+Open data
-Basic information
Entry | Database: PDB / ID: 7zc2 | ||||||
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Title | Dipeptide and tripeptide Permease C (DtpC) | ||||||
Components | Amino acid/peptide transporter | ||||||
Keywords | TRANSPORT PROTEIN / Membrane protein / Peptide transporter / Proton coupled oligopeptide transporter / POT / MFS / DtpC. | ||||||
Function / homology | Function and homology information oligopeptide transport / peptide transmembrane transporter activity / membrane => GO:0016020 / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å | ||||||
Authors | Killer, M. / Finocchio, G. / Pardon, E. / Steyaert, J. / Loew, C. | ||||||
Funding support | 1items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Cryo-EM Structure of an Atypical Proton-Coupled Peptide Transporter: Di- and Tripeptide Permease C. Authors: Maxime Killer / Giada Finocchio / Haydyn D T Mertens / Dmitri I Svergun / Els Pardon / Jan Steyaert / Christian Löw / Abstract: Proton-coupled Oligopeptide Transporters (POTs) of the Major Facilitator Superfamily (MFS) mediate the uptake of short di- and tripeptides in all phyla of life. POTs are thought to constitute the ...Proton-coupled Oligopeptide Transporters (POTs) of the Major Facilitator Superfamily (MFS) mediate the uptake of short di- and tripeptides in all phyla of life. POTs are thought to constitute the most promiscuous class of MFS transporters, with the potential to transport more than 8400 unique substrates. Over the past two decades, transport assays and biophysical studies have shown that various orthologues and paralogues display differences in substrate selectivity. The genome codes for four different POTs, known as Di- and tripeptide permeases A-D (DtpA-D). DtpC was shown previously to favor positively charged peptides as substrates. In this study, we describe, how we determined the structure of the 53 kDa DtpC by cryogenic electron microscopy (cryo-EM), and provide structural insights into the ligand specificity of this atypical POT. We collected and analyzed data on the transporter fused to split superfolder GFP (split sfGFP), in complex with a 52 kDa Pro-macrobody and with a 13 kDa nanobody. The latter sample was more stable, rigid and a significant fraction dimeric, allowing us to reconstruct a 3D volume of DtpC at a resolution of 2.7 Å. This work provides a molecular explanation for the selectivity of DtpC, and highlights the value of small and rigid fiducial markers such as nanobodies for structure determination of low molecular weight integral membrane proteins lacking soluble domains. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zc2.cif.gz | 163.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zc2.ent.gz | 128.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zc2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zc2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7zc2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7zc2_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 7zc2_validation.cif.gz | 43.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/7zc2 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/7zc2 | HTTPS FTP |
-Related structure data
Related structure data | 14618MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 53090.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: dtpD_2, dtpC, dtpD_1, yjdL, AM464_14395, AT845_002896, AWP93_17895, BANRA_02817, BGZ_01664, BGZ_05066, BJI68_16865, BJJ90_24000, BO068_004094, BON64_05130, BON69_04615, BON71_15930, BON73_ ...Gene: dtpD_2, dtpC, dtpD_1, yjdL, AM464_14395, AT845_002896, AWP93_17895, BANRA_02817, BGZ_01664, BGZ_05066, BJI68_16865, BJJ90_24000, BO068_004094, BON64_05130, BON69_04615, BON71_15930, BON73_07300, BON74_00740, BON75_25330, BON77_18065, BON80_13570, BON89_26025, BON93_12630, BON97_19640, BvCmsF30A_02788, BvCmsHHP019_00793, BvCmsHHP056_00023, BvCmsKKP061_00271, C2U48_11920, C3F40_14675, C5N07_06940, C5Y87_09615, CA593_05175, CG831_003409, CIG67_08950, COD53_12960, CWS33_03315, D0X26_12710, D9D77_08965, DAH17_08915, DAH18_16490, DAH34_18055, DAH35_18055, DAH36_09805, DAH37_06440, DEN87_12425, DEO12_13910, DEO20_13520, DXT71_14295, DXT73_07155, E0I42_01290, E2119_15085, E2121_02870, E2122_03065, E2131_09650, E2135_09870, E4K51_08850, E5M02_11420, E5P26_01815, E5P27_12215, E5P28_03135, E5P29_19355, E5P31_11330, E5P32_03320, E5P33_11435, E5P35_07320, E5P36_20530, E5P40_16720, E5S34_00615, E5S35_05230, E5S36_08360, E5S37_06350, E5S42_15010, E5S43_14690, E5S45_06265, E5S51_06500, E5S54_12820, E5S57_19065, EC1094V2_4123, EC3234A_78c00250, EI021_09455, EIZ93_10840, EL79_4257, EL80_4164, ELT20_09370, ELT41_02450, ELV08_11600, ELY39_09460, ERS139208_00804, EYV17_05270, EYV18_19620, F2N31_14570, F9V24_13955, F9X20_06665, FDM60_18295, FOI11_014975, FOI11_20705, FQ007_15450, FQF29_19850, FV293_00630, G5632_13435, GF699_20045, GIB53_13155, GKF89_08690, GKG12_11445, GNZ05_19605, GP662_06300, GQF59_12650, GRW05_17855, GRW57_10485, GRW81_08175, H0O72_04690, HHH44_003360, HMV95_08810, HNC36_09415, HV109_21715, HVY77_23340, HX136_22920, I6H02_16470, IH768_20930, IH772_00050, J0541_004579, J4S20_000461, JFD_00784, JNP96_02330, NCTC10429_06294, NCTC11126_02220, NCTC11181_01802, NCTC13216_02261, NCTC8008_04125, NCTC9037_04624, NCTC9045_05367, NCTC9073_04059, PGD_03312, SAMEA3472067_03850, SAMEA3472080_00141, SAMEA3752557_02097, WP2S18E08_44130, WR15_07240 Production host: Escherichia coli (E. coli) / References: UniProt: W8TWZ0 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dipeptide and tripeptide permease C (DtpC) / Type: CELL / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 900 nm |
Image recording | Electron dose: 75 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 24333 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 6464070 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 878428 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.73 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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