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Yorodumi- PDB-6zbv: Inward-open structure of human glycine transporter 1 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zbv | |||||||||||||||
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Title | Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor and sybody Sb_GlyT1#7 | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / secondary active transport / neurotransmitter-sodium symport / amino acid transport / SLC6A9 / inward open state / inhibitor bound complex | |||||||||||||||
Function / homology | Function and homology information glycine:sodium symporter activity / regulation of synaptic transmission, glycinergic / glycine transmembrane transporter activity / negative regulation of NMDA glutamate receptor activity / positive regulation of heme biosynthetic process / glycine import across plasma membrane / glycine transport / synaptic transmission, glycinergic / positive regulation of hemoglobin biosynthetic process / dense core granule ...glycine:sodium symporter activity / regulation of synaptic transmission, glycinergic / glycine transmembrane transporter activity / negative regulation of NMDA glutamate receptor activity / positive regulation of heme biosynthetic process / glycine import across plasma membrane / glycine transport / synaptic transmission, glycinergic / positive regulation of hemoglobin biosynthetic process / dense core granule / Na+/Cl- dependent neurotransmitter transporters / neurotransmitter transport / parallel fiber to Purkinje cell synapse / transport across blood-brain barrier / lateral plasma membrane / sodium ion transmembrane transport / hippocampal mossy fiber to CA3 synapse / basal plasma membrane / synaptic vesicle membrane / presynaptic membrane / basolateral plasma membrane / postsynaptic membrane / postsynaptic density / endosome / apical plasma membrane / membrane / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) unidentified (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | |||||||||||||||
Authors | Shahsavar, A. / Stohler, P. / Bourenkov, G. / Zimmermann, I. / Siegrist, M. / Guba, W. / Pinard, E. / Sinning, S. / Seeger, M.A. / Schneider, T.R. ...Shahsavar, A. / Stohler, P. / Bourenkov, G. / Zimmermann, I. / Siegrist, M. / Guba, W. / Pinard, E. / Sinning, S. / Seeger, M.A. / Schneider, T.R. / Dawson, R.J.P. / Nissen, P. | |||||||||||||||
Funding support | Denmark, Switzerland, Germany, 4items
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Citation | Journal: Nature / Year: 2021 Title: Structural insights into the inhibition of glycine reuptake. Authors: Shahsavar, A. / Stohler, P. / Bourenkov, G. / Zimmermann, I. / Siegrist, M. / Guba, W. / Pinard, E. / Sinning, S. / Seeger, M.A. / Schneider, T.R. / Dawson, R.J.P. / Nissen, P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zbv.cif.gz | 254.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zbv.ent.gz | 205.2 KB | Display | PDB format |
PDBx/mmJSON format | 6zbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/6zbv ftp://data.pdbj.org/pub/pdb/validation_reports/zb/6zbv | HTTPS FTP |
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-Related structure data
Related structure data | 6zplC 4us3S 6dzzS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64801.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A9 / Plasmid: pCDNA3.1 / Cell (production host): HEK293 Production host: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others) References: UniProt: P48067 |
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#2: Antibody | Mass: 13303.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli MC1061 (bacteria) |
#3: Chemical | ChemComp-QET / [ |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.89 % Description: Crystals appeared in 3-10 days with the longest dimension of 2-5 um. |
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Crystal grow | Temperature: 292.75 K / Method: lipidic cubic phase / pH: 7 Details: 0.1M ADA pH 7, 13-25% PEG600, 4-14% v/v-1,3-Butanediol |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.4→30 Å / Num. obs: 12641 / % possible obs: 99.71 % / Redundancy: 12.1 % / Biso Wilson estimate: 103.12 Å2 / CC1/2: 0.985 / CC star: 0.997 / Rmerge(I) obs: 0.42 / Rpim(I) all: 0.1225 / Rrim(I) all: 0.44 / Net I/σ(I): 6.57 | |||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 3.4→3.5 Å / Redundancy: 11.9 % / Rmerge(I) obs: 2.688 / Mean I/σ(I) obs: 1.69 / Num. unique obs: 1232 / CC1/2: 0.541 / CC star: 0.838 / Rpim(I) all: 0.7956 / Rrim(I) all: 2.809 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4us3, 6dzz Resolution: 3.4→29.67 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.861 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.547
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Displacement parameters | Biso max: 196.18 Å2 / Biso mean: 113.5 Å2 / Biso min: 77.2 Å2
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Refinement step | Cycle: final / Resolution: 3.4→29.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 32
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