[English] 日本語
Yorodumi
- PDB-6zbv: Inward-open structure of human glycine transporter 1 in complex w... -

+
Open data


ID or keywords:

Loading...

-
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


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 / transport across blood-brain barrier / sodium ion transmembrane transport / lateral plasma membrane / 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
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.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more