[English] 日本語
Yorodumi
- PDB-5ig3: Crystal structure of the human CaMKII-alpha hub -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ig3
TitleCrystal structure of the human CaMKII-alpha hub
ComponentsCalcium/calmodulin-dependent protein kinase type II subunit alpha
KeywordsTRANSFERASE / Ca2+/CaM-dependent kinase alpha / hub
Function / homology
Function and homology information


peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / regulation of neuron migration / dendritic spine development / Trafficking of AMPA receptors / positive regulation of calcium ion transport / negative regulation of hydrolase activity ...peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / regulation of neuron migration / dendritic spine development / Trafficking of AMPA receptors / positive regulation of calcium ion transport / negative regulation of hydrolase activity / Assembly and cell surface presentation of NMDA receptors / calcium/calmodulin-dependent protein kinase activity / regulation of mitochondrial membrane permeability involved in apoptotic process / CaMK IV-mediated phosphorylation of CREB / positive regulation of cardiac muscle cell apoptotic process / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / regulation of neuronal synaptic plasticity / Ion transport by P-type ATPases / Long-term potentiation / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / glutamate receptor binding / cellular response to interferon-beta / Ion homeostasis / Ras activation upon Ca2+ influx through NMDA receptor / response to ischemia / angiotensin-activated signaling pathway / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / cellular response to type II interferon / G1/S transition of mitotic cell cycle / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / calcium ion transport / Interferon gamma signaling / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / kinase activity / positive regulation of NF-kappaB transcription factor activity / Ca2+ pathway / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / protein autophosphorylation / dendritic spine / postsynaptic density / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / 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 type II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMcSpadden, E. / Cao, Y.M. / Bhattacharyya, 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 1.1Apr 6, 2016Group: Structure summary
Revision 1.2Jul 13, 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: Calcium/calmodulin-dependent protein kinase type II subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
F: Calcium/calmodulin-dependent protein kinase type II subunit alpha


Theoretical massNumber of molelcules
Total (without water)105,1246
Polymers105,1246
Non-polymers00
Water27015
1
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
F: Calcium/calmodulin-dependent protein kinase type II subunit alpha

A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Calcium/calmodulin-dependent protein kinase type II subunit alpha
E: Calcium/calmodulin-dependent protein kinase type II subunit alpha
F: Calcium/calmodulin-dependent protein kinase type II subunit alpha


Theoretical massNumber of molelcules
Total (without water)210,24812
Polymers210,24812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area27640 Å2
ΔGint-221 kcal/mol
Surface area66900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.888, 89.888, 226.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
Calcium/calmodulin-dependent protein kinase type II subunit alpha / CaMK-II subunit alpha


Mass: 17520.680 Da / Num. of mol.: 6 / Fragment: UNP residues 345-475
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2A, CAMKA, KIAA0968 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 35 % (v/v) MPD, 0.1 M HEPES pH 7.3

-
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: Jul 16, 2015 / Details: M1: parabola M2: torroid
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→48.64 Å / Num. obs: 25096 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 78 Å2 / CC1/2: 0.946 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 14.4
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.124 / Mean I/σ(I) obs: 2.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HKX

1hkx


Resolution: 2.75→48.631 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 31.54
RfactorNum. reflection% reflection
Rfree0.2684 1184 4.71 %
Rwork0.22 --
obs0.2225 23820 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.75→48.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6297 0 0 15 6312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026459
X-RAY DIFFRACTIONf_angle_d0.5058727
X-RAY DIFFRACTIONf_dihedral_angle_d11.4993798
X-RAY DIFFRACTIONf_chiral_restr0.042921
X-RAY DIFFRACTIONf_plane_restr0.0031131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.8140.43631460.40932950X-RAY DIFFRACTION100
2.814-2.88430.36181020.33792969X-RAY DIFFRACTION100
2.8843-2.96230.36411240.30732914X-RAY DIFFRACTION100
2.9623-3.04950.33511540.28792909X-RAY DIFFRACTION100
3.0495-3.14790.3021600.2622930X-RAY DIFFRACTION100
3.1479-3.26040.3071530.24882910X-RAY DIFFRACTION100
3.2604-3.39090.33521320.26552910X-RAY DIFFRACTION100
3.3909-3.54520.36121240.24652977X-RAY DIFFRACTION100
3.5452-3.7320.30041450.2222945X-RAY DIFFRACTION100
3.732-3.96570.28041400.2032907X-RAY DIFFRACTION100
3.9657-4.27180.24211620.18452938X-RAY DIFFRACTION100
4.2718-4.70130.20271510.16542894X-RAY DIFFRACTION100
4.7013-5.38090.22221450.17452919X-RAY DIFFRACTION100
5.3809-6.77640.27371700.24392904X-RAY DIFFRACTION100
6.7764-48.63840.25081610.21662914X-RAY DIFFRACTION100
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)
14.3460.57620.80263.6227-2.0144.626-0.03420.3885-0.1134-0.6569-0.048-0.25420.15480.5510.04780.6364-0.04220.17660.6067-0.09590.5676-7.072875.2717-10.6222
23.68770.6597-0.41395.4568-1.01125.3146-0.02760.4719-0.42-0.7411-0.03120.08580.4074-0.16360.0390.69170.0791-0.05060.5191-0.0430.5444-55.085349.4096-27.8143
33.8488-1.73091.63024.3143-0.81916.06670.21550.0288-0.7827-0.67410.00570.35481.05980.0127-0.17510.80460.036-0.06250.46160.02180.6548-51.002924.3888-5.559
45.5725-0.0061.48124.8471-0.2243.73950.10720.2654-0.6975-0.3122-0.1248-0.33760.81250.60890.08020.68920.25130.03740.6674-0.00210.7338-24.725824.651815.0052
57.4790.62520.40261.44671.29984.1374-0.04440.89490.2399-0.8751-0.045-0.0139-1.04880.43950.07041.1827-0.0432-0.03780.65040.04750.5702-32.936475.3487-29.6994
64.156-0.2782-0.49645.0761-0.91691.8555-0.1455-0.6869-0.4616-0.2924-0.0542-1.13310.02061.29630.09540.52750.02780.06571.17710.0690.8518-2.004149.323812.868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 329 through 472)
2X-RAY DIFFRACTION2(chain 'B' and resid 344 through 473)
3X-RAY DIFFRACTION3(chain 'C' and resid 331 through 472)
4X-RAY DIFFRACTION4(chain 'D' and resid 331 through 473)
5X-RAY DIFFRACTION5(chain 'E' and resid 344 through 473)
6X-RAY DIFFRACTION6(chain 'F' and resid 344 through 472)

+
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