[English] 日本語
Yorodumi
- PDB-6hin: Mouse serotonin 5-HT3 receptor, serotonin-bound, F conformation -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6hin
TitleMouse serotonin 5-HT3 receptor, serotonin-bound, F conformation
Components5-hydroxytryptamine receptor 3A
KeywordsMEMBRANE PROTEIN / Ion channel / serotonin receptor / pentameric ligand-gated channel
Function / homologyNeurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / 5-hydroxytryptamine 3 receptor, A subunit / Neurotransmitter receptors and postsynaptic signal transmission / 5-hydroxytryptamine 3 receptor / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain ...Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / 5-hydroxytryptamine 3 receptor, A subunit / Neurotransmitter receptors and postsynaptic signal transmission / 5-hydroxytryptamine 3 receptor / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / serotonin-activated cation-selective channel complex / serotonin-gated cation-selective channel activity / serotonin binding / positive regulation of ion transmembrane transporter activity / integral component of postsynaptic membrane / integral component of presynaptic membrane / cleavage furrow / response to cocaine / cellular response to growth factor stimulus / transmembrane signaling receptor activity / response to ethanol / glutamatergic synapse / axon / neuronal cell body / cytoplasm / 5-hydroxytryptamine receptor 3A
Function and homology information
Specimen sourceMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsPolovinkin, L. / Neumann, E. / Schoehn, G. / Nury, H.
CitationJournal: Nature / Year: 2018
Title: Conformational transitions of the serotonin 5-HT3 receptor
Authors: Polovinkin, L. / Hassaine, G. / Perot, J. / Neumann, E. / Jensen, A.A. / Lefebvre, S.N. / Corringer, P.J. / Neyton, J. / Chipot, C. / Dehez, F. / Schoehn, G. / Nury, H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 30, 2018 / Release: Nov 7, 2018

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0225
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5-hydroxytryptamine receptor 3A
B: 5-hydroxytryptamine receptor 3A
C: 5-hydroxytryptamine receptor 3A
D: 5-hydroxytryptamine receptor 3A
E: 5-hydroxytryptamine receptor 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,94135
Polyers259,5305
Non-polymers6,41130
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)36790
ΔGint (kcal/M)-175
Surface area (Å2)72860
MethodPISA

-
Components

#1: Protein/peptide
5-hydroxytryptamine receptor 3A


Mass: 51906.031 Da / Num. of mol.: 5 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Htr3a / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: E9QLC0
#2: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 25 / Formula: C8H15NO6 / N-Acetylglucosamine
#3: Chemical
ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 5 / Formula: C10H12N2O / Serotonin

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: 5-HT3 receptor, serotonin-bound / Type: COMPLEX / Entity ID: 1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Cell: HEK 293 / Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 10667 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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