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- PDB-6zl4: the structure of glutamate transporter homologue GltTk in complex... -

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Basic information

Entry
Database: PDB / ID: 6zl4
Titlethe structure of glutamate transporter homologue GltTk in complex with the photo switchable compound (cis)
ComponentsProton/glutamate symporter, SDF family
KeywordsTRANSPORT PROTEIN / glutamate transporter / amino acid transporter / photoisomerization / membrane protein
Function / homology
Function and homology information


carboxylic acid transport / symporter activity / membrane
Similarity search - Function
Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1.
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-QM5 / Proton/glutamate symporter, SDF family
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsArkhipova, V. / Slotboom, D.J. / Guskov, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Structural Aspects of Photopharmacology: Insight into the Binding of Photoswitchable and Photocaged Inhibitors to the Glutamate Transporter Homologue.
Authors: Arkhipova, V. / Fu, H. / Hoorens, M.W.H. / Trinco, G. / Lameijer, L.N. / Marin, E. / Feringa, B.L. / Poelarends, G.J. / Szymanski, W. / Slotboom, D.J. / Guskov, A.
History
DepositionJun 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 31, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proton/glutamate symporter, SDF family
B: Proton/glutamate symporter, SDF family
C: Proton/glutamate symporter, SDF family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,04442
Polymers140,0563
Non-polymers5,98839
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16020 Å2
ΔGint-101 kcal/mol
Surface area50950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.210, 117.210, 309.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 186 or resid 188 through 430))
21(chain B and (resid 8 through 186 or resid 188 through 430))
31(chain C and (resid 8 through 186 or resid 188 through 430))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEU(chain A and (resid 8 through 186 or resid 188 through 430))AA8 - 1868 - 186
12VALVALSERSER(chain A and (resid 8 through 186 or resid 188 through 430))AA188 - 430188 - 430
21ARGARGLEULEU(chain B and (resid 8 through 186 or resid 188 through 430))BB8 - 1868 - 186
22VALVALSERSER(chain B and (resid 8 through 186 or resid 188 through 430))BB188 - 430188 - 430
31ARGARGLEULEU(chain C and (resid 8 through 186 or resid 188 through 430))CC8 - 1868 - 186
32VALVALSERSER(chain C and (resid 8 through 186 or resid 188 through 430))CC188 - 430188 - 430

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

#1: Protein Proton/glutamate symporter, SDF family


Mass: 46685.363 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: 8His tag at C-terminus / Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JID0
#3: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 6 types, 36 molecules

#2: Chemical ChemComp-QM5 / (2~{S},3~{S})-2-azanyl-3-[[4-[2-(4-methoxyphenyl)hydrazinyl]phenyl]methoxy]butanedioic acid


Mass: 375.376 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H21N3O6
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM

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Details

Has ligand of interestN

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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: 4.38 Å3/Da / Density % sol: 71.92 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 23% PEG 400, 100 mM sodium acetate, 50 mM NaCl, 20 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→48.225 Å / Num. obs: 50233 / % possible obs: 99.9 % / Redundancy: 15.3 % / CC1/2: 0.998 / Net I/σ(I): 10.12
Reflection shellResolution: 3→3.08 Å / Mean I/σ(I) obs: 0.31 / Num. unique obs: 3663 / CC1/2: 0.124 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XSCALEdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E9S

5e9s


Resolution: 3→48.225 Å / SU ML: 0.82 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 41.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2876 2495 5 %
Rwork0.2545 47357 -
obs0.2562 49852 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 418.84 Å2 / Biso mean: 172.7568 Å2 / Biso min: 109.76 Å2
Refinement stepCycle: final / Resolution: 3→48.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9463 0 402 0 9865
Biso mean--194.91 --
Num. residues----1270
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5782X-RAY DIFFRACTION10.581TORSIONAL
12B5782X-RAY DIFFRACTION10.581TORSIONAL
13C5782X-RAY DIFFRACTION10.581TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3-3.05770.6151210.5369232990
7.8516-48.22050.3021510.252284799
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)
13.021.56840.22551.6051.56932.1754-0.05260.105-0.14560.2892-0.2980.23610.98140.045-0.06212.09180.24940.32531.881-0.00320.977740.503819.8686-23.7818
21.1631-0.11090.55563.40020.09981.54740.11660.14430.3775-0.5209-0.2793-0.27-0.1947-0.4928-0.13221.5260.1637-0.04022.03030.0840.90876.644146.9394-32.2415
32.2109-1.5064-0.52112.09320.46380.44570.0743-0.4022-0.2184-0.6218-0.06870.194-0.54480.5864-0.16511.8985-0.18730.25271.43280.2250.845147.21663.4016-26.9017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 8 through 501)A8 - 501
2X-RAY DIFFRACTION2(chain 'B' and resid 8 through 501)B8 - 501
3X-RAY DIFFRACTION3(chain 'C' and resid 8 through 501)C8 - 501

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