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- PDB-7ahk: Crystal structure of the outward-facing state of the substrate-fr... -

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Basic information

Entry
Database: PDB / ID: 7ahk
TitleCrystal structure of the outward-facing state of the substrate-free Na+-only bound glutamate transporter homolog GltPh
ComponentsGlutamate transporter homolog
KeywordsMEMBRANE PROTEIN / glutamate transporter / aminoacid transport / homologue
Function / homology
Function and homology information


amino acid:sodium symporter activity / L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / chloride transmembrane transporter activity / protein homotrimerization / chloride transmembrane transport / identical protein binding / metal ion binding / plasma 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
EICOSANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PHOSPHATE ION / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKovalev, K. / Alleva, C. / Astashkin, A. / Machtens, J.-P. / Fahlke, C. / Gordeliy, V.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
CitationJournal: Sci Adv / Year: 2020
Title: Na + -dependent gate dynamics and electrostatic attraction ensure substrate coupling in glutamate transporters.
Authors: Alleva, C. / Kovalev, K. / Astashkin, R. / Berndt, M.I. / Baeken, C. / Balandin, T. / Gordeliy, V. / Fahlke, C. / Machtens, J.P.
History
DepositionSep 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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
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: Glutamate transporter homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,56421
Polymers44,8431
Non-polymers4,72120
Water43224
1
A: Glutamate transporter homolog
hetero molecules

A: Glutamate transporter homolog
hetero molecules

A: Glutamate transporter homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,69363
Polymers134,5293
Non-polymers14,16360
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area19620 Å2
ΔGint-164 kcal/mol
Surface area47180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.011, 152.011, 57.521
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glutamate transporter homolog / Glt(Ph) / Sodium-aspartate symporter Glt(Ph) / Sodium-dependent aspartate transporter


Mass: 44843.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1295 / Production host: Escherichia coli (E. coli) / References: UniProt: O59010
#3: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 43 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
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H42
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 4.28 Å3/Da / Density % sol: 71.25 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.2 / Details: 1M KH2PO4/Na2HPO4, pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.5→45.87 Å / Num. obs: 25571 / % possible obs: 96.4 % / Redundancy: 2.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.122 / Rrim(I) all: 0.211 / Net I/σ(I): 5.4 / Num. measured all: 65714 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.5-2.62.61.365758029050.250.9681.6840.898.5
9.01-45.872.50.02113525370.9990.0150.02626.488.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NWW

2nww


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1179 4.6 %RANDOM
Rwork0.2114 ---
obs0.2133 24338 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 420 Å2 / Biso mean: 45.012 Å2 / Biso min: 19.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å2-0 Å2
2--0.27 Å20 Å2
3----0.88 Å2
Refinement stepCycle: final / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 207 24 3250
Biso mean--73.25 44.77 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133264
X-RAY DIFFRACTIONr_bond_other_d0.0330.0173441
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.654383
X-RAY DIFFRACTIONr_angle_other_deg2.0981.5897940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62522.596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.12415495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.454158
X-RAY DIFFRACTIONr_chiral_restr0.0640.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023398
X-RAY DIFFRACTIONr_gen_planes_other0.020.02594
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 88 -
Rwork0.342 1757 -
all-1845 -
obs--98.3 %

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