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- PDB-6m7h: Structure of calmodulin with KN93 -

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Basic information

Entry
Database: PDB / ID: 6m7h
TitleStructure of calmodulin with KN93
ComponentsCalmodulin-1
KeywordsSIGNALING PROTEIN / Ca2+ binding EF-hand inhibitor complex
Function / homology
Function and homology information


CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / 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 / PKA activation ...CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / 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 / PKA activation / CaMK IV-mediated phosphorylation of CREB / 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 calcium ion export across plasma membrane / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / presynaptic endocytosis / regulation of cardiac muscle cell action potential / positive regulation of ryanodine-sensitive calcium-release channel activity / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / negative regulation of ryanodine-sensitive calcium-release channel activity / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / calcineurin-mediated signaling / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / Long-term potentiation / Regulation of MECP2 expression and activity / Calcineurin activates NFAT / protein phosphatase activator activity / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Smooth Muscle Contraction / catalytic complex / detection of calcium ion / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / presynaptic cytosol / calcium channel inhibitor activity / cellular response to interferon-beta / Protein methylation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / regulation of calcium-mediated signaling / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / voltage-gated potassium channel complex / sperm midpiece / substantia nigra development / calcium channel complex / calyx of Held / FCERI mediated Ca+2 mobilization / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / adenylate cyclase activator activity / regulation of heart rate / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / sarcomere / regulation of cytokinesis / VEGFR2 mediated vascular permeability / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of receptor signaling pathway via JAK-STAT / spindle microtubule / RAF activation / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / cellular response to type II interferon / long-term synaptic potentiation / response to calcium ion / RAS processing / spindle pole / 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-dependent protein binding / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Inactivation, recovery and regulation of the phototransduction cascade / Platelet degranulation / myelin sheath / Ca2+ pathway / RAF/MAP kinase cascade / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / vesicle / transmembrane transporter binding / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / centrosome
Similarity search - Function
EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / 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 ...EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-KN9 / Calmodulin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsDamo, S.M. / Pattanayek, R. / Johnson, C.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)HRD-1547757 United States
CitationJournal: Cell Calcium / Year: 2019
Title: The CaMKII inhibitor KN93-calmodulin interaction and implications for calmodulin tuning of NaV1.5 and RyR2 function.
Authors: Johnson, C.N. / Pattanayek, R. / Potet, F. / Rebbeck, R.T. / Blackwell, D.J. / Nikolaienko, R. / Sequeira, V. / Le Meur, R. / Radwanski, P.B. / Davis, J.P. / Zima, A.V. / Cornea, R.L. / ...Authors: Johnson, C.N. / Pattanayek, R. / Potet, F. / Rebbeck, R.T. / Blackwell, D.J. / Nikolaienko, R. / Sequeira, V. / Le Meur, R. / Radwanski, P.B. / Davis, J.P. / Zima, A.V. / Cornea, R.L. / Damo, S.M. / Gyorke, S. / George Jr., A.L. / Knollmann, B.C.
History
DepositionAug 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: audit_author / entity_src_gen ...audit_author / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Calmodulin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6318
Polymers16,9671
Non-polymers1,6637
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.511, 40.511, 348.785
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Calmodulin-1


Mass: 16967.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DP23
#2: Chemical ChemComp-KN9 / N-[2-[[[3-(4'-Chlorophenyl)-2-propenyl]methylamino]methyl]phenyl]-N-(2-hydroxyethyl)-4'-methoxybenzenesulfonamide / N-[2-({[(2E)-3-(4-chlorophenyl)prop-2-en-1-yl](methyl)amino}methyl)phenyl]-N-(2-hydroxyethyl)-4-methoxybenzene-1-sulfonamide


Mass: 501.037 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H29ClN2O4S
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: bis tris ph 6.5, peg 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→38.8 Å / Num. obs: 50207 / % possible obs: 99.8 % / Redundancy: 15.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 18
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 4 / Num. unique obs: 2264 / CC1/2: 0.929 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→35.084 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 26.82
RfactorNum. reflection% reflection
Rfree0.2666 3097 7.6 %
Rwork0.2282 --
obs0.2311 40767 96.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→35.084 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 106 79 1306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081247
X-RAY DIFFRACTIONf_angle_d0.9811680
X-RAY DIFFRACTIONf_dihedral_angle_d8.6491001
X-RAY DIFFRACTIONf_chiral_restr0.049169
X-RAY DIFFRACTIONf_plane_restr0.005222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6250.32061390.28511647X-RAY DIFFRACTION92
1.625-1.65170.30551180.28091587X-RAY DIFFRACTION92
1.6517-1.68020.36441410.2741695X-RAY DIFFRACTION93
1.6802-1.71070.30521370.29451640X-RAY DIFFRACTION93
1.7107-1.74360.36041330.28021626X-RAY DIFFRACTION93
1.7436-1.77920.31741500.29151647X-RAY DIFFRACTION93
1.7792-1.81790.33941310.2711705X-RAY DIFFRACTION95
1.8179-1.86020.29951460.26941682X-RAY DIFFRACTION96
1.8602-1.90670.27931490.26341709X-RAY DIFFRACTION96
1.9067-1.95820.29271280.24791724X-RAY DIFFRACTION97
1.9582-2.01580.30421480.24981744X-RAY DIFFRACTION97
2.0158-2.08090.34191360.24321694X-RAY DIFFRACTION97
2.0809-2.15530.25971420.24691744X-RAY DIFFRACTION97
2.1553-2.24150.27431480.24561758X-RAY DIFFRACTION98
2.2415-2.34350.2711420.23451742X-RAY DIFFRACTION98
2.3435-2.46710.28151390.22341715X-RAY DIFFRACTION98
2.4671-2.62160.3021430.23351769X-RAY DIFFRACTION99
2.6216-2.82390.27391400.22711766X-RAY DIFFRACTION99
2.8239-3.1080.25191490.23171764X-RAY DIFFRACTION99
3.108-3.55730.23681430.20821761X-RAY DIFFRACTION100
3.5573-4.48040.27641440.1751793X-RAY DIFFRACTION100
4.4804-35.0920.16841510.21051758X-RAY DIFFRACTION100

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