[English] 日本語
Yorodumi
- PDB-6kux: Crystal structures of the alpha2A adrenergic receptor in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kux
TitleCrystal structures of the alpha2A adrenergic receptor in complex with an antagonist RSC.
Componentsalpha2A adrenergic receptor
KeywordsSIGNALING PROTEIN / alpha2A adrenergic receptor / antagonist / GPCR
Function / homology
Function and homology information


negative regulation of uterine smooth muscle contraction / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / phospholipase C-activating adrenergic receptor signaling pathway / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / alpha-2C adrenergic receptor binding / receptor transactivation / epinephrine binding / alpha-1B adrenergic receptor binding / negative regulation of norepinephrine secretion ...negative regulation of uterine smooth muscle contraction / adenylate cyclase-inhibiting adrenergic receptor signaling pathway / phospholipase C-activating adrenergic receptor signaling pathway / alpha2-adrenergic receptor activity / Adrenaline signalling through Alpha-2 adrenergic receptor / alpha-2C adrenergic receptor binding / receptor transactivation / epinephrine binding / alpha-1B adrenergic receptor binding / negative regulation of norepinephrine secretion / negative regulation of calcium ion transmembrane transporter activity / negative regulation of epinephrine secretion / heterotrimeric G-protein binding / dopaminergic synapse / negative regulation of calcium ion-dependent exocytosis / Surfactant metabolism / positive regulation of potassium ion transport / thermoception / fear response / thioesterase binding / negative regulation of insulin secretion involved in cellular response to glucose stimulus / norepinephrine binding / Adrenoceptors / intestinal absorption / positive regulation of membrane protein ectodomain proteolysis / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of wound healing / adrenergic receptor signaling pathway / activation of protein kinase activity / negative regulation of calcium ion transport / Rho protein signal transduction / regulation of vasoconstriction / negative regulation of insulin secretion / GABA-ergic synapse / negative regulation of lipid catabolic process / axon terminus / presynaptic active zone membrane / adenylate cyclase-activating adrenergic receptor signaling pathway / cellular response to hormone stimulus / presynaptic modulation of chemical synaptic transmission / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / activation of protein kinase B activity / positive regulation of cytokine production / female pregnancy / postsynaptic density membrane / positive regulation of MAP kinase activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / platelet activation / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / vasodilation / glucose homeostasis / G alpha (i) signalling events / actin cytoskeleton organization / basolateral plasma membrane / DNA replication / Ras protein signal transduction / positive regulation of MAPK cascade / receptor complex / positive regulation of cell migration / G protein-coupled receptor signaling pathway / protein heterodimerization activity / neuronal cell body / glutamatergic synapse / positive regulation of cell population proliferation / protein kinase binding / protein homodimerization activity / plasma membrane / cytoplasm
Similarity search - Function
Alpha 2A adrenoceptor / Adrenoceptor family / 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
Chem-E3F / CITRATE ANION / OLEIC ACID / DI(HYDROXYETHYL)ETHER / Alpha-2A adrenergic receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsQu, L. / Zhou, Q.T. / Wu, D. / Zhao, S.W.
CitationJournal: To Be Published
Title: Crystal structures of the alpha2A adrenergic receptor in complex with an antagonist RSC.
Authors: Qu, L. / Zhou, Q.T. / Wu, D. / Zhao, S.W.
History
DepositionSep 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 22, 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: alpha2A adrenergic receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8589
Polymers44,4911
Non-polymers1,3678
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-1 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.170, 71.790, 284.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein alpha2A adrenergic receptor


Mass: 44490.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P08913*PLUS
#2: Chemical ChemComp-E3F / (8~{a}~{R},12~{a}~{S},13~{a}~{S})-12-ethylsulfonyl-3-methoxy-5,6,8,8~{a},9,10,11,12~{a},13,13~{a}-decahydroisoquinolino[2,1-g][1,6]naphthyridine


Mass: 364.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28N2O3S
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.25 Å3/Da / Density % sol: 71.06 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1M Sodium citrate tribasic dihydrate pH 5.0, 290mM Ammonium chloride, 30% PEG400, 7% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→49.7 Å / Num. obs: 18743 / % possible obs: 91.4 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.7
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.487 / Num. unique obs: 2155 / CC1/2: 0.46 / % possible all: 73.4
Serial crystallography sample deliveryMethod: fixed target

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y02

2y02


Resolution: 2.7→47.385 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.41
RfactorNum. reflection% reflection
Rfree0.2669 867 4.63 %
Rwork0.2511 --
obs0.252 18724 91.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.385 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 79 0 2979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033043
X-RAY DIFFRACTIONf_angle_d0.5264135
X-RAY DIFFRACTIONf_dihedral_angle_d15.6421802
X-RAY DIFFRACTIONf_chiral_restr0.039487
X-RAY DIFFRACTIONf_plane_restr0.003508
LS refinement shellResolution: 2.7→2.8691 Å
RfactorNum. reflection% reflection
Rfree0.2669 109 -
Rwork0.2511 2332 -
obs--73 %
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)
13.88630.62151.08990.27591.52256.0010.0278-0.96940.10750.18970.55630.0659-1.14641.7109-0.22381.7608-0.18290.18121.4739-0.51170.7221-2.3629-4.9629-33.3038
26.75892.12120.95627.9903-0.10523.92720.02680.0133-0.14150.1850.08380.17860.2116-0.2315-0.13690.3097-0.0049-0.00750.3075-0.01090.7441-11.3049-34.386-70.0184
34.6540.1353.77810.5670.16792.6944-0.1833-0.0066-0.18160.8070.343-0.53681.51692.9610.05281.75870.33650.02471.6924-0.42920.83470.0879-15.3426-35.5685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 227 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1001 through 1106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 365 through 443 )

+
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