[English] 日本語
Yorodumi
- PDB-2vz6: Structure of human calcium calmodulin dependent protein kinase ty... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vz6
TitleStructure of human calcium calmodulin dependent protein kinase type II alpha (CAMK2A) in complex with Indirubin E804
ComponentsCALCIUM CALMODULIN DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CELL JUNCTION / CELL MEMBRANE / LONG TERM POTENTIATION / BRAIN / KINASE / SYNAPSE / MEMBRANE / NMDA RECEPTOR SIGNALLING / PHOSPHOPROTEIN / CALMODULIN-BINDING / NUCLEOTIDE-BINDING
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 / 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
Chem-FEF / S-1,2-PROPANEDIOL / Calcium/calmodulin-dependent protein kinase type II subunit alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPike, A.C.W. / Rellos, P. / King, O. / Salah, E. / Parizotto, E. / Fedorov, O. / Shrestha, L. / Burgess-Brown, N. / Roos, A. / Murray, J.W. ...Pike, A.C.W. / Rellos, P. / King, O. / Salah, E. / Parizotto, E. / Fedorov, O. / Shrestha, L. / Burgess-Brown, N. / Roos, A. / Murray, J.W. / von Delft, F. / Edwards, A. / Arrowsmith, C.H. / Wikstroem, M. / Bountra, C. / 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 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: 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 / Category: citation_author / Item: _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 / struct_ncs_dom_lim / 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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
B: CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2437
Polymers71,2842
Non-polymers9595
Water5,603311
1
A: CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1594
Polymers35,6421
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CALCIUM CALMODULIN DEPENDENT PROTEIN KINASE TYPE II ALPHA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0833
Polymers35,6421
Non-polymers4412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.244, 113.621, 131.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111TYRTYRLYSLYS1AA13 - 2124 - 32
211TYRTYRLYSLYS1BB13 - 2124 - 32
121VALVALVALVAL1AA26 - 3137 - 42
221VALVALVALVAL1BB26 - 3137 - 42
131LYSLYSGLNGLN6AA32 - 3743 - 48
231LYSLYSGLNGLN6BB32 - 3743 - 48
141GLUGLULYSLYS1AA38 - 4749 - 58
241GLUGLULYSLYS1BB38 - 4749 - 58
151LYSLYSPROPRO6AA48 - 7059 - 81
251LYSLYSPROPRO6BB48 - 7059 - 81
161ASNASNGLUGLU4AA71 - 8182 - 92
261ASNASNGLUGLU4BB71 - 8182 - 92
171PHEPHEMETMET6AA-3 - 020 - 23
271PHEPHEMETMET6BB-3 - 020 - 23
112HISHISTRPTRP1AA84 - 27095 - 281
212HISHISTRPTRP1BB84 - 27095 - 281
122ILEILECYSCYS4AA271 - 280282 - 291
222ILEILECYSCYS4BB271 - 280282 - 291
132METMETASNASN1AA281 - 294292 - 305
232METMETASNASN1BB281 - 294292 - 305
142ALAALALEULEU4AA295 - 299306 - 310
242ALAALALEULEU4BB295 - 299306 - 310

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.986, -0.109, 0.124), (0.13, -0.048, 0.99), (-0.102, 0.993, 0.062)
Vector: 63.29433, 28.29945, -15.66426)

-
Components

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


Mass: 35641.898 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 13-302
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) / Variant (production host): R3-PRARE2
References: UniProt: Q9UQM7, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-FEF / (2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME}


Mass: 365.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19N3O4
#3: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.98 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growpH: 8.5 / Details: 12% PEG6000, 0.1M TRIS PH8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9828
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9828 Å / Relative weight: 1
ReflectionResolution: 2.3→49.88 Å / Num. obs: 51687 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V7O

2v7o


Resolution: 2.3→43.15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.292 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2269 4.4 %RANDOM
Rwork0.163 ---
obs0.165 49347 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: 21.77 Å2
Baniso -1Baniso -2Baniso -3
1-3.58 Å20 Å20 Å2
2---0.76 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4654 0 69 311 5034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224862
X-RAY DIFFRACTIONr_bond_other_d0.0010.023324
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9676586
X-RAY DIFFRACTIONr_angle_other_deg0.9433.0018044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26223.5220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.71615825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7731530
X-RAY DIFFRACTIONr_chiral_restr0.0940.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215329
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02987
X-RAY DIFFRACTIONr_nbd_refined0.1960.2846
X-RAY DIFFRACTIONr_nbd_other0.2360.23136
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22262
X-RAY DIFFRACTIONr_nbtor_other0.1110.22229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0730.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.17732920
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.53554694
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.90781942
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.025111892
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A354tight positional0.210.05
12B354tight positional0.210.05
21A2710tight positional0.280.05
22B2710tight positional0.280.05
11A155medium positional0.460.5
12B155medium positional0.460.5
21A190medium positional0.510.5
22B190medium positional0.510.5
11A453loose positional0.745
12B453loose positional0.745
11A354tight thermal0.920.5
12B354tight thermal0.920.5
21A2710tight thermal1.020.5
22B2710tight thermal1.020.5
11A155medium thermal0.812
12B155medium thermal0.812
21A190medium thermal1.112
22B190medium thermal1.112
11A453loose thermal1.0110
12B453loose thermal1.0110
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 171
Rwork0.246 3586
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)
18.5879-0.96874.23773.5651-0.248911.047-0.10410.07130.19620.28950.0286-0.2547-0.11570.57550.0756-0.0378-0.0043-0.01380.20170.08240.135863.996862.415721.2157
22.7664-0.6889-0.48024.36810.31281.93550.2494-0.31180.5160.2651-0.3714-0.7486-0.49610.60180.1220.1188-0.0953-0.09480.09830.05880.160454.418770.651525.9448
32.08130.5410.55532.0985-0.1141.8450.01910.03980.0992-0.003-0.0548-0.0722-0.11710.03010.0357-0.1141-0.00040.0275-0.14830.0057-0.188134.053965.925716.2342
41.73280.6077-0.46742.5564-0.28153.98270.05710.1062-0.1145-0.1552-0.0422-0.07480.14830.0868-0.0149-0.16070.0258-0.0445-0.1385-0.0052-0.195431.448356.80514.0852
59.5331-0.9931-2.829410.32672.309211.9296-0.35740.16620.19510.47550.17390.8693-0.2037-0.9460.1836-0.1222-0.1446-0.05210.3037-0.06470.0991-3.235754.584641.6888
61.95840.1571-1.68030.52540.22796.7951-0.02250.08860.3140.0150.01580.27510.0015-0.92840.0067-0.0080.0262-0.00460.06820.0033-0.00585.215757.191951.0527
71.4079-0.4887-0.60931.21190.13872.5437-0.1009-0.1149-0.08590.16990.07930.06080.2944-0.08470.0216-0.084-0.0404-0.0092-0.18230.0359-0.155524.911546.181247.3837
83.48782.1937-0.9874.6223-0.66242.5876-0.05040.101-0.1233-0.0667-0.02490.25310.3986-0.10110.0753-0.05480.0126-0.0337-0.18940.0134-0.128926.511441.373635.6347
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-5 - 38
2X-RAY DIFFRACTION2A39 - 94
3X-RAY DIFFRACTION3A95 - 257
4X-RAY DIFFRACTION4A258 - 299
5X-RAY DIFFRACTION5B-5 - 39
6X-RAY DIFFRACTION6B40 - 93
7X-RAY DIFFRACTION7B94 - 266
8X-RAY DIFFRACTION8B267 - 300

+
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