[English] 日本語
Yorodumi
- PDB-2v7o: Crystal structure of human calcium-calmodulin-dependent protein k... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v7o
TitleCrystal structure of human calcium-calmodulin-dependent protein kinase II gamma
ComponentsCALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II GAMMA CHAIN
KeywordsTRANSFERASE / KINASE / S/T KINASE / ATP-BINDING / SERINE/THREONINE-PROTEIN KINASE / NUCLEOTIDE-BINDING / PHOSPHORYLATION / CALMODULIN-BINDING
Function / homology
Function and homology information


regulation of skeletal muscle adaptation / calcium-dependent protein serine/threonine phosphatase activity / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / Trafficking of AMPA receptors / Assembly and cell surface presentation of NMDA receptors / calcium/calmodulin-dependent protein kinase activity / insulin secretion / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB ...regulation of skeletal muscle adaptation / calcium-dependent protein serine/threonine phosphatase activity / calcium- and calmodulin-dependent protein kinase complex / Ca2+/calmodulin-dependent protein kinase / Trafficking of AMPA receptors / Assembly and cell surface presentation of NMDA receptors / calcium/calmodulin-dependent protein kinase activity / insulin secretion / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / CaMK IV-mediated phosphorylation of CREB / regulation of neuron projection development / Negative regulation of NMDA receptor-mediated neuronal transmission / Phase 0 - rapid depolarisation / Unblocking of NMDA receptors, glutamate binding and activation / Ion transport by P-type ATPases / regulation of calcium ion transport / Long-term potentiation / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / Ion homeostasis / sarcoplasmic reticulum membrane / Ras activation upon Ca2+ influx through NMDA receptor / RAF activation / 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 / Interferon gamma signaling / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / nervous system development / RAF/MAP kinase cascade / cell differentiation / calmodulin binding / neuron projection / protein serine kinase activity / protein homodimerization activity / nucleoplasm / ATP binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / NTF2-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BISINDOLYLMALEIMIDE IX / Calcium/calmodulin-dependent protein kinase type II subunit gamma / Calcium/calmodulin-dependent protein kinase type II subunit gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPike, A.C.W. / Rellos, P. / Fedorov, O. / Burgess-Brown, N. / Shrestha, L. / Ugochukwu, E. / Pilka, E.S. / von Delft, F. / Edwards, A. / Weigelt, J. ...Pike, A.C.W. / Rellos, P. / Fedorov, O. / Burgess-Brown, N. / Shrestha, L. / Ugochukwu, E. / Pilka, E.S. / von Delft, F. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Knapp, S.
CitationJournal: Plos Biol. / Year: 2010
Title: Structure of the Camkiidelta/Calmodulin Complex Reveals the Molecular Mechanism of Camkii Kinase Activation.
Authors: Rellos, P. / Pike, A.C.W. / Niesen, F.H. / Salah, E. / Lee, W.H. / von Delft, F. / Knapp, S.
History
DepositionJul 31, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references / Derived calculations
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II GAMMA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0844
Polymers38,5021
Non-polymers5823
Water1,982110
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.703, 117.226, 75.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2030-

HOH

-
Components

#1: Protein CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II GAMMA CHAIN / CAM-KINASE II GAMMA CHAIN / CAM KINASE II GAMMA SUBUNIT / CAMK-II SUBUNIT GAMMA / CALCIUM- ...CAM-KINASE II GAMMA CHAIN / CAM KINASE II GAMMA SUBUNIT / CAMK-II SUBUNIT GAMMA / CALCIUM-CALMODULIN-DEPENDENT PROTEIN KINASE II GAMMA


Mass: 38501.922 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 5-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) ROSETTA / Variant (production host): R3
References: UniProt: Q8N4I3, UniProt: Q13555*PLUS, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-DRN / BISINDOLYLMALEIMIDE IX


Mass: 457.547 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23N5O2S / Comment: inhibitor*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsBISINDOLYLMALEIMIDE IX (DRN): BIM-9

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 50.7 % / Description: NONE
Crystal growpH: 7
Details: 0.10M MAGNESIUM CHLORIDE, 0.1M HEPES PH7, 20% PEG6K, 10% ETHYLENE GLYCOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00721
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00721 Å / Relative weight: 1
ReflectionResolution: 2.25→42.33 Å / Num. obs: 18326 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.4
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 1.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BDW

1bdw


Resolution: 2.25→35.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 14.48 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 936 5.1 %RANDOM
Rwork0.176 ---
obs0.179 17388 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.45 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2---0.43 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.25→35.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 41 110 2568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212524
X-RAY DIFFRACTIONr_bond_other_d0.0010.021706
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.9633424
X-RAY DIFFRACTIONr_angle_other_deg1.333.0034123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40423.793116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65315.036415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8181515
X-RAY DIFFRACTIONr_chiral_restr0.0750.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02513
X-RAY DIFFRACTIONr_nbd_refined0.190.2458
X-RAY DIFFRACTIONr_nbd_other0.180.21718
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21192
X-RAY DIFFRACTIONr_nbtor_other0.0890.21267
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2590.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1920.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 55 -
Rwork0.231 1265 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: -17.835 Å / Origin y: -36.744 Å / Origin z: -5.995 Å
111213212223313233
T-0.0227 Å2-0.0031 Å20.0264 Å2--0.0818 Å20.0157 Å2---0.1926 Å2
L0.5622 °20.2605 °2-0.0332 °2-2.6013 °20.0891 °2--1.0305 °2
S-0.0035 Å °0.0256 Å °0.1641 Å °-0.1753 Å °0.0276 Å °0.0708 Å °-0.2573 Å °0.0334 Å °-0.0241 Å °

+
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