[English] 日本語
Yorodumi
- PDB-5ig5: Crystal structure of N. vectensis CaMKII-B hub at pH 4.2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ig5
TitleCrystal structure of N. vectensis CaMKII-B hub at pH 4.2
ComponentsCaMKII-B hub
KeywordsTRANSFERASE / Ca2+/CaM-dependent kinase / sea anemone / peptide docking / open-spiral
Function / homology
Function and homology information


protein serine/threonine kinase activity => GO:0004674 / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / calmodulin binding / neuron projection / protein serine kinase activity / ATP binding / cytoplasm
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 speciesNematostella vectensis (starlet sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBhattacharyya, M. / Gee, C.L. / Barros, T. / Kuriyan, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)NA 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 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Structure summary
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: CaMKII-B hub
F: CaMKII-B hub
C: CaMKII-B hub
D: CaMKII-B hub
E: CaMKII-B hub
B: CaMKII-B hub
G: CaMKII-B hub


Theoretical massNumber of molelcules
Total (without water)115,8057
Polymers115,8057
Non-polymers00
Water21612
1
A: CaMKII-B hub
F: CaMKII-B hub
C: CaMKII-B hub
D: CaMKII-B hub
E: CaMKII-B hub
B: CaMKII-B hub
G: CaMKII-B hub

A: CaMKII-B hub
F: CaMKII-B hub
C: CaMKII-B hub
D: CaMKII-B hub
E: CaMKII-B hub
B: CaMKII-B hub
G: CaMKII-B hub


Theoretical massNumber of molelcules
Total (without water)231,61014
Polymers231,61014
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area35740 Å2
ΔGint-198 kcal/mol
Surface area83260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.974, 113.974, 241.645
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11G-454-

VAL

21G-468-

HIS

-
Components

#1: Protein
CaMKII-B hub / Predicted protein


Mass: 16543.576 Da / Num. of mol.: 7 / Fragment: UNP residues 335-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nematostella vectensis (starlet sea anemone)
Gene: v1g157808 / Production host: Escherichia coli (E. coli) / References: UniProt: A7RF52
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.91 Å3/Da / Density % sol: 64.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 2.5 M sodium chloride, 0.1 M acetate pH 4.2, and 0.25 M lithium sulphate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→49.352 Å / Num. obs: 37190 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 11.1
Reflection shellResolution: 3→3.13 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.373 / Mean I/σ(I) obs: 1.5 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_2229: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HKX

1hkx


Resolution: 3→49.352 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 1816 4.89 %
Rwork0.2324 --
obs0.2342 37120 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7792 0 0 12 7804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039093
X-RAY DIFFRACTIONf_angle_d0.62512321
X-RAY DIFFRACTIONf_dihedral_angle_d13.2245471
X-RAY DIFFRACTIONf_chiral_restr0.0431409
X-RAY DIFFRACTIONf_plane_restr0.0041583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.08120.41461290.35162676X-RAY DIFFRACTION100
3.0812-3.17190.3451580.32812638X-RAY DIFFRACTION100
3.1719-3.27430.3681640.30272634X-RAY DIFFRACTION100
3.2743-3.39130.36361510.2942690X-RAY DIFFRACTION100
3.3913-3.5270.33921470.28072668X-RAY DIFFRACTION100
3.527-3.68750.31831360.24382704X-RAY DIFFRACTION100
3.6875-3.88180.27811400.22372668X-RAY DIFFRACTION100
3.8818-4.12490.24021130.2152729X-RAY DIFFRACTION100
4.1249-4.44320.23571250.19372731X-RAY DIFFRACTION100
4.4432-4.890.19741240.1712737X-RAY DIFFRACTION100
4.89-5.59670.20791230.19422764X-RAY DIFFRACTION100
5.5967-7.0480.31181370.26462791X-RAY DIFFRACTION100
7.048-49.35880.24571690.23322874X-RAY DIFFRACTION99
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)
15.4217-1.52831.74614.09720.32595.55160.2014-0.45420.0519-0.39490.41760.2346-0.3776-0.5054-0.39130.6144-0.1883-0.12750.95310.32090.4997-89.860813.9148-71.7594
25.8438-0.838-0.70796.2856-1.42856.8808-0.10340.5478-0.3805-0.45580.1737-0.02710.7069-0.141-0.02040.536-0.05670.05220.749-0.2610.3754-35.7399-8.369-61.5629
32.14541.6993-1.92383.0117-1.54881.8826-0.10371.32021.0784-0.6182-0.1454-0.28-0.00980.98060.02710.5924-0.06070.01031.71580.40750.8409-56.553515.0171-75.8785
41.05960.81071.05172.68590.66844.72820.46841.2917-1.1123-1.11990.22190.2250.77150.3007-0.83981.01030.1909-0.49121.8501-0.35450.7998-63.2022-6.2532-80.0677
55.42451.1339-0.65975.9169-1.09296.78690.0693-0.11790.46480.09450.202-0.2054-0.63850.0938-0.18880.3505-0.01560.02150.7528-0.20130.4776-32.94712.717-52.0203
62.96190.85660.84470.87260.63941.5290.3396-0.2739-0.77860.00450.10540.50080.8616-0.7522-0.51490.6799-0.8453-0.96011.4290.69611.2802-94.889-8.313-68.7599
75.02950.1337-0.24417.66180.19566.5350.0421-0.8486-0.10070.52080.0154-0.5352-0.02350.29260.03460.3738-0.09540.10330.8267-0.04250.4812-105.6786-12.9568-38.5158
82.4979-0.4815-0.70414.13910.54372.7969-0.21320.1571-0.2515-0.0731-0.30110.62890.4239-0.28080.40990.447-0.28310.00271.20560.15840.3988-106.9704-9.8192-36.7785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'F'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'B'
7X-RAY DIFFRACTION7chain 'G'
8X-RAY DIFFRACTION8chain 'G'

+
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://pdbjlvh1.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