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- PDB-7q0m: Crystal structure of the peptide transporter YePEPT-K314A in comp... -

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Basic information

Entry
Database: PDB / ID: 7q0m
TitleCrystal structure of the peptide transporter YePEPT-K314A in complex with LZNV at 2.66 A
ComponentsPeptide transporter YePEPT
KeywordsMEMBRANE PROTEIN / MFS / peptide transporter / solute transporter / Inhibitor bound / LZNV / PEPT1
Function / homology
Function and homology information


oligopeptide transport / peptide transmembrane transporter activity / protein transport / plasma membrane
Similarity search - Function
: / Dipeptide/tripeptide permease / 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 / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Chem-OPK / Peptide transporter YePEPT
Similarity search - Component
Biological speciesYersinia enterocolitica subsp. palearctica YE-P4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsJeckelmann, J.M. / Stauffer, M. / Ilgue, H. / Fotiadis, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_184980 Switzerland
CitationJournal: Commun Chem / Year: 2022
Title: Peptide transporter structure reveals binding and action mechanism of a potent PEPT1 and PEPT2 inhibitor.
Authors: Stauffer, M. / Jeckelmann, J.M. / Ilgu, H. / Ucurum, Z. / Boggavarapu, R. / Fotiadis, D.
History
DepositionOct 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide transporter YePEPT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3733
Polymers56,4521
Non-polymers9212
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-6 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.398, 100.372, 103.084
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptide transporter YePEPT


Mass: 56451.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica subsp. palearctica YE-P4 (bacteria)
Gene: YEP4_02370 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R9TD79
#2: Chemical ChemComp-OPK / (2~{S})-2-[[(2~{S})-2-azanyl-6-[(4-nitrophenyl)methoxycarbonylamino]hexanoyl]amino]-3-methyl-butanoic acid


Mass: 424.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N4O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9.25 / Details: PEG 300, glycine, LZNV

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.54→45.85 Å / Num. obs: 24643 / % possible obs: 95.1 % / Redundancy: 10.9 % / CC1/2: 0.998 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
2.54-2.6611.51.211580.543179.3
2.657-2.74811.71.3711410.579181.9

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.1data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Q0L

7q0l


Resolution: 2.54→24.96 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2914 1223 4.97 %
Rwork0.2671 23379 -
obs0.2683 24602 79.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 232.9 Å2 / Biso mean: 96.0658 Å2 / Biso min: 44.9 Å2
Refinement stepCycle: final / Resolution: 2.54→24.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 135 0 3827
Biso mean--126.57 --
Num. residues----482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.54-2.640.3402490.3291951100030
2.64-2.760.3684780.32781434151245
2.76-2.910.3515970.33221897199460
2.91-3.090.3561420.3152652279482
3.09-3.330.31061660.30243215338199
3.33-3.660.29671720.265732463418100
3.66-4.190.26721680.256432623430100
4.19-5.270.29131720.259832993471100
5.27-24.960.28181790.257534233602100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9375-0.3157-0.76813.257-1.10064.53410.0846-0.12620.11950.04030.035-0.1776-0.06710.4911-0.11910.3075-0.0251-0.00660.4141-0.06360.3105-7.1642-0.480630.673
26.73790.4332-0.62274.902-0.76843.3728-0.2384-0.53640.1295-0.0281-0.43010.09020.6515-0.49890.62890.47540.01170.08410.4581-0.1410.377-16.5836-6.042337.9006
34.99271.67173.64046.90651.66525.57770.1983-0.72060.09550.8391-0.0653-0.46360.15570.04380.24630.6810.08240.08240.7323-0.14550.5342-6.63775.048841.742
42.3050.0673-0.01777.205-3.66363.65560.11740.12010.612-0.3402-0.458-1.03020.36730.40420.25930.5920.06550.05650.4961-0.21020.5477.4974-14.743126.0745
56.6297-1.2246-1.00878.7073-1.85696.7037-0.23150.05650.00850.00090.06260.7966-0.3247-1.04540.07640.4356-0.1047-0.02850.4094-0.14940.6038-23.2352-15.821928.9843
63.46310.0055-1.62394.6809-0.50831.99-0.13970.1892-0.2231-0.32450.09280.19780.52020.0896-0.02870.7119-0.06280.03650.3975-0.09160.3933-8.7799-24.84528.2715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 143 )A6 - 143
2X-RAY DIFFRACTION2chain 'A' and (resid 144 through 180 )A144 - 180
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 232 )A181 - 232
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 313 )A233 - 313
5X-RAY DIFFRACTION5chain 'A' and (resid 314 through 370 )A314 - 370
6X-RAY DIFFRACTION6chain 'A' and (resid 371 through 503 )A371 - 503

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