+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12528 | ||||||||||||||||||||||||||||||||||||
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Title | Cryo-EM structure of the mammalian peptide transporter PepT2 | ||||||||||||||||||||||||||||||||||||
Map data | cryoSPARC local refinement, sharpened | ||||||||||||||||||||||||||||||||||||
Sample |
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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 / peptide transport / renal absorption / phagocytic vesicle membrane / protein transport / apical plasma membrane / membrane / plasma membrane Similarity search - Function | ||||||||||||||||||||||||||||||||||||
Biological species | Rattus norvegicus (Norway rat) / Lama glama (llama) | ||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||||||||||||||||||||||||||||||||
Authors | Parker JL / Deme JC / Lea SM / Newstead S | ||||||||||||||||||||||||||||||||||||
Funding support | United Kingdom, 11 items
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Citation | Journal: Sci Adv / Year: 2021 Title: Cryo-EM structure of PepT2 reveals structural basis for proton-coupled peptide and prodrug transport in mammals. Authors: Joanne L Parker / Justin C Deme / Zhiyi Wu / Gabriel Kuteyi / Jiandong Huo / Raymond J Owens / Philip C Biggin / Susan M Lea / Simon Newstead / Abstract: The SLC15 family of proton-coupled solute carriers PepT1 and PepT2 play a central role in human physiology as the principal route for acquiring and retaining dietary nitrogen. A remarkable feature of ...The SLC15 family of proton-coupled solute carriers PepT1 and PepT2 play a central role in human physiology as the principal route for acquiring and retaining dietary nitrogen. A remarkable feature of the SLC15 family is their extreme substrate promiscuity, which has enabled the targeting of these transporters for the improvement of oral bioavailability for several prodrug molecules. Although recent structural and biochemical studies on bacterial homologs have identified conserved sites of proton and peptide binding, the mechanism of peptide capture and ligand promiscuity remains unclear for mammalian family members. Here, we present the cryo-electron microscopy structure of the outward open conformation of the rat peptide transporter PepT2 in complex with an inhibitory nanobody. Our structure, combined with molecular dynamics simulations and biochemical and cell-based assays, establishes a framework for understanding peptide and prodrug recognition within this pharmaceutically important transporter family. | ||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12528.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-12528-v30.xml emd-12528.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12528_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_12528.png | 131.3 KB | ||
Masks | emd_12528_msk_1.map | 125 MB | Mask map | |
Others | emd_12528_additional_1.map.gz emd_12528_half_map_1.map.gz emd_12528_half_map_2.map.gz | 61.8 MB 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12528 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12528 | HTTPS FTP |
-Validation report
Summary document | emd_12528_validation.pdf.gz | 640.4 KB | Display | EMDB validaton report |
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Full document | emd_12528_full_validation.pdf.gz | 639.9 KB | Display | |
Data in XML | emd_12528_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | emd_12528_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12528 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12528 | HTTPS FTP |
-Related structure data
Related structure data | 7nqkMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12528.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryoSPARC local refinement, sharpened | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12528_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: cryoSPARC local refinement, unsharpened
File | emd_12528_additional_1.map | ||||||||||||
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Annotation | cryoSPARC local refinement, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_12528_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_12528_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of the mammalian peptide transporter PepT2 with nanobody
Entire | Name: Complex of the mammalian peptide transporter PepT2 with nanobody |
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Components |
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-Supramolecule #1: Complex of the mammalian peptide transporter PepT2 with nanobody
Supramolecule | Name: Complex of the mammalian peptide transporter PepT2 with nanobody type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: PepT2
Supramolecule | Name: PepT2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Homo sapiens (human) |
-Supramolecule #3: nanobody
Supramolecule | Name: nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Lama glama (llama) |
-Macromolecule #1: Solute carrier family 15 member 2
Macromolecule | Name: Solute carrier family 15 member 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 82.477766 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MNPFQKNESK ETLFSPVSTE EMLPRPPSPP KKSPPKIFGS SYPVSIAFIV VNEFCERFSY YGMKAVLTLY FLYFLHWNED TSTSVYHAF SSLCYFTPIL GAAIADSWLG KFKTIIYLSL VYVLGHVFKS LGAIPILGGK MLHTILSLVG LSLIALGTGG I KPCVAAFG ...String: MNPFQKNESK ETLFSPVSTE EMLPRPPSPP KKSPPKIFGS SYPVSIAFIV VNEFCERFSY YGMKAVLTLY FLYFLHWNED TSTSVYHAF SSLCYFTPIL GAAIADSWLG KFKTIIYLSL VYVLGHVFKS LGAIPILGGK MLHTILSLVG LSLIALGTGG I KPCVAAFG GDQFEEEHAE ARTRYFSVFY LAINAGSLIS TFITPMLRGD VKCFGQDCYA LAFGVPGLLM VLALVVFAMG SK MYRKPPP EGNIVAQVIK CIWFALCNRF RNRSGDLPKR QHWLDWAAEK YPKHLIADVK ALTRVLFLYI PLPMFWALLD QQG SRWTLQ ANKMNGDLGF FVLQPDQMQV LNPFLVLIFI PLFDLVIYRL ISKCRINFSS LRKMAVGMIL ACLAFAVAAL VETK INGMI HPQPASQEIF LQVLNLADGD VKVTVLGSRN NSLLVESVSS FQNTTHYSKL HLEAKSQDLH FHLKYNSLSV HNDHS VEEK NCYQLLIHQD GESISSMLVK DTGIKPANGM AAIRFINTLH KDLNISLDTD APLSVGKDYG VSAYRTVLRG KYPAVH CET EDKVFSLDLG QLDFGTTYLF VITNITSQGL QAWKAEDIPV NKLSIAWQLP QYVLVTAAEV MFSVTGLEFS YSQAPSS MK SVLQAAWLLT VAVGNIIVLV VAQFSGLAQW AEFVLFSCLL LVVCLIFSVM AYYYVPLKSE DTREATDKQI PAVQGNMI N LETKNTRLVE GENLYFQ |
-Macromolecule #2: nanobody
Macromolecule | Name: nanobody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 14.494183 KDa |
Sequence | String: GPSQVQLVES GGGLVQPGGS LRLLCVASGR PFNDYDMGWF RQAPGKEREF VASISWSGRV TDYSDSMKGR CTVSRDNAKG TMFLQMSNL VPRDTAVYYC AAARRRWTFK ATNTEEFYET WGQGTQVTVS SA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |