[English] 日本語
Yorodumi
- PDB-6mh8: High-viscosity injector-based Pink Beam Serial Crystallography of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mh8
TitleHigh-viscosity injector-based Pink Beam Serial Crystallography of Micro-crystals at a Synchrotron Radiation Source
ComponentsAdenosine receptor A2a, Soluble cytochrome b562 chimeric construct
KeywordsMEMBRANE PROTEIN / GPCR / Pink beam serial crystallography
Function / homology
Function and homology information


regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / sensory perception ...regulation of norepinephrine secretion / positive regulation of circadian sleep/wake cycle, sleep / positive regulation of acetylcholine secretion, neurotransmission / negative regulation of alpha-beta T cell activation / Adenosine P1 receptors / G protein-coupled adenosine receptor activity / response to purine-containing compound / G protein-coupled adenosine receptor signaling pathway / NGF-independant TRKA activation / sensory perception / Surfactant metabolism / positive regulation of urine volume / synaptic transmission, dopaminergic / inhibitory postsynaptic potential / type 5 metabotropic glutamate receptor binding / negative regulation of vascular permeability / positive regulation of glutamate secretion / synaptic transmission, cholinergic / response to caffeine / blood circulation / intermediate filament / eating behavior / alpha-actinin binding / presynaptic active zone / regulation of calcium ion transport / membrane depolarization / asymmetric synapse / axolemma / phagocytosis / prepulse inhibition / cellular defense response / presynaptic modulation of chemical synaptic transmission / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / regulation of mitochondrial membrane potential / central nervous system development / positive regulation of apoptotic signaling pathway / positive regulation of long-term synaptic potentiation / excitatory postsynaptic potential / positive regulation of synaptic transmission, GABAergic / synaptic transmission, glutamatergic / positive regulation of protein secretion / locomotory behavior / astrocyte activation / apoptotic signaling pathway / electron transport chain / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of inflammatory response / adenylate cyclase-activating G protein-coupled receptor signaling pathway / blood coagulation / vasodilation / cell-cell signaling / presynaptic membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / negative regulation of neuron apoptotic process / postsynaptic membrane / periplasmic space / electron transfer activity / positive regulation of ERK1 and ERK2 cascade / calmodulin binding / inflammatory response / iron ion binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / neuronal cell body / apoptotic process / lipid binding / heme binding / dendrite / regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / enzyme binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
Adenosine A2A receptor / Adenosine receptor / 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-ZMA / Soluble cytochrome b562 / Adenosine receptor A2a
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 Å
AuthorsMartin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. ...Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhan, S. / Weierstall, U. / Spence, J.C.H. / Fromme, P. / Zatsepin, N.A. / Fischetti, R.F. / Cherezov, V. / Liu, W.
Funding support United States, 10items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Science Foundation (NSF, United States)1565180 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21DA042298 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124152 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095583 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127086 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM111072 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)ACB-12002 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AGM12006 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Iucrj / Year: 2019
Title: High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source.
Authors: Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M.Y. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhang, S. / ...Authors: Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M.Y. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhang, S. / Weierstall, U. / Spence, J.C.H. / Fromme, P. / Zatsepin, N.A. / Fischetti, R.F. / Cherezov, V. / Liu, W.
History
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_R_split / _reflns_shell.pdbx_R_split
Revision 1.3Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 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
Revision 1.6Nov 1, 2023Group: Refinement description / Category: software / Item: _software.name
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adenosine receptor A2a, Soluble cytochrome b562 chimeric construct
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3122
Polymers49,9741
Non-polymers3371
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.000, 179.000, 142.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Adenosine receptor A2a, Soluble cytochrome b562 chimeric construct / Cytochrome b-562


Mass: 49974.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: ADORA2A, ADORA2, cybC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P29274, UniProt: P0ABE7
#2: 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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 5 / Details: sodium citrate pH 5.0, PEG 400, sodium thiocyanate

-
Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.033-1.67
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Jun 24, 2017
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0331
21.671
ReflectionResolution: 4.2→50 Å / Num. obs: 4021 / % possible obs: 87.8 % / Redundancy: 11.5 % / R split: 0.27 / Net I/σ(I): 4.5
Reflection shellResolution: 4.2→4.3 Å / R split: 0.262

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
CrystFELdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UVI

5uvi


Resolution: 4.2→50 Å / Cor.coef. Fo:Fc: 0.841 / Cor.coef. Fo:Fc free: 0.798 / SU B: 84.914 / SU ML: 1.114 / Cross valid method: THROUGHOUT / ESU R Free: 1.27 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28767 353 10 %RANDOM
Rwork0.24997 ---
obs0.25385 3179 87.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.074 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å2-0 Å2
2--0.82 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 4.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 25 0 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193073
X-RAY DIFFRACTIONr_bond_other_d0.0020.022985
X-RAY DIFFRACTIONr_angle_refined_deg1.0431.9584192
X-RAY DIFFRACTIONr_angle_other_deg0.86136789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0735387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.51823.675117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45815475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1281513
X-RAY DIFFRACTIONr_chiral_restr0.0450.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02731
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4025.9511560
X-RAY DIFFRACTIONr_mcbond_other2.3825.9461559
X-RAY DIFFRACTIONr_mcangle_it4.2228.9061943
X-RAY DIFFRACTIONr_mcangle_other4.2238.9111944
X-RAY DIFFRACTIONr_scbond_it1.8535.9221513
X-RAY DIFFRACTIONr_scbond_other1.8525.9211514
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.478.822250
X-RAY DIFFRACTIONr_long_range_B_refined11.52254.85413268
X-RAY DIFFRACTIONr_long_range_B_other11.52254.85313269
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.2→4.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 22 -
Rwork0.208 209 -
obs--78.84 %

+
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