[English] 日本語
Yorodumi
- EMDB-12566: Structure of human excitatory amino acid transporter 3 (EAAT3) in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12566
TitleStructure of human excitatory amino acid transporter 3 (EAAT3) in complex with HIP-B
Map data
Sample
  • Complex: Ternary complex of excitatory amino acid transporter 3 with inhibitor HIP-B
    • Protein or peptide: Excitatory amino acid transporter 3
  • Ligand: (+)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-carboxylic acid
  • Ligand: (-)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-carboxylic acid
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Function / homology
Function and homology information


response to decreased oxygen levels / D-aspartate transmembrane transport / response to anesthetic / regulation of protein targeting to membrane / neurotransmitter receptor transport to plasma membrane / D-aspartate transmembrane transporter activity / Defective SLC1A1 is implicated in schizophrenia 18 (SCZD18) and dicarboxylic aminoaciduria (DCBXA) / distal dendrite / cysteine transmembrane transporter activity / cysteine transport ...response to decreased oxygen levels / D-aspartate transmembrane transport / response to anesthetic / regulation of protein targeting to membrane / neurotransmitter receptor transport to plasma membrane / D-aspartate transmembrane transporter activity / Defective SLC1A1 is implicated in schizophrenia 18 (SCZD18) and dicarboxylic aminoaciduria (DCBXA) / distal dendrite / cysteine transmembrane transporter activity / cysteine transport / monoatomic anion channel activity / high-affinity L-glutamate transmembrane transporter activity / glutamate:sodium symporter activity / L-glutamate import / cellular response to mercury ion / Transport of inorganic cations/anions and amino acids/oligopeptides / conditioned place preference / zinc ion transmembrane transport / L-glutamate transmembrane transport / retina layer formation / cellular response to bisphenol A / L-glutamate transmembrane transporter activity / L-aspartate transmembrane transport / D-aspartate import across plasma membrane / cellular response to ammonium ion / proximal dendrite / glutathione biosynthetic process / righting reflex / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / grooming behavior / intracellular glutamate homeostasis / Glutamate Neurotransmitter Release Cycle / L-glutamate import across plasma membrane / apical dendrite / neurotransmitter transport / transepithelial transport / response to morphine / intracellular zinc ion homeostasis / glutamate receptor signaling pathway / cellular response to cocaine / chloride transmembrane transporter activity / motor neuron apoptotic process / blood vessel morphogenesis / motor behavior / glutamate binding / dopamine receptor signaling pathway / maintenance of blood-brain barrier / positive regulation of heart rate / adult behavior / dopamine metabolic process / postsynaptic modulation of chemical synaptic transmission / superoxide metabolic process / heart contraction / perisynaptic space / glial cell projection / transport across blood-brain barrier / cellular response to organic cyclic compound / asymmetric synapse / response to axon injury / behavioral fear response / synaptic cleft / axon terminus / monoatomic ion transport / chloride transmembrane transport / response to amphetamine / neurogenesis / dendritic shaft / locomotory behavior / long-term synaptic potentiation / cell periphery / synapse organization / regulation of protein phosphorylation / brain development / Schaffer collateral - CA1 synapse / memory / cytokine-mediated signaling pathway / recycling endosome membrane / presynapse / late endosome membrane / gene expression / cellular response to oxidative stress / perikaryon / chemical synaptic transmission / early endosome membrane / negative regulation of neuron apoptotic process / dendritic spine / response to xenobiotic stimulus / membrane raft / apical plasma membrane / axon / dendrite / neuronal cell body / cell surface / endoplasmic reticulum / extracellular exosome / membrane / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Sodium:dicarboxylate symporter family signature 2. / 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
Excitatory amino acid transporter 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsBaronina A / Pike ACW / Yu X / Dong YY / Shintre CA / Tessitore A / Chu A / Rotty B / Venkaya S / Mukhopadhyay SMM ...Baronina A / Pike ACW / Yu X / Dong YY / Shintre CA / Tessitore A / Chu A / Rotty B / Venkaya S / Mukhopadhyay SMM / Borkowska O / Chalk R / Shrestha L / Burgess-Brown NA / Edwards AM / Arrowsmith CH / Bountra C / Han S / Carpenter EP / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Wellcome Trust106169/Z/14/Z United Kingdom
CitationJournal: TO BE PUBLISHED
Title: Structure of human excitatory amino acid transporter 3 (EAAT3) in complex with HIP-B
Authors: Baronina A / Pike ACW / Yu X / Dong YY / Shintre CA / Tessitore A / Chu A / Rotty B / Venkaya S / Mukhopadhyay SMM / Borkowska O / Chalk R / Shrestha L / Burgess-Brown NA / Edwards AM / ...Authors: Baronina A / Pike ACW / Yu X / Dong YY / Shintre CA / Tessitore A / Chu A / Rotty B / Venkaya S / Mukhopadhyay SMM / Borkowska O / Chalk R / Shrestha L / Burgess-Brown NA / Edwards AM / Arrowsmith CH / Bountra C / Han S / Carpenter EP
History
DepositionMar 5, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7nsg
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12566.png

