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

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Basic information

Entry
Database: PDB / ID: 6zpl
TitleInward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions.
Components
  • Endoglucanase H
  • 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


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 / positive regulation of hemoglobin biosynthetic process / dense core granule / synaptic transmission, glycinergic ...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 / positive regulation of hemoglobin biosynthetic process / dense core granule / synaptic transmission, glycinergic / Na+/Cl- dependent neurotransmitter transporters / neurotransmitter transport / parallel fiber to Purkinje cell synapse / cellulase / cellulase activity / beta-glucosidase activity / transport across blood-brain barrier / sodium ion transmembrane transport / lateral plasma membrane / cellulose catabolic process / 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 / cell surface / extracellular region / membrane / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter, glycine, type 1 / Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Clostridium cellulosome enzymes repeated domain signature. / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Glycoside hydrolase, family 5, conserved site ...Sodium:neurotransmitter symporter, glycine, type 1 / Carbohydrate binding module family 11 / Carbohydrate binding domain (family 11) / Glycosyl hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Clostridium cellulosome enzymes repeated domain signature. / Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Glycoside hydrolase, family 5, conserved site / Glycosyl hydrolases family 5 signature. / Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile. / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Galactose-binding-like domain superfamily / EF-hand calcium-binding domain. / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-QET / Endoglucanase H / Sodium- and chloride-dependent glycine transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Hungateiclostridium thermocellum (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.945 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
F. Hoffmann-La Roche LTD 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
DepositionJul 8, 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 31, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Sodium- and chloride-dependent glycine transporter 1
A: Sodium- and chloride-dependent glycine transporter 1
C: Endoglucanase H
E: Sybody Sb_GlyT1#7
F: Sybody Sb_GlyT1#7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,48411
Polymers187,2325
Non-polymers1,2526
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.410, 69.710, 149.430
Angle α, β, γ (deg.)90.000, 92.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 3 molecules BAC

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


Mass: 64730.410 Da / Num. of mol.: 2
Mutation: L153A, S297A, I368A, C633A. N-terminal deletion of residues 1-91 and residues 9-281 of Lichenase (PDB ID 2CIT) have been fused at the N-terminal. C- terminal deletion of residues 685-706 as ...Mutation: L153A, S297A, I368A, C633A. N-terminal deletion of residues 1-91 and residues 9-281 of Lichenase (PDB ID 2CIT) have been fused at the N-terminal. C- terminal deletion of residues 685-706 as well as a deletion in the extracellular loop 2 (EL2) between residues 240-256.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC6A9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P48067
#2: Protein Endoglucanase H / Cellulase H / Endo-1 / 4-beta-glucanase H / EgH


Mass: 31163.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: celH, Cthe_1472 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P16218, cellulase

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Antibody , 1 types, 2 molecules EF

#3: Antibody Sybody Sb_GlyT1#7


Mass: 13303.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli MC1061 (bacteria)

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Non-polymers , 3 types, 6 molecules

#4: 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.: 2 / Source method: obtained synthetically / Formula: C24H23F6NO6S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl

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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: 3.24 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 292.75 K / Method: lipidic cubic phase / pH: 7
Details: Crystals appeared in 3-10 days in 0.1 M ADA pH 7, 13-25% PEG600, 4-14% v/v, 1,3-Butanediol with the longest dimension of 2-5 um.

