[English] 日本語
Yorodumi
- PDB-6hyi: Regulatory subunit of a cAMP-independent protein kinase A from Tr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hyi
TitleRegulatory subunit of a cAMP-independent protein kinase A from Trypanosoma cruzi at 1.4 A resolution in complex with inosine
ComponentsProtein kinase A regulatory subunit
KeywordsSIGNALING PROTEIN / protein kinase A / regulatory subunit / cell signalling
Function / homology
Function and homology information


cilium / kinase activity / phosphorylation
Similarity search - Function
Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
INOSINE / Protein kinase A regulatory subunit
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3994484654 Å
AuthorsVolpato Santos, Y. / Lorentzen, E. / Basquin, J. / Boshart, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationBo1100/7-1 Germany
CitationJournal: Elife / Year: 2024
Title: Purine nucleosides replace cAMP in allosteric regulation of PKA in trypanosomatid pathogens.
Authors: Ober, V.T. / Githure, G.B. / Volpato Santos, Y. / Becker, S. / Moya Munoz, G. / Basquin, J. / Schwede, F. / Lorentzen, E. / Boshart, M.
History
DepositionOct 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0133
Polymers34,4761
Non-polymers5362
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint3 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.740, 88.529, 46.020
Angle α, β, γ (deg.)90.000, 98.280, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Protein kinase A regulatory subunit


Mass: 34476.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: PKAR, C3747_37g237
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q86RB0
#2: Chemical ChemComp-NOS / INOSINE / Inosine


Mass: 268.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M Magnesium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979179 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979179 Å / Relative weight: 1
ReflectionResolution: 1.399→88.529 Å / Num. obs: 124652 / % possible obs: 99.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.7880344982 Å2 / Rrim(I) all: 0.047 / Net I/σ(I): 10.01
Reflection shellResolution: 1.399→1.407 Å / Rrim(I) all: 0.643

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FLO

6flo


Resolution: 1.3994484654→45.5402929781 Å / SU ML: 0.187171574567 / Cross valid method: FREE R-VALUE / σ(F): 1.31669947668 / Phase error: 22.1960421157
RfactorNum. reflection% reflection
Rfree0.201100708418 6956 5.58351594545 %
Rwork0.180305526381 --
obs0.181488713943 124652 99.2898814078 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.2332091284 Å2
Refinement stepCycle: LAST / Resolution: 1.3994484654→45.5402929781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 38 415 2732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005558861994992384
X-RAY DIFFRACTIONf_angle_d0.8801759218123241
X-RAY DIFFRACTIONf_chiral_restr0.326378568589370
X-RAY DIFFRACTIONf_plane_restr0.0049647390279411
X-RAY DIFFRACTIONf_dihedral_angle_d20.1093705895859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3994-1.41540.3662694953952100.3797471341853754X-RAY DIFFRACTION95.472061657
1.4154-1.4320.3725913856412240.346084992853916X-RAY DIFFRACTION99.4236311239
1.432-1.44950.3477530795352360.339138799193941X-RAY DIFFRACTION99.310508797
1.4495-1.46780.3308947759362270.3162196281393922X-RAY DIFFRACTION99.4487056568
1.4678-1.48710.3141278711662290.303529412863932X-RAY DIFFRACTION99.5454545455
1.4871-1.50750.2986837534022100.2816360172633992X-RAY DIFFRACTION99.5262908574
1.5075-1.5290.2721697144882250.2699147205463885X-RAY DIFFRACTION99.4435035083
1.529-1.55190.2791479622962490.2649576062973930X-RAY DIFFRACTION99.5236961181
1.5519-1.57610.2601150210452550.2452909363043925X-RAY DIFFRACTION99.358212503
1.5761-1.6020.258874634062260.2336488148943894X-RAY DIFFRACTION99.4448467294
1.602-1.62960.2460891066912480.230114460143953X-RAY DIFFRACTION99.8099311
1.6296-1.65920.2127528270672350.1889291468923916X-RAY DIFFRACTION99.6399423908
1.6592-1.69110.2383616744562000.1857884469063995X-RAY DIFFRACTION99.5018975332
1.6911-1.72570.1978367454292320.1862035529773897X-RAY DIFFRACTION99.6861419604
1.7257-1.76320.2149460389312290.1962569498573969X-RAY DIFFRACTION99.643959174
1.7632-1.80420.2380201520682330.1892333426973915X-RAY DIFFRACTION99.8315282792
1.8042-1.84930.2234983793832420.1793697136663985X-RAY DIFFRACTION99.7404436055
1.8493-1.89930.2227025616022310.1818569101673882X-RAY DIFFRACTION99.636627907
1.8993-1.95520.1935216968082360.1753770586183961X-RAY DIFFRACTION99.5729537367
1.9552-2.01830.1791685468022340.175210916623911X-RAY DIFFRACTION99.7113302863
2.0183-2.09050.2124132128622420.1757175009483935X-RAY DIFFRACTION99.6421755725
2.0905-2.17410.1988837171732350.1707040305553910X-RAY DIFFRACTION99.4004796163
2.1741-2.27310.1918536723132330.1694283963563964X-RAY DIFFRACTION99.5021337127
2.2731-2.39290.195761189112330.1784634635863923X-RAY DIFFRACTION99.3545302415
2.3929-2.54280.2201252098762350.1800917662793927X-RAY DIFFRACTION99.3317422434
2.5428-2.73920.232045766722360.1823431831023916X-RAY DIFFRACTION99.4491017964
2.7392-3.01480.193163930682310.1781130689733879X-RAY DIFFRACTION98.6794717887
3.0148-3.45090.1903028637382340.163505428933898X-RAY DIFFRACTION98.5687022901
3.4509-4.34720.1514722223882280.1404640121193888X-RAY DIFFRACTION98.7998079693
4.3472-45.56440.1576806916912380.1567395964833910X-RAY DIFFRACTION98.7148976678
Refinement TLS params.Method: refined / Origin x: -72.2164423019 Å / Origin y: 85.1051645921 Å / Origin z: 19.0661017941 Å
111213212223313233
T0.144349122125 Å20.0081203287666 Å2-0.00577895369345 Å2-0.14049020947 Å2-0.020201450923 Å2--0.123784630793 Å2
L0.417255774798 °20.105540116029 °2-0.0791999594545 °2-0.700627338206 °2-0.356987370112 °2--0.284255140835 °2
S-0.0115733560285 Å °0.0224291256908 Å °0.0080856029203 Å °0.0196862915377 Å °0.0577894319747 Å °0.033393258439 Å °0.0215948899987 Å °0.0102644191205 Å °6.38164315988E-6 Å °
Refinement TLS groupSelection details: all

+
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