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- PDB-6a93: Crystal structure of 5-HT2AR in complex with risperidone -

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Basic information

Entry
Database: PDB / ID: 6a93
TitleCrystal structure of 5-HT2AR in complex with risperidone
Components5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


protein localization to cytoskeleton / 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 / serotonin receptor signaling pathway / Serotonin receptors / artery smooth muscle contraction ...protein localization to cytoskeleton / 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 / serotonin receptor signaling pathway / Serotonin receptors / artery smooth muscle contraction / cell body fiber / urinary bladder smooth muscle contraction / serotonin binding / negative regulation of synaptic transmission, glutamatergic / G protein-coupled serotonin receptor activity / neurotransmitter receptor activity / temperature homeostasis / regulation of dopamine secretion / detection of temperature stimulus involved in sensory perception of pain / protein tyrosine kinase activator activity / behavioral response to cocaine / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / negative regulation of potassium ion transport / activation of phospholipase C activity / positive regulation of fat cell differentiation / detection of mechanical stimulus involved in sensory perception of pain / release of sequestered calcium ion into cytosol / positive regulation of vasoconstriction / presynaptic modulation of chemical synaptic transmission / positive regulation of glycolytic process / dendritic shaft / phosphatidylinositol 3-kinase/protein kinase B signal transduction / caveola / glycolytic process / memory / intracellular calcium ion homeostasis / positive regulation of neuron apoptotic process / positive regulation of peptidyl-tyrosine phosphorylation / virus receptor activity / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / chemical synaptic transmission / cytoplasmic vesicle / postsynaptic membrane / G alpha (q) signalling events / electron transfer activity / periplasmic space / positive regulation of ERK1 and ERK2 cascade / response to xenobiotic stimulus / iron ion binding / axon / neuronal cell body / dendrite / glutamatergic synapse / heme binding / positive regulation of cell population proliferation / protein-containing complex binding / identical protein binding / plasma membrane
Similarity search - Function
5-Hydroxytryptamine 2A 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
Chem-8NU / CHOLESTEROL / PALMITIC ACID / Soluble cytochrome b562 / 5-hydroxytryptamine receptor 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKimura, T.K. / Asada, H. / Inoue, A. / Kadji, F.M.N. / Im, D. / Mori, C. / Arakawa, T. / Hirata, K. / Nomura, Y. / Nomura, N. ...Kimura, T.K. / Asada, H. / Inoue, A. / Kadji, F.M.N. / Im, D. / Mori, C. / Arakawa, T. / Hirata, K. / Nomura, Y. / Nomura, N. / Aoki, J. / Iwata, S. / Shimamura, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structures of the 5-HT2Areceptor in complex with the antipsychotics risperidone and zotepine.
Authors: Kimura, K.T. / Asada, H. / Inoue, A. / Kadji, F.M.N. / Im, D. / Mori, C. / Arakawa, T. / Hirata, K. / Nomura, Y. / Nomura, N. / Aoki, J. / Iwata, S. / Shimamura, T.
History
DepositionJul 11, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
B: 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,49311
Polymers83,8622
Non-polymers2,6319
Water0
1
A: 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5087
Polymers41,9311
Non-polymers1,5776
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9854
Polymers41,9311
Non-polymers1,0543
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)277.720, 42.150, 91.940
Angle α, β, γ (deg.)90.00, 92.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5-hydroxytryptamine receptor 2A,Soluble cytochrome b562 / 5-HT-2A / Serotonin receptor 2A / Cytochrome b-562


Mass: 41931.051 Da / Num. of mol.: 2 / Mutation: S162K, M164W, R120I, H124I, R128G, M29W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: HTR2A, HTR2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P28223, UniProt: P0ABE7

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Non-polymers , 5 types, 9 molecules

#2: Chemical ChemComp-8NU / 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one / Risperidone


Mass: 410.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27FN4O2 / Comment: antipsychotic*YM
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.62 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 100 mM MES, pH 6.0-6.5, 28-31% (v/v) PEG 400, 120-200 mM Am-formate, 1-2% (v/v) DMSO
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.707→46.241 Å / Num. obs: 29971 / % possible obs: 83.96 % / Redundancy: 22.4 % / CC1/2: 0.993 / Net I/σ(I): 6.63
Reflection shellResolution: 2.707→2.8 Å / CC1/2: 0.677

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Processing

Software
NameVersionClassification
PHENIX(dev_3150)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RH1
Resolution: 3→46.241 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 26.96
RfactorNum. reflection% reflection
Rfree0.2747 1011 5.49 %
Rwork0.2435 --
obs0.2452 18429 83.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→46.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5723 0 166 0 5889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036018
X-RAY DIFFRACTIONf_angle_d0.6518173
X-RAY DIFFRACTIONf_dihedral_angle_d12.0153602
X-RAY DIFFRACTIONf_chiral_restr0.04969
X-RAY DIFFRACTIONf_plane_restr0.004974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.15810.339620.29071095X-RAY DIFFRACTION38
3.1581-3.3560.32541140.27471851X-RAY DIFFRACTION63
3.356-3.6150.31511370.25652511X-RAY DIFFRACTION86
3.615-3.97860.28831800.24482927X-RAY DIFFRACTION100
3.9786-4.55390.25751680.22522965X-RAY DIFFRACTION100
4.5539-5.73570.24481680.23152976X-RAY DIFFRACTION100
5.7357-46.24630.24341820.23723093X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1936-1.16970.59051.8780.06481.1415-0.1091-1.34210.42840.45940.30770.10810.1091-0.2851-0.13250.5154-0.08690.19161.3779-0.55430.97820.68084.507670.7583
20.44970.00880.07430.86510.08151.22570.0286-0.22350.05840.2888-0.06920.4928-0.0268-0.86470.06870.21090.08720.1726-0.27130.06720.400241.8946-1.37553.2675
31.7848-0.7023-2.13473.7405-0.27192.9094-0.0123-0.7017-0.19770.28840.17190.32550.04620.1452-0.0980.3981-0.13960.20181.3501-0.00120.798124.5504-3.46169.6949
46.546-1.8029-0.90273.7576-0.37793.83120.3680.3353-0.04670.3171-0.02030.48780.7016-0.5326-0.33840.4906-0.10530.12530.7173-0.10530.30724.603-7.512229.8674
51.16420.5428-0.75271.05630.22820.91910.06030.33860.70290.0412-0.1023-0.1685-0.1471-0.09620.08830.4610.10310.35981.23190.35621.247823.09757.898820.9241
63.2142-0.081-0.9690.82590.18380.49750.2516-0.04890.4006-0.13740.2494-0.1415-0.2423-0.0994-0.27760.54660.0040.25131.63440.24050.75564.23436.03491.4453
73.3432-0.2925-1.96350.81750.09751.16610.0383-0.01520.2078-0.1792-0.0915-0.24370.0368-0.168-0.01780.48540.07820.23651.43830.08080.571847.5158-0.45839.8685
80.1001-0.19160.12515.6639-0.66330.23810.25581.19270.4267-0.6346-0.21871.03250.0815-0.55610.00720.4964-0.08760.04591.7777-0.1810.675518.1288-6.554715.568
90.8963-1.78790.87654.4756-2.18792.82690.28530.90820.05840.1828-0.0835-0.40920.72840.586-0.22480.3547-0.072-0.13930.7142-0.07950.37944.3721-7.126832.173
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 144 )
2X-RAY DIFFRACTION2chain 'A' and ((resid 145 through 265 ) or (resid 1001 through 1106 ) or (resid 313 through 348 ))
3X-RAY DIFFRACTION3chain 'A' and (resid 349 through 399 )
4X-RAY DIFFRACTION4chain 'B' and (resid 72 through 101 )
5X-RAY DIFFRACTION5chain 'B' and (resid 102 through 243 )
6X-RAY DIFFRACTION6chain 'B' and ((resid 244 through 265 ) or (resid 1001 through 1083 ))
7X-RAY DIFFRACTION7chain 'B' and ((resid 1084 through 1106 ) or (resid 313 through 348 ))
8X-RAY DIFFRACTION8chain 'B' and (resid 349 through 382 )
9X-RAY DIFFRACTION9chain 'B' and (resid 383 through 401 )

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