[English] 日本語
Yorodumi
- PDB-3vg9: Crystal structure of human adenosine A2A receptor with an alloste... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vg9
TitleCrystal structure of human adenosine A2A receptor with an allosteric inverse-agonist antibody at 2.7 A resolution
Components
  • (antibody fab fragment ...) x 2
  • Adenosine receptor A2a
KeywordsSIGNALING PROTEIN / 7 transmembrane receptor / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / NGF-independant TRKA activation ...positive regulation of acetylcholine secretion, neurotransmission / positive regulation of circadian sleep/wake cycle, sleep / regulation of norepinephrine secretion / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / G protein-coupled adenosine receptor signaling pathway / response to purine-containing compound / sensory perception / NGF-independant TRKA activation / Surfactant metabolism / positive regulation of urine volume / positive regulation of glutamate secretion / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / : / negative regulation of vascular permeability / type 5 metabotropic glutamate receptor binding / synaptic transmission, cholinergic / blood circulation / response to caffeine / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / cellular defense response / prepulse inhibition / phagocytosis / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / excitatory postsynaptic potential / regulation of mitochondrial membrane potential / apoptotic signaling pathway / positive regulation of long-term synaptic potentiation / synaptic transmission, glutamatergic / central nervous system development / positive regulation of synaptic transmission, GABAergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / positive regulation of apoptotic signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / vasodilation / blood coagulation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / postsynaptic membrane / negative regulation of neuron apoptotic process / calmodulin binding / inflammatory response / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / lipid binding / glutamatergic synapse / dendrite / regulation of DNA-templated transcription / protein-containing complex binding / apoptotic process / enzyme binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) ...Adenosine A2A receptor / Adenosine receptor / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / 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) / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
STEARIC ACID / Chem-ZMA / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. ...Hino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. / Cameron, A.D. / Kobayashi, T. / Hamakubo, T. / Iwata, S. / Murata, T.
CitationJournal: Nature / Year: 2012
Title: G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody
Authors: Hino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. / Cameron, A.D. / Kobayashi, T. / ...Authors: Hino, T. / Arakawa, T. / Iwanari, H. / Yurugi-Kobayashi, T. / Ikeda-Suno, C. / Nakada-Nakura, Y. / Kusano-Arai, O. / Weyand, S. / Shimamura, T. / Nomura, N. / Cameron, A.D. / Kobayashi, T. / Hamakubo, T. / Iwata, S. / Murata, T.
History
DepositionAug 4, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Database references
Revision 1.2Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine receptor A2a
B: antibody fab fragment light chain
C: antibody fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,91811
Polymers84,3633
Non-polymers2,5558
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-20 kcal/mol
Surface area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.180, 90.150, 113.550
Angle α, β, γ (deg.)90.00, 98.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-235-

HOH

-
Components

-
Antibody , 2 types, 2 molecules BC

#2: Antibody antibody fab fragment light chain


Mass: 23527.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody antibody fab fragment heavy chain


Mass: 24294.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Adenosine receptor A2a


Mass: 36540.266 Da / Num. of mol.: 1 / Fragment: UNP residues 1-316 / Mutation: N154Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADORA2A, ADORA2 / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / References: UniProt: P29274
#6: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 3 types, 77 molecules

#4: Chemical ChemComp-ZMA / 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol


Mass: 337.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N7O2 / Comment: antagonist*YM
#5: Chemical
ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H36O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 400, 0.1M MES, 0.2M magnesium chloride, 0.5% octhyl thioglucoside, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2010
RadiationMonochromator: ACCEL Fixed exit Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→72.1 Å / Num. all: 31030 / Num. obs: 31030 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 64.5 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 4.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.3 / % possible all: 92.9

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EML and 1P7K

3eml

1p7k


Resolution: 2.7→19.995 Å / SU ML: 0.34 / σ(F): 0 / Phase error: 27.35 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 1554 5.03 %RANDOM
Rwork0.206 ---
all0.2079 30910 --
obs0.2079 30910 92.81 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.619 Å2 / ksol: 0.293 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--16.8209 Å20 Å2-20.1804 Å2
2--1.4061 Å2-0 Å2
3---15.4147 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5651 0 180 70 5901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016230
X-RAY DIFFRACTIONf_angle_d1.0328082
X-RAY DIFFRACTIONf_dihedral_angle_d17.832147
X-RAY DIFFRACTIONf_chiral_restr0.072916
X-RAY DIFFRACTIONf_plane_restr0.005996
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.7870.38721450.3616265093
2.787-2.88630.36561360.3323256690
2.8863-3.00150.33021470.2701264993
3.0015-3.13760.25591520.2303272395
3.1376-3.30230.26971390.2177270394
3.3023-3.50820.25831380.2083259292
3.5082-3.77740.21971450.185271593
3.7774-4.15440.22041500.1644269994
4.1544-4.74860.20221480.1554262792
4.7486-5.95630.18911250.1718276695
5.9563-19.99570.27431290.2375266690
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)
10.04950.01970.02820.0531-0.02870.08480.10390.0805-0.0055-0.10230.07140.110.036-0.14160.13090.2194-0.0516-0.56990.78870.12940.4834-61.2381-9.3148-37.205
20.19240.05370.06010.13340.02710.0697-0.0204-0.0975-0.033-0.06260.00690.0222-0.0023-0.0953-0.00340.3031-0.0412-0.05390.32690.01770.315-20.5598-16.59384.8453
30.0967-0.0018-0.00060.1638-0.02560.02940.022-0.01470.0651-0.0342-0.0121-0.1105-0.0499-0.00270.00510.30890.0471-0.05430.269-0.07580.3964-19.3680.44090.3
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'

+
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