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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6flo
TitleRegulatory subunit of a cAMP-independent protein kinase A from Trypanosoma brucei at 2.1 Angstrom resolution
ComponentsProtein kinase A regulatory subunit
KeywordsSIGNALING PROTEIN / Protein kinase A / Regulatory Subunit / Nucleoside-binding protein
Function / homology
Function and homology information


paraflagellar rod / modulation of formation of structure involved in a symbiotic process / cilium movement involved in cell motility / cAMP-dependent protein kinase regulator activity / quorum sensing / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / protein kinase A catalytic subunit binding / cAMP binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway ...paraflagellar rod / modulation of formation of structure involved in a symbiotic process / cilium movement involved in cell motility / cAMP-dependent protein kinase regulator activity / quorum sensing / cAMP-dependent protein kinase inhibitor activity / cAMP-dependent protein kinase complex / protein kinase A catalytic subunit binding / cAMP binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / kinase activity / intracellular signal transduction / cilium / protein phosphorylation / cytosol
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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
INOSINE / Protein kinase A regulatory subunit / Protein kinase A regulatory subunit
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.138686637 Å
AuthorsVolpato Santos, Y. / Lorentzen, E. / Basquin, J. / Boshart, M.
Funding support Brazil, Germany, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development233134/2014-0 Brazil
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
DepositionJan 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Apr 10, 2024Group: Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct_ref / struct_ref_seq
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 / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein kinase A regulatory subunit
B: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0838
Polymers68,8262
Non-polymers1,2576
Water2,342130
1
A: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9493
Polymers34,4131
Non-polymers5362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein kinase A regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1345
Polymers34,4131
Non-polymers7214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.460, 71.550, 122.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRSERSER(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA219 - 22721 - 29
12ASPASPASPASP(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA229 - 33531 - 137
13ASPASPILEILE(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA337 - 348139 - 150
14ARGARGARGARG(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA350 - 413152 - 215
15GLYGLYHISHIS(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA417 - 451219 - 253
16VALVALASNASN(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA453 - 458255 - 260
17ARGARGLYSLYS(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA460 - 474262 - 276
18THRTHRLYSLYS(chain A and (resseq 219:227 or resseq 229:235 or (resid...AA476 - 488278 - 290
29TYRTYRSERSER(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB219 - 22721 - 29
210ASPASPASPASP(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB229 - 33531 - 137
211ASPASPILEILE(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB337 - 348139 - 150
212ARGARGARGARG(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB350 - 413152 - 215
213GLYGLYHISHIS(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB417 - 451219 - 253
214VALVALASNASN(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB453 - 458255 - 260
215ARGARGLYSLYS(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB460 - 474262 - 276
216THRTHRLYSLYS(chain B and (resseq 219:227 or resseq 229:235 or (resid...BB476 - 488278 - 290

-
Components

#1: Protein Protein kinase A regulatory subunit


Mass: 34413.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb11.02.2210
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q385V6, UniProt: Q9GU80*PLUS
#2: Chemical
ChemComp-NOS / INOSINE


Mass: 268.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N4O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 32% PEG 3350, 50 mM Tris pH 8.0, 4% MPD, 0.2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.13→49.09 Å / Num. obs: 30014 / % possible obs: 89 % / Redundancy: 4 % / Biso Wilson estimate: 21.3717547556 Å2 / Net I/σ(I): 9.2
Reflection shellResolution: 2.14→2.22 Å / Num. unique obs: 30009

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
BUCCANEERmodel building
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.138686637→49.0836704952 Å / SU ML: 0.371269280305 / Cross valid method: FREE R-VALUE / σ(F): 0.0277024936218 / Phase error: 29.6760677529
RfactorNum. reflection% reflection
Rfree0.274742492489 1998 6.65733706517 %
Rwork0.220238891841 --
obs0.223883743113 30012 89.3320633409 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.0426550602 Å2
Refinement stepCycle: LAST / Resolution: 2.138686637→49.0836704952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 88 130 4514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005720106371144482
X-RAY DIFFRACTIONf_angle_d0.8528454672896094
X-RAY DIFFRACTIONf_chiral_restr0.0484989913175695
X-RAY DIFFRACTIONf_plane_restr0.00456508320636762
X-RAY DIFFRACTIONf_dihedral_angle_d11.22114499972602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1387-2.19220.534745023221800.5532771160831242X-RAY DIFFRACTION55.3601340034
2.1922-2.25140.4490042008471120.414591674011678X-RAY DIFFRACTION75.8474576271
2.2514-2.31770.3924791287891260.3033143198751793X-RAY DIFFRACTION81.9735155916
2.3177-2.39250.3114545939861420.2730397223091863X-RAY DIFFRACTION84.1376416282
2.3925-2.4780.3640946308911280.258841483641943X-RAY DIFFRACTION88.5042735043
2.478-2.57720.3448495631071480.2430154718471988X-RAY DIFFRACTION89.4847088395
2.5772-2.69450.2875663495291510.2322312047112012X-RAY DIFFRACTION90.8441831163
2.6945-2.83650.2856246126771490.2309299966962043X-RAY DIFFRACTION92.5675675676
2.8365-3.01420.2709835995771510.2423009902952125X-RAY DIFFRACTION95.4697986577
3.0142-3.24690.2994083559791530.2265085224262212X-RAY DIFFRACTION98.2142857143
3.2469-3.57360.2665612243161570.1994936256872217X-RAY DIFFRACTION98.3429991715
3.5736-4.09050.2165275445411590.1602425054122224X-RAY DIFFRACTION99.1264559068
4.0905-5.15270.1950961708051680.1396266514152292X-RAY DIFFRACTION99.5951417004
5.1527-49.09660.2100572666761740.1701295434722382X-RAY DIFFRACTION99.6102883866
Refinement TLS params.Method: refined / Origin x: 21.6494457721 Å / Origin y: -12.5074641799 Å / Origin z: 99.1971935704 Å
111213212223313233
T-0.0145814098939 Å20.0152468295041 Å20.183494336358 Å2-0.049165020948 Å2-0.0158532331543 Å2---0.0565203601001 Å2
L0.0809483828147 °2-0.0226684639225 °2-0.0531013411907 °2--0.030022833883 °20.175563258114 °2--0.08929968789 °2
S-0.0441257754618 Å °0.00370709979848 Å °0.14371457232 Å °0.138299645218 Å °-0.00615336465535 Å °-0.113956739444 Å °0.149920343416 Å °-0.0680023481305 Å °8.54241233166E-12 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