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- EMDB-44601: Cryo-EM structure of the mammalian peptide transporter PepT2 boun... -
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Open data
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Basic information
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Title | Cryo-EM structure of the mammalian peptide transporter PepT2 bound to cloxacillin, pose 1 | |||||||||||||||
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![]() | protein-coupled peptide transporter / peptide transport / antibiotics / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() 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 | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
![]() | Parker JL / Deme JC / Lea SM / Newstead S | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural basis for antibiotic transport and inhibition in the mammalian proton-coupled peptide transporter, PepT2 Authors: Parker JL / Deme JC / Lichtinger SM / Kuteyi G / Biggin PC / Lea SM / Newstead S | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 307.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.8 KB 18.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.5 KB | Display | ![]() |
Images | ![]() | 117.8 KB | ||
Masks | ![]() | 325 MB | ![]() | |
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() ![]() | 293.1 MB 301.6 MB 301.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 942.4 KB | Display | ![]() |
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Full document | ![]() | 942 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9bitMC ![]() 9birC ![]() 9bisC ![]() 9biuC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.732 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: unsharpened map
File | emd_44601_additional_1.map | ||||||||||||
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-Half map: unsharpened map
File | emd_44601_half_map_1.map | ||||||||||||
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-Half map: unsharpened map
File | emd_44601_half_map_2.map | ||||||||||||
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Sample components
-Entire : Complex of the mammalian peptide transporter PepT2 with nanobody ...
Entire | Name: Complex of the mammalian peptide transporter PepT2 with nanobody and bound cloxacillin, pose 1 |
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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 and bound cloxacillin, pose 1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: PepT2
Supramolecule | Name: PepT2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: nanobody
Supramolecule | Name: nanobody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 82.477766 KDa |
Recombinant expression | Organism: ![]() |
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 UniProtKB: Solute carrier family 15 member 2 |
-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: ![]() ![]() |
Molecular weight | Theoretical: 14.494183 KDa |
Sequence | String: GPSQVQLVES GGGLVQPGGS LRLLCVASGR PFNDYDMGWF RQAPGKEREF VASISWSGRV TDYSDSMKGR CTVSRDNAKG TMFLQMSNL VPRDTAVYYC AAARRRWTFK ATNTEEFYET WGQGTQVTVS SA |
-Macromolecule #3: CLOXACILLIN
Macromolecule | Name: CLOXACILLIN / type: ligand / ID: 3 / Number of copies: 1 / Formula: CXN |
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Molecular weight | Theoretical: 435.881 Da |
Chemical component information | ![]() ChemComp-CXN: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 57.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |