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- PDB-2kyg: Structure of the AML1-ETO Nervy Domain - PKA(RIIa) complex and it... -

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Basic information

Entry
Database: PDB / ID: 2kyg
TitleStructure of the AML1-ETO Nervy Domain - PKA(RIIa) complex and its contribution to AML1-ETO activity
Components
  • Protein CBFA2T1
  • cAMP-dependent protein kinase type II-alpha regulatory subunit
KeywordsPROTEIN BINDING / protein/protein / homodimer bound to monomer
Function / homology
Function and homology information


ROBO receptors bind AKAP5 / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / cAMP-dependent protein kinase complex / negative regulation of fat cell differentiation ...ROBO receptors bind AKAP5 / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase inhibitor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / cAMP-dependent protein kinase complex / negative regulation of fat cell differentiation / plasma membrane raft / protein kinase A catalytic subunit binding / PKA activation in glucagon signalling / DARPP-32 events / Hedgehog 'off' state / cAMP binding / FCGR3A-mediated IL10 synthesis / nuclear matrix / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / transcription corepressor activity / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / intracellular signal transduction / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / DNA-templated transcription / centrosome / ubiquitin protein ligase binding / protein-containing complex / DNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Protein CBFA2T1 / CBFA2T family / NHR2-like / NHR2 domain like / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit ...Protein CBFA2T1 / CBFA2T family / NHR2-like / NHR2 domain like / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
cAMP-dependent protein kinase type II-alpha regulatory subunit / Protein CBFA2T1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsCorpora, T.A. / Cierpecki, T. / Bushweller, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure of the AML1-ETO NHR3-PKA(RIIalpha) complex and its contribution to AML1-ETO activity.
Authors: Corpora, T. / Roudaia, L. / Oo, Z.M. / Chen, W. / Manuylova, E. / Cai, X. / Chen, M.J. / Cierpicki, T. / Speck, N.A. / Bushweller, J.H.
History
DepositionMay 25, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase type II-alpha regulatory subunit
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
C: Protein CBFA2T1


Theoretical massNumber of molelcules
Total (without water)15,4283
Polymers15,4283
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)15 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide cAMP-dependent protein kinase type II-alpha regulatory subunit


Mass: 5621.425 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR2A, PKR2, PRKAR2 / Plasmid: pHis Parallel 2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13861
#2: Protein/peptide Protein CBFA2T1 / Protein MTG8 / Protein ETO / Eight twenty one protein / Cyclin-D-related protein / Zinc finger MYND ...Protein MTG8 / Protein ETO / Eight twenty one protein / Cyclin-D-related protein / Zinc finger MYND domain-containing protein 2


Mass: 4184.722 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUNX1T1, AML1T1, CBFA2T1, CDR, ETO, MTG8, ZMYND2 / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q06455

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HN(CA)CB
1513D (H)CCH-TOCSY
1613D HNHA
1713D H(CCO)NH
1813D 1H-15N NOESY
1913D 1H-13C NOESY
NMR detailsText: The structure was determined using a combination of NOE and residual dipolar coupling data.

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Sample preparation

DetailsContents: 2 mM [U-99% 13C; U-99% 15N] NHR3, 2 mM [U-99% 13C; U-99% 15N] PKA(RIIa), 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMNHR3[U-99% 13C; U-99% 15N]1
2 mMPKA(RIIa)[U-99% 13C; U-99% 15N]1
Sample conditionsIonic strength: 0.0 / pH: 4.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian AvanceVarianAVANCE6001
Varian AvanceVarianAVANCE5002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TALOSCornilescu, Delaglio and Baxstructure solution
CNSBrunger, A. et al.refinement
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thodata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 15

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