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- PDB-6v8g: GltPh mutant - Y204L A345V V366A -

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Basic information

Entry
Database: PDB / ID: 6v8g
TitleGltPh mutant - Y204L A345V V366A
ComponentsGlutamate transporter homolog
KeywordsMEMBRANE PROTEIN / aspartate transporter / substrate bound / fast mutant
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
ASPARTIC ACID / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsBoudker, O. / Huysmans, G.H.M.
Funding support United States, France, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
Marie Sklodowska-Curie Actions, FragNET ITN France
CitationJournal: Embo J. / Year: 2021
Title: The high-energy transition state of the glutamate transporter homologue GltPh.
Authors: Huysmans, G.H.M. / Ciftci, D. / Wang, X. / Blanchard, S.C. / Boudker, O.
History
DepositionDec 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Oct 11, 2023Group: 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
B: Glutamate transporter homolog
C: Glutamate transporter homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,38215
Polymers133,7763
Non-polymers60612
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.416, 109.416, 305.227
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain 'A' and (resid 12 through 416 or resid 501 through 503))
221(chain 'B' and (resid 12 through 416 or resid 501 through 503))
331(chain 'C' and (resid 12 through 416 or resid 501 through 503))

NCS oper:
IDCodeMatrixVector
1given(-0.418290921611, 0.79131385098, 0.445931714666), (-0.882826475641, -0.469669025291, 0.00533109642688), (0.213658884217, -0.391450374797, 0.895051107628)-0.838689671478, -53.3663543271, -7.20305318757
2given(-0.423621518811, -0.878334715474, 0.221524121473), (0.786760685784, -0.477964676436, -0.390585959021), (0.448945912228, 0.00882585254081, 0.893515345263)-45.5505971513, -27.4465615302, 7.26988645315

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Components

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


Mass: 44591.930 Da / Num. of mol.: 3 / Mutation: Y204L, A345V, V366A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1295 / Production host: Escherichia coli (E. coli) / References: UniProt: O59010
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4 / Feature type: SUBJECT OF INVESTIGATION
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: 4.15 Å3/Da / Density % sol: 70.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: Potassium citrate, PEG 400 / PH range: 4.75 - 4.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 3.375→47.38 Å / Num. obs: 30612 / % possible obs: 99.54 % / Redundancy: 10.5 % / Biso Wilson estimate: 114.03 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.03574 / Rrim(I) all: 0.1212 / Net I/σ(I): 10.87
Reflection shellResolution: 3.375→3.496 Å / Num. unique obs: 2964 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2nwx

2nwx


Resolution: 3.38→47.38 Å / SU ML: 0.4226 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.3006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2574 1400 4.58 %
Rwork0.2324 29166 -
obs0.2336 30566 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 132.82 Å2
Refinement stepCycle: LAST / Resolution: 3.38→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8643 0 36 0 8679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00248814
X-RAY DIFFRACTIONf_angle_d0.453112018
X-RAY DIFFRACTIONf_chiral_restr0.03871548
X-RAY DIFFRACTIONf_plane_restr0.00341470
X-RAY DIFFRACTIONf_dihedral_angle_d1.87455178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.38-3.50.38711560.33212800X-RAY DIFFRACTION98.4
3.5-3.640.30841270.27742909X-RAY DIFFRACTION99.84
3.64-3.80.28141370.24872868X-RAY DIFFRACTION99.8
3.8-40.30061190.2432881X-RAY DIFFRACTION99.83
4-4.250.26651580.21432880X-RAY DIFFRACTION100
4.25-4.580.2041570.18522886X-RAY DIFFRACTION99.84
4.58-5.040.22451460.17972891X-RAY DIFFRACTION99.84
5.04-5.770.25141020.21052999X-RAY DIFFRACTION99.97
5.77-7.260.27651480.25842975X-RAY DIFFRACTION100
7.26-47.380.24841500.2473077X-RAY DIFFRACTION98.59
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)
13.157533715390.1627818305160.8273565701121.41684195547-0.1252808885133.772565789940.2255340012230.205972554283-0.159008635441-0.268882496591-0.0140230584044-0.09863516268410.910042719331.10894724115-0.2288705079591.119584242060.1845690216520.09828107561390.865490713424-0.09690584438790.6184097021362.74563203086-26.4455492603-32.5566216425
29.003061458894.543389306666.660053084854.843082172757.46582410911.999998201762.23091550123-2.51633774608-1.963104635290.4288395365590.9790471419150.7294755416882.31584850738-4.78769734267-3.210366385042.06886613793-0.6788662452961.041805751721.66124941656-0.1466650241872.991861000443.91017328834-26.0387975051-26.9708268651
30.876591713845-0.120635734093-0.4396834138131.57273375912-0.2438166830992.483393389210.180768342661-0.01693532460350.179322385054-0.140768825788-0.0557088128789-0.0540897831598-1.05747724472-0.77502379554-0.00836078556161.064357588320.1707578272820.009569640071580.9359817512220.04954076610980.67431692007-30.68282289620.117767116089-20.9513246323
45.676730772197.009089049361.48922949678.690850273192.712515453751.99999608396-0.738715619830.2638189822820.8165204628961.36328296848-1.55941988906-0.834849974679-1.590054891650.7949207147642.315744416761.689084237250.5100438326580.1422920904171.496622255510.07549300523313.37289017296-30.3298736861-1.33783504003-15.431825862
51.856163576190.512138249973-0.006679285680972.539626689920.2153659152051.979318339820.129954220192-0.345564349659-0.0133707948406-0.1116951367650.183434757070.4695811574830.977863150279-1.469246590440.2537847798261.39668007309-0.60748114076-0.2124926690931.164787107390.01374391639910.623861126747-37.5508349914-43.2508638915-25.2764062294
67.307132838736.45601948873-3.720415234549.05349956422-9.975536036291.999996814580.220105674505-0.156483681162-0.4003683952960.51337891291-0.67401594659-1.67187089647-0.4258412146250.5420885715810.4673807615922.66402935863-0.6203822184270.8612571803811.30260267433-0.3699871680612.99218936167-35.2150144513-44.4169686643-20.1874768049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 12 through 416)
2X-RAY DIFFRACTION2(chain 'A' and resid 503 through 503)
3X-RAY DIFFRACTION3(chain 'B' and resid 12 through 416)
4X-RAY DIFFRACTION4(chain 'B' and resid 503 through 503)
5X-RAY DIFFRACTION5(chain 'C' and resid 12 through 416)
6X-RAY DIFFRACTION6(chain 'C' and resid 503 through 503)

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