[English] 日本語
Yorodumi
- PDB-5ig0: Crystal structure of S. rosetta CaMKII hub -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ig0
TitleCrystal structure of S. rosetta CaMKII hub
ComponentsCAMK/CAMK2 protein kinase
KeywordsTRANSFERASE / Ca2+/CaM-dependent kinase / choanoflagellate / open-spiral
Function / homology
Function and homology information


cellular anatomical entity / Ca2+/calmodulin-dependent protein kinase / calmodulin-dependent protein kinase activity / calmodulin binding / protein phosphorylation / ATP binding
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
calcium/calmodulin-dependent protein kinase
Similarity search - Component
Biological speciesSalpingoeca rosetta (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBhattacharyya, M. / Gee, C.L. / Barros, T. / Kuriyan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Elife / Year: 2016
Title: Molecular mechanism of activation-triggered subunit exchange in Ca(2+)/calmodulin-dependent protein kinase II.
Authors: Bhattacharyya, M. / Stratton, M.M. / Going, C.C. / McSpadden, E.D. / Huang, Y. / Susa, A.C. / Elleman, A. / Cao, Y.M. / Pappireddi, N. / Burkhardt, P. / Gee, C.L. / Barros, T. / Schulman, H. ...Authors: Bhattacharyya, M. / Stratton, M.M. / Going, C.C. / McSpadden, E.D. / Huang, Y. / Susa, A.C. / Elleman, A. / Cao, Y.M. / Pappireddi, N. / Burkhardt, P. / Gee, C.L. / Barros, T. / Schulman, H. / Williams, E.R. / Kuriyan, J.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Structure summary
Revision 1.2Sep 28, 2016Group: Data collection
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CAMK/CAMK2 protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6225
Polymers16,2491
Non-polymers3724
Water1,58588
1
A: CAMK/CAMK2 protein kinase
hetero molecules

A: CAMK/CAMK2 protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,24310
Polymers32,4992
Non-polymers7458
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area3740 Å2
ΔGint-53 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.805, 96.805, 58.416
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-655-

HOH

21A-682-

HOH

-
Components

#1: Protein CAMK/CAMK2 protein kinase


Mass: 16249.354 Da / Num. of mol.: 1 / Fragment: UNP residues 335-479
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salpingoeca rosetta (strain ATCC 50818 / BSB-021) (eukaryote)
Strain: ATCC 50818 / BSB-021 / Gene: PTSG_10090 / Production host: Escherichia coli (E. coli) / References: UniProt: F2UPG5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulphate, 0.1 M Tris pH 7.0, 2.0 M ammonium sulphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2013 / Details: M1: parabola M2: torroid
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→48.4 Å / Num. obs: 16674 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 22.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HKX

1hkx


Resolution: 1.75→41.918 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.21
RfactorNum. reflection% reflection
Rfree0.2111 853 5.12 %
Rwork0.1913 --
obs0.1923 16670 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→41.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1019 0 23 88 1130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041066
X-RAY DIFFRACTIONf_angle_d0.8331445
X-RAY DIFFRACTIONf_dihedral_angle_d12.686372
X-RAY DIFFRACTIONf_chiral_restr0.034157
X-RAY DIFFRACTIONf_plane_restr0.005184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.85970.311570.27122577X-RAY DIFFRACTION100
1.8597-2.00320.29511550.22952587X-RAY DIFFRACTION100
2.0032-2.20480.21441400.19732600X-RAY DIFFRACTION100
2.2048-2.52380.23921140.19722645X-RAY DIFFRACTION99
2.5238-3.17960.20211460.18942636X-RAY DIFFRACTION99
3.1796-41.92980.18181410.1762772X-RAY DIFFRACTION98

+
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