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- PDB-6gs4: Crystal structure of peptide transporter DtpA-nanobody in complex... -

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Basic information

Entry
Database: PDB / ID: 6gs4
TitleCrystal structure of peptide transporter DtpA-nanobody in complex with valganciclovir
Components
  • Dipeptide and tripeptide permease A
  • nanobodySingle-domain antibody
KeywordsMEMBRANE PROTEIN / peptide transporter / complex with nanobody / SLC15 family member
Function / homology
Function and homology information


tripeptide transmembrane transport / dipeptide transmembrane transport / tripeptide transmembrane transporter activity / peptide:proton symporter activity / dipeptide transmembrane transporter activity / proton transmembrane transporter activity / proton transmembrane transport / protein transport / membrane / plasma membrane
Similarity search - Function
Amino acid/peptide transporter family, dipeptide and tripeptide permease A / Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / 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. ...Amino acid/peptide transporter family, dipeptide and tripeptide permease A / Dipeptide/tripeptide permease / PTR2 family proton/oligopeptide symporters signature 1. / MFS general substrate transporter like domains / 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. / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-F9E / Dipeptide and tripeptide permease A
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.645 Å
AuthorsUral-Blimke, Y. / Flayhan, A. / Quistgaard, E.M. / Loew, C.
Funding support Sweden, 2items
OrganizationGrant numberCountry
European UnioniNEXT grant, project no. 653706
Swedish Research Council621-2013-5905 Sweden
CitationJournal: J. Am. Chem. Soc. / Year: 2019
Title: Structure of Prototypic Peptide Transporter DtpA from E. coli in Complex with Valganciclovir Provides Insights into Drug Binding of Human PepT1.
Authors: Ural-Blimke, Y. / Flayhan, A. / Strauss, J. / Rantos, V. / Bartels, K. / Nielsen, R. / Pardon, E. / Steyaert, J. / Kosinski, J. / Quistgaard, E.M. / Low, C.
History
DepositionJun 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptide and tripeptide permease A
H: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2354
Polymers69,3702
Non-polymers8652
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-3 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.940, 120.190, 163.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dipeptide and tripeptide permease A


Mass: 54969.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 / Gene: dtpA, tppB, ydgR, b1634, JW1626 / Production host: Escherichia coli (E. coli) / Variant (production host): C41 / References: UniProt: P77304
#2: Antibody nanobody / Single-domain antibody


Mass: 14400.683 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli) / Variant (production host): WK6
#3: Chemical ChemComp-F9E / [(2~{S})-2-[(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)methoxy]-3-oxidanyl-propyl] (2~{S})-2-azanyl-3-methyl-butanoate


Mass: 354.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 3.89 Å3/Da / Density % sol: 68.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: PEG 400, calcium chloride, glycine buffer, Anapoe-C12E10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.645→19.68 Å / Num. all: 206943 / Num. obs: 32188 / % possible obs: 98.98 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.1074 / Net I/σ(I): 10.74
Reflection shellResolution: 2.645→2.74 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GS1

6gs1


Resolution: 2.645→19.68 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 29.09
RfactorNum. reflection% reflection
Rfree0.2394 3044 5.03 %
Rwork0.2157 --
obs0.2169 60493 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.645→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4542 0 60 7 4609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034715
X-RAY DIFFRACTIONf_angle_d0.5716397
X-RAY DIFFRACTIONf_dihedral_angle_d17.1172706
X-RAY DIFFRACTIONf_chiral_restr0.042721
X-RAY DIFFRACTIONf_plane_restr0.004787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6455-2.68670.39621290.39392432X-RAY DIFFRACTION93
2.6867-2.73070.38711410.37172666X-RAY DIFFRACTION100
2.7307-2.77760.37391380.34382591X-RAY DIFFRACTION99
2.7776-2.8280.38991370.35292618X-RAY DIFFRACTION99
2.828-2.88220.341400.3362648X-RAY DIFFRACTION99
2.8822-2.94090.33411340.31982601X-RAY DIFFRACTION100
2.9409-3.00460.36591360.30662626X-RAY DIFFRACTION99
3.0046-3.07420.31341440.30052634X-RAY DIFFRACTION99
3.0742-3.15080.30861340.30092586X-RAY DIFFRACTION99
3.1508-3.23570.29121370.28432630X-RAY DIFFRACTION99
3.2357-3.33040.27321410.23842593X-RAY DIFFRACTION99
3.3304-3.43740.25781450.21742639X-RAY DIFFRACTION100
3.4374-3.55960.22861360.21912613X-RAY DIFFRACTION100
3.5596-3.70120.23361420.20492625X-RAY DIFFRACTION100
3.7012-3.86850.27181370.20832609X-RAY DIFFRACTION100
3.8685-4.07080.24641360.2092619X-RAY DIFFRACTION100
4.0708-4.32340.21371430.19542617X-RAY DIFFRACTION99
4.3234-4.65320.17811400.17212631X-RAY DIFFRACTION100
4.6532-5.11410.18781350.1722640X-RAY DIFFRACTION100
5.1141-5.83760.21251390.19812601X-RAY DIFFRACTION100
5.8376-7.29330.21841410.21142630X-RAY DIFFRACTION99
7.2933-19.82090.22011390.18842600X-RAY DIFFRACTION99
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)
13.6624-1.7583-1.39262.18811.1833.2367-0.15510.0363-0.33060.06120.06840.0010.29870.04410.04480.5519-0.03070.07250.47310.05280.6761-2.6825-12.449635.1185
22.2540.04420.34781.139-0.05771.0323-0.12840.2895-0.1276-0.20440.008-0.02320.0446-0.12020.11980.73770.00090.10790.55440.04760.7235-18.8563-4.978225.6679
35.4467-0.0117-1.2034.88211.66437.070.1848-0.45750.19260.4314-0.20040.08820.0522-0.42580.01490.7475-0.02630.09260.5183-0.01550.7596-18.266718.082661.1654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 488 )
3X-RAY DIFFRACTION3chain 'H' and (resid 1 through 125 )

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