[English] 日本語
Yorodumi
- PDB-6bqg: Crystal structure of 5-HT2C in complex with ergotamine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bqg
TitleCrystal structure of 5-HT2C in complex with ergotamine
Components5-hydroxytryptamine receptor 2C,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / human 5-HT2C receptor / GPCR / ergotamine / polypharmacology / BRIL / LCP
Function / homology
Function and homology information


regulation of corticotropin-releasing hormone secretion / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / regulation of appetite / regulation of nervous system process / Serotonin receptors ...regulation of corticotropin-releasing hormone secretion / 1-(4-iodo-2,5-dimethoxyphenyl)propan-2-amine binding / Gq/11-coupled serotonin receptor activity / phospholipase C-activating serotonin receptor signaling pathway / positive regulation of phosphatidylinositol biosynthetic process / G protein-coupled serotonin receptor signaling pathway / G protein-coupled serotonin receptor complex / regulation of appetite / regulation of nervous system process / Serotonin receptors / serotonin receptor signaling pathway / serotonin binding / G protein-coupled serotonin receptor activity / feeding behavior / neurotransmitter receptor activity / cGMP-mediated signaling / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / behavioral fear response / positive regulation of fat cell differentiation / release of sequestered calcium ion into cytosol / positive regulation of calcium-mediated signaling / locomotory behavior / electron transport chain / intracellular calcium ion homeostasis / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / chemical synaptic transmission / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / iron ion binding / synapse / dendrite / heme binding / identical protein binding / plasma membrane
Similarity search - Function
5-Hydroxytryptamine 2C receptor / 5-hydroxytryptamine receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Ergotamine / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Soluble cytochrome b562 / 5-hydroxytryptamine receptor 2C
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPeng, Y. / McCorvy, J.D. / Harpsoe, K. / Lansu, K. / Yuan, S. / Popov, P. / Qu, L. / Pu, M. / Che, T. / Nikolajse, L.F. ...Peng, Y. / McCorvy, J.D. / Harpsoe, K. / Lansu, K. / Yuan, S. / Popov, P. / Qu, L. / Pu, M. / Che, T. / Nikolajse, L.F. / Huang, X.P. / Wu, Y. / Shen, L. / Bjorn-Yoshimoto, W.E. / Ding, K. / Wacker, D. / Han, G.W. / Cheng, J. / Katritch, V. / Jensen, A.A. / Hanson, M.A. / Zhao, S. / Gloriam, D.E. / Roth, B.L. / Stevens, R.C. / Liu, Z.
CitationJournal: Cell / Year: 2018
Title: 5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology.
Authors: Peng, Y. / McCorvy, J.D. / Harpsoe, K. / Lansu, K. / Yuan, S. / Popov, P. / Qu, L. / Pu, M. / Che, T. / Nikolajsen, L.F. / Huang, X.P. / Wu, Y. / Shen, L. / Bjorn-Yoshimoto, W.E. / Ding, K. ...Authors: Peng, Y. / McCorvy, J.D. / Harpsoe, K. / Lansu, K. / Yuan, S. / Popov, P. / Qu, L. / Pu, M. / Che, T. / Nikolajsen, L.F. / Huang, X.P. / Wu, Y. / Shen, L. / Bjorn-Yoshimoto, W.E. / Ding, K. / Wacker, D. / Han, G.W. / Cheng, J. / Katritch, V. / Jensen, A.A. / Hanson, M.A. / Zhao, S. / Gloriam, D.E. / Roth, B.L. / Stevens, R.C. / Liu, Z.J.
History
DepositionNov 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 4, 2023Group: 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: 5-hydroxytryptamine receptor 2C,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2483
Polymers51,3101
Non-polymers9382
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.840, 94.580, 145.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN

-
Components

#1: Protein 5-hydroxytryptamine receptor 2C,Soluble cytochrome b562 / 5-HTR2C / 5-hydroxytryptamine receptor 1C / 5-HT1C / Serotonin receptor 2C / Cytochrome b-562


Mass: 51310.055 Da / Num. of mol.: 1 / Mutation: M29W, H124I, R128L, C360N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: HTR2C, HTR1C, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28335, UniProt: P0ABE7
#2: Chemical ChemComp-ERM / Ergotamine


Mass: 581.661 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H35N5O5 / Comment: neurotransmitter, alkaloid*YM
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.11 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1 M sodium citrate pH 6.0, 100mM (NH4)2SO4, 30% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 12052 / % possible obs: 83.4 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Net I/σ(I): 21.6
Reflection shellResolution: 3→3.1 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 5 / Num. unique obs: 943 / CC1/2: 0.9 / % possible all: 67.8

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IB4

4ib4


Resolution: 3→47.29 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2909 550 4.58 %
Rwork0.2612 --
obs0.2627 12007 83.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 54 0 3030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033098
X-RAY DIFFRACTIONf_angle_d0.5154221
X-RAY DIFFRACTIONf_dihedral_angle_d10.9351836
X-RAY DIFFRACTIONf_chiral_restr0.037501
X-RAY DIFFRACTIONf_plane_restr0.003516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.30190.4618850.44182298X-RAY DIFFRACTION68
3.3019-3.77960.37731260.33822651X-RAY DIFFRACTION79
3.7796-4.76110.26141510.24253095X-RAY DIFFRACTION91
4.7611-47.29590.27051880.22853413X-RAY DIFFRACTION96

+
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://pdbjlc1.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