[English] 日本語
Yorodumi
- PDB-2wel: Crystal structure of SU6656-bound calcium/calmodulin-dependent pr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wel
TitleCrystal structure of SU6656-bound calcium/calmodulin-dependent protein kinase II delta in complex with calmodulin
Components
  • CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE II DELTA CHAIN
  • CALMODULIN
KeywordsTRANSFERASE / CELLULAR DIFFERENTIATION / SERINE/THREONINE-PROTEIN KINASE / PHOSPHOPROTEIN / CALMODULIN-BINDING / CALMODULIN BINDING / KINASE / ATP-BINDING / NUCLEOTIDE-BINDING / VASCULAR SMOOTH MUSCLE / SERINE-THREONINE KINASE
Function / homology
Function and homology information


regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / regulation of cardiac muscle cell action potential involved in regulation of contraction / calcium- and calmodulin-dependent protein kinase complex / regulation of cell communication by electrical coupling / Ca2+/calmodulin-dependent protein kinase / : / : / : ...regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / regulation of cardiac muscle cell action potential involved in regulation of contraction / calcium- and calmodulin-dependent protein kinase complex / regulation of cell communication by electrical coupling / Ca2+/calmodulin-dependent protein kinase / : / : / : / : / regulation of membrane depolarization / : / positive regulation of protein autophosphorylation / regulation of the force of heart contraction / negative regulation of peptidyl-threonine phosphorylation / Trafficking of AMPA receptors / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / endoplasmic reticulum calcium ion homeostasis / sodium channel inhibitor activity / cardiac muscle cell contraction / calcium/calmodulin-dependent protein kinase activity / Assembly and cell surface presentation of NMDA receptors / relaxation of cardiac muscle / CaM pathway / positive regulation of peptidyl-threonine phosphorylation / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / positive regulation of DNA binding / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / CaMK IV-mediated phosphorylation of CREB / PKA activation / response to corticosterone / negative regulation of high voltage-gated calcium channel activity / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / positive regulation of cardiac muscle hypertrophy / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / regulation of heart contraction / presynaptic endocytosis / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / protein phosphatase activator activity / Long-term potentiation / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / positive regulation of protein serine/threonine kinase activity / DARPP-32 events / regulation of neuronal synaptic plasticity / catalytic complex / Smooth Muscle Contraction / HSF1-dependent transactivation / detection of calcium ion / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / positive regulation of cardiac muscle cell apoptotic process / activation of adenylate cyclase activity / regulation of protein localization to plasma membrane / cellular response to interferon-beta / Protein methylation / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / positive regulation of nitric-oxide synthase activity / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / enzyme regulator activity / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling
Similarity search - Function
Helix Hairpins - #620 / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Helix Hairpins / NTF2-like domain superfamily / : / Helix non-globular / EF-hand domain pair / Special / EF-hand, calcium binding motif ...Helix Hairpins - #620 / Calcium/calmodulin-dependent protein kinase II, association-domain / Calcium/calmodulin dependent protein kinase II association domain / Helix Hairpins / NTF2-like domain superfamily / : / Helix non-globular / EF-hand domain pair / Special / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-K88 / PHOSPHATE ION / Calmodulin-1 / Calmodulin-3 / Calcium/calmodulin-dependent protein kinase type II subunit delta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPike, A.C.W. / Rellos, P. / Salah, E. / Burgess-Brown, N. / Keates, T. / Muniz, J. / Sethi, R. / Roos, A. / Filippakopoulos, P. / von Delft, F. ...Pike, A.C.W. / Rellos, P. / Salah, E. / Burgess-Brown, N. / Keates, T. / Muniz, J. / Sethi, R. / Roos, A. / Filippakopoulos, P. / von Delft, F. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / 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
DepositionMar 31, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 10, 2011Group: Database references / Non-polymer description / Refinement description
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_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
D: CALMODULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,04015
Polymers53,9462
Non-polymers1,09413
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-31.5 kcal/mol
Surface area28670 Å2
MethodPQS
Unit cell
Length a, b, c (Å)68.260, 68.850, 121.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 2 molecules AD

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


Mass: 37006.500 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, RESIDUES 11-335
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: Q13557, Ca2+/calmodulin-dependent protein kinase
#2: Protein CALMODULIN / CAM


Mass: 16939.623 Da / Num. of mol.: 1
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: P62158, UniProt: P0DP23*PLUS

-
Non-polymers , 5 types, 418 molecules

#3: Chemical ChemComp-K88 / (3Z)-N,N-DIMETHYL-2-OXO-3-(4,5,6,7-TETRAHYDRO-1H-INDOL-2-YLMETHYLIDENE)-2,3-DIHYDRO-1H-INDOLE-5-SULFONAMIDE


Mass: 371.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N3O3S
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer details(2-OXO-3-(4,5,6,7-TETRAHYDRO-1 H-INDOL-2-YLMETHYLENE)-2, 3-DIHYDRO-1H-INDOLE-5-SULFONIC ACID ...(2-OXO-3-(4,5,6,7-TETRAHYDRO-1 H-INDOL-2-YLMETHYLENE)-2, 3-DIHYDRO-1H-INDOLE-5-SULFONIC ACID DIMETHYLAMIDE) (K88): SU6656

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.72 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M SODIUM POTASSIUM PHOSPHATE, 20% PEG3350 10% ETHYLENE GLYCOL, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9787
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.9→33.13 Å / Num. obs: 45901 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 20.729 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.6 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2VN9, 1MXE

2vn9

1mxe


Resolution: 1.9→33.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.064 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19929 827 1.8 %RANDOM
Rwork0.16057 ---
obs0.1613 45074 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.066 Å2
Baniso -1Baniso -2Baniso -3
1--1.92 Å20 Å20 Å2
2--1.02 Å20 Å2
3---0.9 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3544 0 64 405 4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223702
X-RAY DIFFRACTIONr_bond_other_d0.0010.022529
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9734991
X-RAY DIFFRACTIONr_angle_other_deg0.9113.0016148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2075446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51824.59183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97215657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4031525
X-RAY DIFFRACTIONr_chiral_restr0.0850.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02728
X-RAY DIFFRACTIONr_nbd_refined0.2160.2755
X-RAY DIFFRACTIONr_nbd_other0.170.22422
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21791
X-RAY DIFFRACTIONr_nbtor_other0.0870.21772
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2330
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0960.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1630.214
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.230
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0470.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.30632233
X-RAY DIFFRACTIONr_mcbond_other1.1013909
X-RAY DIFFRACTIONr_mcangle_it4.70953596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.0781469
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.372111395
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 50 -
Rwork0.235 3286 -
obs--100 %
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)
10.50990.0989-0.22620.4313-0.15341.74130.00210.01630.0196-0.04110.03830.036-0.0394-0.1191-0.04050.006-0.0012-0.00610.0226-0.00460.075917.2686-14.5916-13.2017
21.2733-0.57230.07132.76360.54651.26720.03050.2130.0167-0.34170.00740.1598-0.2259-0.0702-0.03790.11680.0058-0.0190.09360.04590.079788.1056-20.6549-51.1215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 276
2X-RAY DIFFRACTION2D3 - 147
3X-RAY DIFFRACTION2A294 - 316

+
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