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- PDB-6zbv: Inward-open structure of human glycine transporter 1 in complex w... -

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Basic information

Entry
Database: PDB / ID: 6zbv
TitleInward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor and sybody Sb_GlyT1#7
Components
  • Sodium- and chloride-dependent glycine transporter 1,Sodium- and chloride-dependent glycine transporter 1
  • Sybody Sb_GlyT1#7
KeywordsMEMBRANE PROTEIN / secondary active transport / neurotransmitter-sodium symport / amino acid transport / SLC6A9 / inward open state / inhibitor bound complex
Function / homology
Function and homology information


regulation of synaptic transmission, glycinergic / glycine secretion, neurotransmission / glycine transmembrane transporter activity / glycine:sodium symporter activity / positive regulation of heme biosynthetic process / neurotransmitter uptake / glycine import across plasma membrane / glycine transport / positive regulation of hemoglobin biosynthetic process / amino acid:sodium symporter activity ...regulation of synaptic transmission, glycinergic / glycine secretion, neurotransmission / glycine transmembrane transporter activity / glycine:sodium symporter activity / positive regulation of heme biosynthetic process / neurotransmitter uptake / glycine import across plasma membrane / glycine transport / positive regulation of hemoglobin biosynthetic process / amino acid:sodium symporter activity / dense core granule / SLC-mediated transport of neurotransmitters / parallel fiber to Purkinje cell synapse / lateral plasma membrane / transport across blood-brain barrier / basal plasma membrane / sodium ion transmembrane transport / hippocampal mossy fiber to CA3 synapse / synaptic vesicle membrane / presynaptic membrane / basolateral plasma membrane / postsynaptic membrane / endosome / postsynaptic density / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, glycine, type 1 / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-QET / Sodium- and chloride-dependent glycine transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsShahsavar, 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
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
Lundbeckfonden Denmark
Roche Switzerland
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND664726 Germany
CitationJournal: 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
DepositionJun 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium- and chloride-dependent glycine transporter 1,Sodium- and chloride-dependent glycine transporter 1
B: Sybody Sb_GlyT1#7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6733
Polymers78,1052
Non-polymers5671
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-9 kcal/mol
Surface area27950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.170, 58.140, 122.310
Angle α, β, γ (deg.)90.000, 100.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Sodium- and chloride-dependent glycine transporter 1,Sodium- and chloride-dependent glycine transporter 1 / GlyT1 / Solute carrier family 6 member 9


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
#2: Antibody Sybody Sb_GlyT1#7


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 / [5-fluoranyl-6-(oxan-4-yloxy)-1,3-dihydroisoindol-2-yl]-[5-methylsulfonyl-2-[2,2,3,3,3-pentakis(fluoranyl)propoxy]phenyl]methanone


Mass: 567.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23F6NO6S
Has ligand of interestY
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.89 %
Description: Crystals appeared in 3-10 days with the longest dimension of 2-5 um.
Crystal growTemperature: 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

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
41001N
51001N
61001N
71001N
81001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)10.9801
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)20.9801
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)30.9801
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)40.9801
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)50.9801
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)60.9801
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)70.9801
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)80.9801
Detector
TypeIDDetectorDateDetails
DECTRIS EIGER X 16M1PIXELOct 5, 2019Mirrors
DECTRIS EIGER X 16M2PIXELOct 4, 2019Mirrors
DECTRIS EIGER X 16M3PIXELSep 21, 2019Mirrors
DECTRIS EIGER X 16M4PIXELSep 19, 2019Mirrors
DECTRIS EIGER X 16M5PIXELAug 7, 2019Mirrors
DECTRIS EIGER X 16M6PIXELAug 6, 2019Mirrors
DECTRIS EIGER X 16M7PIXELJul 14, 2019Mirrors
DECTRIS EIGER X 16M8PIXELJun 30, 2019Mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
5SINGLE WAVELENGTHMx-ray5
6SINGLE WAVELENGTHMx-ray6
7SINGLE WAVELENGTHMx-ray7
8SINGLE WAVELENGTHMx-ray8
Radiation wavelength
IDWavelength (Å)Relative weight
10.98011
21
31
41
51
61
71
81
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4us3, 6dzz

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2585 633 5.01 %RANDOM
Rwork0.2144 ---
obs0.2166 12641 99.9 %-
Displacement parametersBiso max: 196.18 Å2 / Biso mean: 113.5 Å2 / Biso min: 77.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.7653 Å20 Å217.4019 Å2
2--3.4775 Å20 Å2
3---0.2879 Å2
Refinement stepCycle: final / Resolution: 3.4→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5222 0 61 0 5283
Biso mean--127.27 --
Num. residues----659
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3011SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1605HARMONIC5
X-RAY DIFFRACTIONt_it5429HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion672SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7457SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10559HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg18959HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.82
X-RAY DIFFRACTIONt_other_torsion13.87
LS refinement shellResolution: 3.4→3.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 32
RfactorNum. reflection% reflection
Rfree0.268 21 5.15 %
Rwork0.2121 387 -
all0.2148 408 -
obs--100 %

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