[English] 日本語
Yorodumi
- PDB-7ujq: Cocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ujq
TitleCocrystal structure of human CaMKII-alpha (CAMK2A)kinase domain and GluN2B
Components
  • Calcium/calmodulin-dependent protein kinase type II subunit alpha
  • Glutamate receptor ionotropic, NMDA 2B
KeywordsTRANSFERASE / CaMKII / Kinase / Human / CAMK2A
Function / homology
Function and homology information


peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / excitatory chemical synaptic transmission / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / Activated NTRK2 signals through FYN / regulation of neuron migration / dendritic spine development / positive regulation of cysteine-type endopeptidase activity ...peptidyl-threonine autophosphorylation / regulation of endocannabinoid signaling pathway / calcium- and calmodulin-dependent protein kinase complex / excitatory chemical synaptic transmission / Ca2+/calmodulin-dependent protein kinase / regulation of neurotransmitter secretion / Activated NTRK2 signals through FYN / regulation of neuron migration / dendritic spine development / positive regulation of cysteine-type endopeptidase activity / Synaptic adhesion-like molecules / negative regulation of dendritic spine maintenance / Trafficking of AMPA receptors / positive regulation of calcium ion transport / negative regulation of hydrolase activity / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / calcium/calmodulin-dependent protein kinase activity / NMDA glutamate receptor activity / Neurexins and neuroligins / NMDA selective glutamate receptor complex / regulation of mitochondrial membrane permeability involved in apoptotic process / calcium ion transmembrane import into cytosol / glutamate binding / glutamate receptor signaling pathway / protein heterotetramerization / CaMK IV-mediated phosphorylation of CREB / glycine binding / 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 / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / Ion transport by P-type ATPases / Long-term potentiation / Regulation of MECP2 expression and activity / positive regulation of excitatory postsynaptic potential / HSF1-dependent transactivation / glutamate receptor binding / cellular response to interferon-beta / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / Ion homeostasis / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / EPHB-mediated forward signaling / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of synaptic transmission, glutamatergic / excitatory postsynaptic potential / synaptic transmission, glutamatergic / synaptic membrane / response to ischemia / angiotensin-activated signaling pathway / long-term synaptic potentiation / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / positive regulation of receptor signaling pathway via JAK-STAT / RAF activation / postsynaptic density membrane / brain development / regulation of synaptic plasticity / 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 / late endosome / kinase activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / Ca2+ pathway / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / chemical synaptic transmission / postsynaptic membrane / response to ethanol / protein autophosphorylation / dendritic spine / lysosome / postsynaptic density / learning or memory / cytoskeleton / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / cell surface / protein homodimerization activity / mitochondrion / zinc ion binding / nucleoplasm / ATP binding / identical protein binding
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / NTF2-like domain superfamily / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / NTF2-like domain superfamily / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-UZD / Glutamate receptor ionotropic, NMDA 2B / Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsOzden, C. / Foster, J.C. / Stratton, M.M. / Garman, S.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
Title: CaMKII binds both substrates and activators at the active site.
Authors: Ozden, C. / Sloutsky, R. / Mitsugi, T. / Santos, N. / Agnello, E. / Gaubitz, C. / Foster, J. / Lapinskas, E. / Esposito, E.A. / Saneyoshi, T. / Kelch, B.A. / Garman, S.C. / Hayashi, Y. / Stratton, M.M.
History
DepositionMar 31, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionApr 13, 2022ID: 6XBP
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

-
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: Glutamate receptor ionotropic, NMDA 2B
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3677
Polymers66,6044
Non-polymers7633
Water2,324129
1
A: Calcium/calmodulin-dependent protein kinase type II subunit alpha
C: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6383
Polymers33,3022
Non-polymers3351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-4 kcal/mol
Surface area13580 Å2
MethodPISA
2
B: Calcium/calmodulin-dependent protein kinase type II subunit alpha
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7304
Polymers33,3022
Non-polymers4272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-4 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.245, 91.784, 91.772
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRARGARGAA7 - 2741 - 268
21THRTHRARGARGBB7 - 2741 - 268
12ARGARGASPASPCC1295 - 13057 - 17
22ARGARGASPASPDD1295 - 13057 - 17

NCS ensembles :
ID
1
2

-
Components

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


Mass: 30548.086 Da / Num. of mol.: 2 / Mutation: D135N, Q223K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK2A, CAMKA, KIAA0968 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Protein/peptide Glutamate receptor ionotropic, NMDA 2B / GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / ...GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NR2B / N-methyl-D-aspartate receptor subunit 3 / hNR3


Mass: 2754.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13224
#3: Chemical ChemComp-UZD / methyl 6-O-(heptylcarbamoyl)-beta-L-altropyranoside


Mass: 335.393 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H29NO7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M Bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane, 0.1 M Ammonium sulfate, 25% PEG 3350, 19mM Methyl 6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K thorughout the collection / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Mar 22, 2019 / Details: Rigaku VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 29074 / % possible obs: 96.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.05 / Rrim(I) all: 0.127 / Χ2: 2.896 / Net I/σ(I): 9.3 / Num. measured all: 182419
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.295.70.37413540.9170.1650.411.53590.1
2.29-2.3360.33413320.9410.1430.3641.45792.9
2.33-2.385.90.30713960.950.1330.3361.5894.7
2.38-2.4260.29714100.9520.1270.3241.75495.1
2.42-2.486.10.26514140.9620.1130.2891.66295.7
2.48-2.536.20.25614130.9670.1090.2791.74695.9
2.53-2.66.30.23314180.960.0990.2531.99595.9
2.6-2.676.40.21214260.9760.0890.231.90796.2
2.67-2.756.50.19214210.9810.080.2082.1696.3
2.75-2.836.60.16914440.9850.070.1842.21896.7
2.83-2.946.60.15314720.9870.0640.1662.52598
2.94-3.056.60.19914550.9890.0870.2173.08398.1
3.05-3.196.60.11814620.990.0490.1283.00898.7
3.19-3.366.60.10514830.9920.0440.1143.0399.1
3.36-3.576.60.09314660.9930.0390.1013.74898.7
3.57-3.856.50.09215090.9930.0390.14.07999.1
3.85-4.236.40.08314970.9930.0360.093.98699.2
4.23-4.856.30.07915280.9940.0340.0874.46899.3
4.85-6.16.10.08615440.9930.0380.0944.49399.6
6.1-505.40.07716300.9920.0370.0866.70199

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6vzk

6vzk


Resolution: 2.25→45.93 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.799 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2711 1376 4.7 %RANDOM
Rwork0.2199 ---
obs0.2223 27648 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.67 Å2 / Biso mean: 24.97 Å2 / Biso min: 9.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å20 Å2
2---1.27 Å20 Å2
3---1.94 Å2
Refinement stepCycle: final / Resolution: 2.25→45.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4507 0 52 129 4688
Biso mean--23.01 21.49 -
Num. residues----562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0134671
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174352
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.6526321
X-RAY DIFFRACTIONr_angle_other_deg1.0881.59410083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79621.928249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.80415786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7351531
X-RAY DIFFRACTIONr_chiral_restr0.0490.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025152
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02996
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A83340.1
12B83340.1
21C2050.15
22D2050.15
LS refinement shellResolution: 2.252→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 93 -
Rwork0.254 1847 -
all-1940 -
obs--89.61 %

+
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