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- EMDB-26489: TBOA-bound GltPh RSMR mutant in OFS state -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-26489
TitleTBOA-bound GltPh RSMR mutant in OFS state
Map dataTBOA-bound RSMR mutant in OFS
Sample
  • Complex: TBOA-bound GltPh RSMR mutant in OFS state
    • Protein or peptide: Glutamate transporter homolog
  • Ligand: (3S)-3-(BENZYLOXY)-L-ASPARTIC ACID
  • Ligand: SODIUM ION
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
Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsHuang Y / Boudker O
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R37NS085318 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Environmentally Ultrasensitive Fluorine Probe to Resolve Protein Conformational Ensembles by 19F NMR and Cryo-EM
Authors: Huang Y / Reddy KD / Bracken C / Qiu B / Zhan W / Eliezer D / Boudker O
History
DepositionMar 24, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateMay 10, 2023-
Current statusMay 10, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26489.png

Downloads & links

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Map

FileDownload / File: emd_26489.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTBOA-bound RSMR mutant in OFS
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 327.168 Å		0.85 Å/pix.
x 384 pix.
= 327.168 Å		0.85 Å/pix.
x 384 pix.
= 327.168 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.852 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.521
Minimum - Maximum-0.72509944 - 1.745412
Average (Standard dev.)0.0006280861 (±0.036075704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 327.168 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_26489_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_26489_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TBOA-bound GltPh RSMR mutant in OFS state

EntireName: TBOA-bound GltPh RSMR mutant in OFS state
Components
  • Complex: TBOA-bound GltPh RSMR mutant in OFS state
    • Protein or peptide: Glutamate transporter homolog
  • Ligand: (3S)-3-(BENZYLOXY)-L-ASPARTIC ACID
  • Ligand: SODIUM ION

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Supramolecule #1: TBOA-bound GltPh RSMR mutant in OFS state

SupramoleculeName: TBOA-bound GltPh RSMR mutant in OFS state / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pyrococcus horikoshii (archaea)

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Macromolecule #1: Glutamate transporter homolog

MacromoleculeName: Glutamate transporter homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Molecular weightTheoretical: 44.13323 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGLYRKYIEY PVLQKILIGL ILGAIVGLIL GHYGYAHAVH TYVKPFGDLF VRLLKMLVMP IVFASLVVGA ASISPARLGR VGVKIVVYY LLTSAFAVTL GIIMARLFNP GAGIHLAVGG QQFQPHQAPP LVHILLDIVP TNPFGALANG QVLPTIFFAI I LGIAITYL ...String:
MGLYRKYIEY PVLQKILIGL ILGAIVGLIL GHYGYAHAVH TYVKPFGDLF VRLLKMLVMP IVFASLVVGA ASISPARLGR VGVKIVVYY LLTSAFAVTL GIIMARLFNP GAGIHLAVGG QQFQPHQAPP LVHILLDIVP TNPFGALANG QVLPTIFFAI I LGIAITYL MNSENEKVRK SAETLLDAIN GLAEAMYKIV NGVMQYAPIG VFALIAHVMA HQGVHVVGEL AKVTAAVYVG LT LQILLVY FVLLKIYGID PISFIKHAKD AMLTAFVTSS SSGTLPVTMR VAKEMGISEG IYSFTLPLGA TINMDGTALY QGV ATFFIA NALGSHLTVG QQLTIVLTAV LASIGTAGVP GAGAIMLAMV LHSVGLPLTD PNVAAAYA(EFC)I LGIDAILDRG RTMVNVTGD LTGTAIVAKT EGT

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Macromolecule #2: (3S)-3-(BENZYLOXY)-L-ASPARTIC ACID

MacromoleculeName: (3S)-3-(BENZYLOXY)-L-ASPARTIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: TB1
Molecular weightTheoretical: 239.225 Da
Chemical component information

ChemComp-TB1:
(3S)-3-(BENZYLOXY)-L-ASPARTIC ACID

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4.5 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.88 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6x17

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 162235
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.1.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6x17


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7ugj:
TBOA-bound GltPh RSMR mutant in OFS state

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