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
31001N
41001N
51001N
61001N
71001N
81001N
91001N
101001N
111001N
121001N
131001N
141001N
151001N
161001N
171001N
181001N
191001N
201001N
211001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)10.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)20.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)30.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)40.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)50.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)60.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)70.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)80.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)90.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)100.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)110.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)120.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)130.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)140.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)150.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)160.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)170.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)180.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)190.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)200.98
SYNCHROTRONPETRA III, EMBL c/o DESY P14 (MX2)210.98
Detector
TypeIDDetectorDateDetails
DECTRIS EIGER X 16M1PIXELDec 20, 2018Mirrors
DECTRIS EIGER X 16M2PIXELDec 17, 2018Mirrors
DECTRIS EIGER X 16M3PIXELDec 16, 2018Mirrors
DECTRIS EIGER X 16M4PIXELDec 13, 2018Mirrors
DECTRIS EIGER X 16M5PIXELDec 9, 2018Mirrors
DECTRIS EIGER X 16M6PIXELDec 8, 2018Mirrors
DECTRIS EIGER X 16M7PIXELDec 5, 2018Mirrors
DECTRIS EIGER X 16M8PIXELDec 4, 2018Mirrors
DECTRIS EIGER X 16M9PIXELDec 2, 2018Mirrors
DECTRIS EIGER X 16M10PIXELDec 1, 2018Mirrors
DECTRIS EIGER X 16M11PIXELNov 29, 2018Mirrors
DECTRIS EIGER X 16M12PIXELNov 28, 2018Mirrors
DECTRIS EIGER X 16M13PIXELNov 20, 2018Mirrors
DECTRIS EIGER X 16M14PIXELNov 6, 2018Mirrors
DECTRIS EIGER X 16M15PIXELOct 23, 2018Mirrors
DECTRIS EIGER X 16M16PIXELSep 24, 2018Mirrors
DECTRIS EIGER X 16M17PIXELSep 2, 2018Mirrors
DECTRIS EIGER X 16M18PIXELJul 13, 2018Mirrors
DECTRIS EIGER X 16M19PIXELJul 12, 2018Mirrors
DECTRIS EIGER X 16M20PIXELJun 12, 2018Mirrors
DECTRIS EIGER X 16M21PIXELMar 26, 2018Mirrors
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
9SINGLE WAVELENGTHMx-ray9
10SINGLE WAVELENGTHMx-ray10
11SINGLE WAVELENGTHMx-ray11
12SINGLE WAVELENGTHMx-ray12
13SINGLE WAVELENGTHMx-ray13
14SINGLE WAVELENGTHMx-ray14
15SINGLE WAVELENGTHMx-ray15
16SINGLE WAVELENGTHMx-ray16
17SINGLE WAVELENGTHMx-ray17
18SINGLE WAVELENGTHMx-ray18
19SINGLE WAVELENGTHMx-ray19
20SINGLE WAVELENGTHMx-ray20
21SINGLE WAVELENGTHMx-ray21
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
ReflectionResolution: 3.9→29.86 Å / Num. obs: 22222 / % possible obs: 99.61 % / Redundancy: 12.6 % / Biso Wilson estimate: 101.5 Å2 / CC1/2: 0.982 / CC star: 0.995 / Rpim(I) all: 0.2571 / Rrim(I) all: 0.9253 / Net I/σ(I): 4.39
Reflection shellResolution: 3.9→4.039 Å / Redundancy: 12 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 2219 / CC1/2: 0.276 / CC star: 0.658 / % possible all: 100

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Processing

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

4us3

6dzz


Resolution: 3.945→29.07 Å / Cor.coef. Fo:Fc: 0.8 / Cor.coef. Fo:Fc free: 0.764 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.845
RfactorNum. reflection% reflectionSelection details
Rfree0.2914 1072 4.99 %RANDOM
Rwork0.2766 ---
obs0.2774 21462 100 %-
Displacement parametersBiso max: 317.82 Å2 / Biso mean: 106.35 Å2 / Biso min: 39.02 Å2
Baniso -1Baniso -2Baniso -3
1-9.39 Å20 Å20.981 Å2
2---27.8287 Å20 Å2
3---18.4387 Å2
Refine analyzeLuzzati coordinate error obs: 0.85 Å
Refinement stepCycle: final / Resolution: 3.945→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12413 0 126 0 12539
Biso mean--99.95 --
Num. residues----1561
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d7186SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3849HARMONIC5
X-RAY DIFFRACTIONt_it12834HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1616SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance13HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17015SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d25069HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg44993HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion3.97
X-RAY DIFFRACTIONt_other_torsion15.66
LS refinement shellResolution: 3.945→3.974 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2871 21 4.88 %
Rwork0.2186 409 -
all0.2222 430 -
obs--100 %
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)
13.2163-0.5169-0.48322.0428-0.85343.1157-0.04720.10990.2841-0.0656-0.004-0.0579-0.4377-0.53940.0512-0.22730.1539-0.0524-0.1074-0.0355-0.2335123.79316.568842.8304
22.3597-0.17150.63552.4588-0.85232.8631-0.1425-0.22380.2103-0.08220.17180.2083-0.4971-0.5561-0.0293-0.29860.1521-0.0533-0.10150.001-0.309365.88926.664442.6878
34.3018-1.1187-0.38812.51210.73095.0118-0.1192-0.16770.31790.25570.00510.2386-0.11660.42420.11410.22770.0929-0.14280.0894-0.14750.02991.3773-18.30034.4362
46.64910.7173-2.05756.5483-1.71554.4490.03080.0815-0.19680.0564-0.0240.3030.0542-0.5409-0.0068-0.29440.0249-0.09670.3040.0987-0.2675128.7208-28.289975.0986
58.49263.0519-1.68526.541-2.76174.7124-0.1322-0.2959-0.56540.3006-0.1556-0.18090.4705-0.55970.2878-0.0748-0.15630.06960.3040.0822-0.202967.1711-28.624673.757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A105 - 650
2X-RAY DIFFRACTION2{ B|* }B107 - 664
3X-RAY DIFFRACTION3{ C|* }C9 - 281
4X-RAY DIFFRACTION4{ E|* }E1 - 120
5X-RAY DIFFRACTION5{ F|* }F1 - 120

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