Downloads & links

-
Map

FileDownload / File: emd_12566.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.086 Å
Density
Contour LevelBy AUTHOR: 0.0252 / Movie #1: 0.03
Minimum - Maximum-0.20561619 - 0.2551124
Average (Standard dev.)3.249621e-05 (±0.007815577)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 217.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0861.0861.086
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z217.200217.200217.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2060.2550.000

-
Supplemental data

-
Mask #1

Fileemd_12566_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_12566_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_12566_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_12566_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of excitatory amino acid transporter 3 with inhib...

EntireName: Ternary complex of excitatory amino acid transporter 3 with inhibitor HIP-B
Components
  • Complex: Ternary complex of excitatory amino acid transporter 3 with inhibitor HIP-B
    • Protein or peptide: Excitatory amino acid transporter 3
  • Ligand: (+)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-carboxylic acid
  • Ligand: (-)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-carboxylic acid
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

-
Supramolecule #1: Ternary complex of excitatory amino acid transporter 3 with inhib...

SupramoleculeName: Ternary complex of excitatory amino acid transporter 3 with inhibitor HIP-B
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant strain: 9
Molecular weightTheoretical: 160 KDa

-
Macromolecule #1: Excitatory amino acid transporter 3

MacromoleculeName: Excitatory amino acid transporter 3 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.252867 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGKPARKGCE WKRFLKNNWV LLSTVAAVVL GITTGVLVRE HRNLSTLEKF YFAFPGEILM RMLKLIILPL IISSMITGVA ALDSNVSGK IGVRAVVYYF CTTLIAVILG IVLVVSIKPG VTQKVGEIAR TGSTPEVSTV DAMLDLIRNM FPENLVQACF Q QYKTKREE ...String:
MGKPARKGCE WKRFLKNNWV LLSTVAAVVL GITTGVLVRE HRNLSTLEKF YFAFPGEILM RMLKLIILPL IISSMITGVA ALDSNVSGK IGVRAVVYYF CTTLIAVILG IVLVVSIKPG VTQKVGEIAR TGSTPEVSTV DAMLDLIRNM FPENLVQACF Q QYKTKREE VKPPSDPEMN MTEESFTAVM TTAISKNKTK EYKIVGMYSD GINVLGLIVF CLVFGLVIGK MGEKGQILVD FF NALSDAT MKIVQIIMCY MPLGILFLIA GKIIEVEDWE IFRKLGLYMA TVLTGLAIHS IVILPLIYFI VVRKNPFRFA MGM AQALLT ALMISSSSAT LPVTFRCAEE NNQVDKRITR FVLPVGATIN MDGTALYEAV AAVFIAQLND LDLGIGQIIT ISIT ATSAS IGAAGVPQAG LVTMVIVLSA VGLPAEDVTL IIAVDWLLDR FRTMVNVLGD AFGTGIVEKL SKKELEQMDV SSEVN AENL YFQ

-
Macromolecule #2: (+)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-c...

MacromoleculeName: (+)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-carboxylic acid
type: ligand / ID: 2 / Number of copies: 3 / Formula: UR5
Molecular weightTheoretical: 172.139 Da
Chemical component information

ChemComp-UR5:
(+)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-carboxylic acid

-
Macromolecule #3: (-)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-c...

MacromoleculeName: (-)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-carboxylic acid
type: ligand / ID: 3 / Number of copies: 3 / Formula: UR8
Molecular weightTheoretical: 172.139 Da
Chemical component information

ChemComp-UR8:
(-)-3-Hydroxy-4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-6-carboxylic acid

-
Macromolecule #4: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

-
Macromolecule #5: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 5 / Number of copies: 15 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium chloridesodium chloride
20.0 mMHEPES(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
0.003 %LMNGlauryl maltose neopentyl glycol
0.0003 %CHScholesteryl hemisuccinate

Details: Solutions were made fresh from pre-made, sterile filtered stocks.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 4s Blot force -15 sample volume 3 uL.
DetailsMonodisperse sample after SEC

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 4947 / Average electron dose: 42.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1169680
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: NONE / Details: Ab-initio models were generated using RELION 2.1
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 127936
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6s3q


Chain - Chain ID: A
DetailsMODEL REFINED USING NCS CONSTRAINTS AND ROTAMER, CBETA, SECONDARY STRUCTURE AND RAMACHANDARN RESTRAINTS AGAINST RELION POST-PROCESSED B-FACTOR SHARPENED (-118A**2) 3.34A FILTERED MAP
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7nsg:
Structure of human excitatory amino acid transporter 3 (EAAT3) in complex with HIP-B

+
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://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