[English] 日本語
Yorodumi
- PDB-2vn9: Crystal Structure of Human Calcium Calmodulin dependent Protein K... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vn9
TitleCrystal Structure of Human Calcium Calmodulin dependent Protein Kinase II delta isoform 1, CAMKD
ComponentsCALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / SERINE-THREONINE KINASE / CELLULAR DIFFERENTIATION / VASCULAR SMOOTH MUSCLE / KINASE / ATP-BINDING / PHOSPHOPROTEIN / CALMODULIN-BINDING / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / calcium- and calmodulin-dependent protein kinase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of the force of heart contraction / Trafficking of AMPA receptors ...regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / calcium- and calmodulin-dependent protein kinase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of the force of heart contraction / Trafficking of AMPA receptors / cardiac muscle cell contraction / endoplasmic reticulum calcium ion homeostasis / Assembly and cell surface presentation of NMDA receptors / sodium channel inhibitor activity / calmodulin-dependent protein kinase activity / regulation of heart contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / relaxation of cardiac muscle / CaMK IV-mediated phosphorylation of CREB / regulation of cardiac muscle cell action potential / regulation of membrane depolarization / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / regulation of heart rate by cardiac conduction / Phase 0 - rapid depolarisation / Long-term potentiation / Ion transport by P-type ATPases / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / sarcoplasmic reticulum membrane / cellular response to calcium ion / Ras activation upon Ca2+ influx through NMDA receptor / regulation of cell growth / peptidyl-threonine phosphorylation / RAF activation / sarcolemma / endocytic vesicle membrane / 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 / Signaling by BRAF and RAF1 fusions / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / transmembrane transporter binding / protein autophosphorylation / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein homodimerization activity / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / 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-GVD / PHOSPHATE ION / Calcium/calmodulin-dependent protein kinase type II subunit delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRoos, A.K. / Rellos, P. / Salah, E. / Pike, A.C.W. / Fedorov, O. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Roos, A.K. / Rellos, P. / Salah, E. / Pike, A.C.W. / Fedorov, O. / Pilka, E.S. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / 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
DepositionJan 31, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references / Derived calculations / Non-polymer description
Revision 1.3Dec 13, 2017Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.gene_src_common_name ..._citation_author.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
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 DELTA CHAIN
B: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,92310
Polymers68,5072
Non-polymers1,4178
Water1,74797
1
A: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0996
Polymers34,2531
Non-polymers8455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8254
Polymers34,2531
Non-polymers5713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.276, 68.276, 313.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: -1 - 309 / Label seq-ID: 1 - 301

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.501, -0.82, 0.275), (-0.865, 0.48, -0.145), (-0.013, -0.311, -0.95)
Vector: 13.43522, 58.73976, 58.85304)

-
Components

-
Protein , 1 types, 2 molecules AB

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


Mass: 34253.457 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 11-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-PRARE2
References: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase

-
Non-polymers , 5 types, 105 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GVD / [4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE


Mass: 381.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H19N7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.85 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.6 M NAKPO4 HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98248
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98248 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 39106 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2 / % 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→43.03 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 15.783 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1960 5 %RANDOM
Rwork0.211 ---
obs0.213 37042 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: 51.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20.57 Å20 Å2
2--1.15 Å20 Å2
3----1.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4721 0 94 97 4912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224928
X-RAY DIFFRACTIONr_bond_other_d0.0020.023332
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.9766686
X-RAY DIFFRACTIONr_angle_other_deg0.9763.0018071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02523.796216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52515820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5221530
X-RAY DIFFRACTIONr_chiral_restr0.080.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215440
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02980
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.68433000
X-RAY DIFFRACTIONr_mcbond_other0.8731210
X-RAY DIFFRACTIONr_mcangle_it2.48154823
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.49581928
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.576111857
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

Ens-ID: 1 / Number: 3959 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
1Atight thermal0.160.5
2Btight thermal0.160.5
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 140 -
Rwork0.298 2704 -
obs--99.89 %
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)
14.7580.43870.72318.4181.91611.652-0.3062-0.30870.5231-0.09870.13270.2238-0.7694-0.41470.1735-0.4185-0.03720.02420.1348-0.02220.059612.480237.930755.7746
26.7529-3.0149-0.35441.81970.94491.3251-0.1694-0.3660.45050.09630.07960.018-0.0176-0.12050.0898-0.4955-0.03430.00550.13710.0496-0.1308-0.275330.218553.5075
33.35980.505-0.23681.90791.25582.0951-0.27710.606-0.3184-0.42130.2423-0.11340.1423-0.07560.0348-0.2976-0.14460.07770.10630.023-0.17767.008415.675736.1947
47.46210.71621.00517.4556-0.382610.1546-0.2801-0.02990.4969-0.46170.29550.2677-0.3389-0.6191-0.01550.1722-0.2799-0.1864-0.09160.06210.0591-8.593957.9775-6.0806
50.21880.32490.72258.9965-2.13543.5945-0.35330.05360.2378-0.98190.11940.2851-0.12040.06870.23390.2174-0.337-0.1012-0.15210.0336-0.14193.795465.3807-1.354
61.55560.15491.60794.0334-2.59825.6129-0.2961-0.52240.11370.13630.1430.0182-0.4519-0.34150.1531-0.1601-0.12170.00390.0152-0.0134-0.25017.059754.94219.5083
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 39
2X-RAY DIFFRACTION2A40 - 83
3X-RAY DIFFRACTION3A84 - 309
4X-RAY DIFFRACTION4B-1 - 39
5X-RAY DIFFRACTION5B40 - 83
6X-RAY DIFFRACTION6B84 - 309

+
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