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- PDB-6yu4: Crystal structure of MhsT in complex with L-4F-phenylalanine -

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Basic information

Entry
Database: PDB / ID: 6yu4
TitleCrystal structure of MhsT in complex with L-4F-phenylalanine
ComponentsSodium-dependent transporter
KeywordsTRANSPORT PROTEIN / LeuT-fold / amino acid transporter / L-4F-phenylalanine
Function / homology
Function and homology information


: / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 4-FLUORO-L-PHENYLALANINE / Na+-dependent transporter / Sodium-dependent transporter
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsFocht, D. / Neumann, C. / Lyons, J. / Eguskiza Bilbao, A. / Blunck, R. / Malinauskaite, L. / Schwarz, I.O. / Javitch, J.A. / Quick, M. / Nissen, P.
Funding support Denmark, 4items
OrganizationGrant numberCountry
Lundbeckfonden2011-3868 Denmark
Lundbeckfonden2015-2704 Denmark
Lundbeckfonden2015-3225 Denmark
Lundbeckfonden2016-2518 Denmark
CitationJournal: Embo J. / Year: 2021
Title: A non-helical region in transmembrane helix 6 of hydrophobic amino acid transporter MhsT mediates substrate recognition.
Authors: Focht, D. / Neumann, C. / Lyons, J. / Eguskiza Bilbao, A. / Blunck, R. / Malinauskaite, L. / Schwarz, I.O. / Javitch, J.A. / Quick, M. / Nissen, P.
History
DepositionApr 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 27, 2021Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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

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Assembly

Deposited unit
A: Sodium-dependent transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,05813
Polymers48,3611
Non-polymers4,69712
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint8 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.150, 49.850, 109.730
Angle α, β, γ (deg.)90.000, 96.080, 90.000
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sodium-dependent transporter


Mass: 48360.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: E2L07_01100 / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: A0A4Y7X244, UniProt: Q9KDT3*PLUS

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Sugars , 2 types, 8 molecules

#5: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#6: Sugar ChemComp-SOG / octyl 1-thio-beta-D-glucopyranoside / 2-HYDROXYMETHYL-6-OCTYLSULFANYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL / 1-S-OCTYL-BETA-D-THIOGLUCOSIDE / octyl 1-thio-beta-D-glucoside / octyl 1-thio-D-glucoside / octyl 1-thio-glucoside


Type: D-saccharide / Mass: 308.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O5S / Comment: detergent*YM

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Non-polymers , 4 types, 32 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PFF / 4-FLUORO-L-PHENYLALANINE


Type: L-peptide linking / Mass: 183.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10FNO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystallized using HiLiDe with DOPC as added lipid. Crystals were obtained in 14-24% PEG400, 0.3-0.5M NaCl, 0.1M Tris-HCl or HEPES-NaOH pH 7.0, 5% Trimethylamine N-oxide (TMANO), 5% or 10% glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.96858 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 2.26→43.9 Å / Num. obs: 20720 / % possible obs: 92.9 % / Redundancy: 2.3 % / CC1/2: 0.991 / Net I/σ(I): 5.3
Reflection shellResolution: 2.26→2.33 Å / Num. unique obs: 2067 / CC1/2: 0.472

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4US3

4us3


Resolution: 2.26→39.313 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.03
RfactorNum. reflection% reflection
Rfree0.2609 752 3.63 %
Rwork0.2233 --
obs0.2247 20719 91.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.57 Å2 / Biso mean: 38.0862 Å2 / Biso min: 19.82 Å2
Refinement stepCycle: final / Resolution: 2.26→39.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 210 28 3562
Biso mean--53.89 43.29 -
Num. residues----442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2601-2.43450.29931220.2912401793
2.4345-2.67950.32331620.2836396192
2.6795-3.06710.31071640.2481401093
3.0671-3.86370.28421490.2032399492
3.8637-39.3130.20451550.197398590

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