transporter PepT2 with nanobody and bound cefadroxilCOMPLEX#1-#20MULTIPLE SOURCES
2PepT2COMPLEX#11RECOMBINANT
3nanobodyCOMPLEX#21NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Rattus norvegicus (Norway rat)10116
32Rattus norvegicus (Norway rat)10116
43Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 54.8 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93759 / Symmetry type: POINT

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