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- PDB-2odd: Solution structure of the MYND domain from AML1-ETO complexed wit... -

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Basic information

Entry
Database: PDB / ID: 2odd
TitleSolution structure of the MYND domain from AML1-ETO complexed with SMRT, a corepressor
Components
  • Protein CBFA2T1
  • SMRT
KeywordsMETAL BINDING PROTEIN / MYND zinc finger / cross-braced topology / poly-proline / proline-tryptophan interaction
Function / homology
Function and homology information


Loss of MECP2 binding ability to the NCoR/SMRT complex / regulation of ketone metabolic process / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / Notch binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / negative regulation of fat cell differentiation / Regulation of MECP2 expression and activity / estrous cycle ...Loss of MECP2 binding ability to the NCoR/SMRT complex / regulation of ketone metabolic process / nuclear glucocorticoid receptor binding / negative regulation of androgen receptor signaling pathway / Notch binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / negative regulation of fat cell differentiation / Regulation of MECP2 expression and activity / estrous cycle / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / lactation / Regulation of lipid metabolism by PPARalpha / transcription repressor complex / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / cerebellum development / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / enzyme activator activity / PPARA activates gene expression / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / NOTCH1 Intracellular Domain Regulates Transcription / Transcriptional regulation of white adipocyte differentiation / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / nuclear matrix / HCMV Early Events / transcription corepressor activity / response to estradiol / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription factor binding / nuclear body / negative regulation of DNA-templated transcription / DNA-templated transcription / chromatin binding / chromatin / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Protein CBFA2T1 / CBFA2T family / NHR2-like / NHR2 domain like / Helix Hairpins - #2220 / N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / TAFH/NHR1 domain superfamily / NHR1 homology to TAF ...Protein CBFA2T1 / CBFA2T family / NHR2-like / NHR2 domain like / Helix Hairpins - #2220 / N-CoR, GPS2-interacting domain / : / G-protein pathway suppressor 2-interacting domain / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / SANT domain profile. / Myb domain / SANT domain / Myb-like DNA-binding domain / Helix Hairpins / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Helix non-globular / Special / Homeobox-like domain superfamily
Similarity search - Domain/homology
Protein CBFA2T1 / Nuclear receptor corepressor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsLiu, Y.Z. / Chen, W. / Gaudet, J. / Cheney, M.D. / Roudaia, L. / Cierpicki, T. / Klet, R.C. / Hartman, K. / Laue, T.M. / Speck, N.A. / Bushweller, J.H.
CitationJournal: Cancer Cell / Year: 2007
Title: Structural basis for recognition of SMRT/N-CoR by the MYND domain and its contribution to AML1/ETO's activity.
Authors: Liu, Y. / Chen, W. / Gaudet, J. / Cheney, M.D. / Roudaia, L. / Cierpicki, T. / Klet, R.C. / Hartman, K. / Laue, T.M. / Speck, N.A. / Bushweller, J.H.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: SMRT
A: Protein CBFA2T1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1064
Polymers8,9752
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide SMRT


Mass: 1613.790 Da / Num. of mol.: 1 / Fragment: SMRT (residues 1101-1113)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMRT / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: Q9Y618*PLUS
#2: Protein 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: 7361.001 Da / Num. of mol.: 1 / Fragment: MYND domain (AML1-ETO, residues 658-707)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AML1-ETO / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL-21 / References: UniProt: Q06455
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

DetailsContents: 2mM SMRT-MYND, 25mM Bis-Tris, pH 6.8, 50uM ZnCl2, 1mM DTT, 95%H2O, 5% D2O
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6.8 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, A.T. et al.structure solution
NMRPipeDelaglio, F. et al.processing
CNSBrunger, A.T. et al.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 25

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