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- PDB-2kqf: Solution structure of MAST205-PDZ complexed with the C-terminus o... -

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Basic information

Entry
Database: PDB / ID: 2kqf
TitleSolution structure of MAST205-PDZ complexed with the C-terminus of a rabies virus G protein
Components
  • C-terminal motif from Glycoprotein
  • Microtubule-associated serine/threonine-protein kinase 2
KeywordsSIGNALING PROTEIN/PEPTIDE BINDING PROTEIN / PDZ domain / MAST205 / kinase / PDZ complex and viral peptide / SIGNALING PROTEIN-PEPTIDE BINDING PROTEIN complex
Function / homology
Function and homology information


spermatid differentiation / regulation of interleukin-12 production / phosphatase binding / cytoskeleton organization / microtubule cytoskeleton / microtubule binding / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity ...spermatid differentiation / regulation of interleukin-12 production / phosphatase binding / cytoskeleton organization / microtubule cytoskeleton / microtubule binding / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / viral envelope / virion membrane / magnesium ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Microtubule-associated serine/threonine-protein kinase, domain / Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily / Microtubule-associated serine/threonine-protein kinase, catalytic domain / Domain of unknown function (DUF1908) / : / Rhabdovirus glycoprotein G PH domain / : / Rhabdovirus spike glycoprotein G central domain / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein fusion domain ...Microtubule-associated serine/threonine-protein kinase, domain / Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily / Microtubule-associated serine/threonine-protein kinase, catalytic domain / Domain of unknown function (DUF1908) / : / Rhabdovirus glycoprotein G PH domain / : / Rhabdovirus spike glycoprotein G central domain / Rhabdovirus glycoprotein / Rhabdovirus spike glycoprotein fusion domain / : / PDZ domain 6 / PDZ domain / PDZ domain / Pdz3 Domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Microtubule-associated serine/threonine-protein kinase 2 / Glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsTerrien, E. / Wolff, N. / Cordier, F. / Simenel, C. / Bernard, A. / Lafon, M. / Delepierre, M.
CitationJournal: To be Published
Title: 1H, 13C and 15N resonance assignments of the PDZ of Microtubule-associated serine/threonine kinase 205 (MAST205) in complex with the C-Terminal motif from the rabies virus glycoprotein
Authors: Terrien, E. / Wolff, N. / Cordier, F. / Simenel, C. / Bernard, A. / Lafon, M. / Delepierre, M. / Buc, H. / Prehaud, C. / Lafage, M.
History
DepositionNov 4, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated serine/threonine-protein kinase 2
B: C-terminal motif from Glycoprotein


Theoretical massNumber of molelcules
Total (without water)11,9292
Polymers11,9292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Microtubule-associated serine/threonine-protein kinase 2


Mass: 10451.940 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAST205 / Plasmid: pDEST15 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) STAR / References: UniProt: Q6P0Q8
#2: Protein/peptide C-terminal motif from Glycoprotein


Mass: 1476.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: Q8JJY9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HN(CA)CB
1713D HN(CO)CA
1813D (H)CCH-TOCSY
1913D HNHA
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D HN(COCA)CB
11313D 13C-selected/12C,14N-selected NOESY
11413D 15N-selected/12C,14N-selected NOESY

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Sample preparation

DetailsContents: 0.8mM [U-100% 13C; U-100% 15N] entity_1-1, 1.6mM entity_2-2, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMentity_1-1[U-100% 13C; U-100% 15N]1
1.6 mMentity_2-21
Sample conditionsIonic strength: 0.2 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIALinge, O'Donoghue and Nilgesstructure solution
TALOSCornilescu, Delaglio and Baxdata analysis
VnmrJVariancollection
ProcheckNMRLaskowski and MacArthurdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
MOLMOLKoradi, Billeter and Wuthrichdata analysis
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1106 / NOE intraresidue total count: 480 / NOE long range total count: 251 / NOE medium range total count: 111 / NOE sequential total count: 264 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 50 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum upper distance constraint violation: 0.812 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.0672 Å / Distance rms dev error: 0.003 Å

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