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- PDB-2w4o: Crystal structure of Human CAMK4 in complex with 4-Amino(sulfamoy... -

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Basic information

Entry
Database: PDB / ID: 2w4o
TitleCrystal structure of Human CAMK4 in complex with 4-Amino(sulfamoyl- phenylamino)-triazole-carbothioic acid (2,6-difluoro-phenyl)-amide)
ComponentsCALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE IV
KeywordsTRANSFERASE / CALMODULIN-BINDING / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / PHOSPHOPROTEIN / KINASE / NUCLEUS
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / Ca2+/calmodulin-dependent protein kinase / regulation of osteoclast differentiation / myeloid dendritic cell differentiation / regulation of T cell differentiation in thymus / calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CaMK IV-mediated phosphorylation of CREB / Negative regulation of NMDA receptor-mediated neuronal transmission ...calcium-dependent protein serine/threonine kinase activity / Ca2+/calmodulin-dependent protein kinase / regulation of osteoclast differentiation / myeloid dendritic cell differentiation / regulation of T cell differentiation in thymus / calmodulin-dependent protein kinase activity / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CaMK IV-mediated phosphorylation of CREB / Negative regulation of NMDA receptor-mediated neuronal transmission / Regulation of MECP2 expression and activity / long-term memory / Transcriptional activation of mitochondrial biogenesis / fibrillar center / peptidyl-serine phosphorylation / adaptive immune response / protein autophosphorylation / calmodulin binding / intracellular signal transduction / inflammatory response / protein phosphorylation / positive regulation of DNA-templated transcription / signal transduction / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
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. ...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-DKI / Calcium/calmodulin-dependent protein kinase type IV
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsMuniz, J.R.C. / Rellos, P. / Gileadi, O. / Fedorov, O. / Filippakopoulos, P. / Salah, E. / Pike, A. / Phillips, C. / Niesen, F. / Shrestha, L. ...Muniz, J.R.C. / Rellos, P. / Gileadi, O. / Fedorov, O. / Filippakopoulos, P. / Salah, E. / Pike, A. / Phillips, C. / Niesen, F. / Shrestha, L. / Burgess-Brown, N. / Bullock, A. / Berridge, G. / von Delft, F. / Edwards, A.M. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of Human Camk4 in Complex with 4-Amino(Sulfamoyl-Phenylamino)-Triazole- Carbothioic Acid (2,6-Difluoro-Phenyl)-Amide)
Authors: Muniz, J.R.C. / Rellos, P. / Gileadi, O. / Fedorov, O. / Filippakopoulos, P. / Salah, E. / Pike, A. / Phillips, C. / Niesen, F. / Shrestha, L. / Burgess-Brown, N. / Bullock, A. / Berridge, G. ...Authors: Muniz, J.R.C. / Rellos, P. / Gileadi, O. / Fedorov, O. / Filippakopoulos, P. / Salah, E. / Pike, A. / Phillips, C. / Niesen, F. / Shrestha, L. / Burgess-Brown, N. / Bullock, A. / Berridge, G. / von Delft, F. / Edwards, A.M. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Knapp, S.
History
DepositionNov 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jul 5, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_refine_tls_group

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7522
Polymers39,3261
Non-polymers4251
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.400, 70.810, 99.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CALCIUM/CALMODULIN-DEPENDENT PROTEIN KINASE TYPE IV / CAM KINASE-GR / CAMK4A


Mass: 39326.285 Da / Num. of mol.: 1 / Fragment: RESIDUES 15-340
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 / Variant (production host): CALM
References: UniProt: Q16566, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-DKI / 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE / CDK 1/2 INHIBITOR


Mass: 425.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13F2N7O2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.05 % / Description: NONE
Crystal growpH: 5.5 / Details: 17% PEG 10K; 0.10M (NH4)(AC); 0.1M BIS-TRIS PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99987
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.05→38.98 Å / Num. obs: 18562 / % possible obs: 95.7 % / Observed criterion σ(I): 1.9 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.9 / % possible all: 74.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JAM

2jam


Resolution: 2.17→36.38 Å / SU ML: 0.26 / σ(F): 0.02 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.237 1570 10.03 %
Rwork0.214 --
obs0.216 15656 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.28 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4301 Å20 Å20 Å2
2--4.8548 Å20 Å2
3----4.4247 Å2
Refinement stepCycle: LAST / Resolution: 2.17→36.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 28 115 2279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072214
X-RAY DIFFRACTIONf_angle_d1.393012
X-RAY DIFFRACTIONf_dihedral_angle_d18.201774
X-RAY DIFFRACTIONf_chiral_restr0.077335
X-RAY DIFFRACTIONf_plane_restr0.009386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.240.26381280.25381115X-RAY DIFFRACTION85
2.24-2.32010.27511330.2361179X-RAY DIFFRACTION91
2.3201-2.4130.29741300.24941237X-RAY DIFFRACTION93
2.413-2.52280.27531370.21311255X-RAY DIFFRACTION94
2.5228-2.65570.25691420.22721251X-RAY DIFFRACTION94
2.6557-2.82210.25831450.23061281X-RAY DIFFRACTION97
2.8221-3.03980.23581470.21691300X-RAY DIFFRACTION97
3.0398-3.34560.24491460.21641314X-RAY DIFFRACTION99
3.3456-3.82920.19291510.19441350X-RAY DIFFRACTION99
3.8292-4.82260.19251510.18021362X-RAY DIFFRACTION100
4.8226-36.38220.25511600.22051442X-RAY DIFFRACTION99
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.66230.18940.92290.63240.21721.0418-0.0834-0.19660.04640.21730.0811-0.00270.0201-0.13630.26040.05330.00170.2324-0.00410.18191.24314.862715.1404
20.4271-0.44750.20840.61320.18570.8420.10320.23060.104-0.1457-0.0686-0.05470.03360.09010.17990.00810.03440.20350.03790.1969-1.21910.4745-6.2216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 112:231 OR RESID 2024:2112 ) )A112 - 231
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 112:231 OR RESID 2024:2112 ) )A2024 - 2112
3X-RAY DIFFRACTION2( CHAIN A AND RESID 232:324 )A232 - 324

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