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- PDB-9de2: ETO2 MYND bound to MPPL peptide from GATAD2A -

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Basic information

Entry
Database: PDB / ID: 9de2
TitleETO2 MYND bound to MPPL peptide from GATAD2A
ComponentsGATAD2A-MPPL motif and ETO2 NHR4 domain fusion protein
KeywordsGENE REGULATION / Zn finger complex / polyproline binder / MYND / NuRD
Function / homology
Function and homology information


granulocyte differentiation / negative regulation of glycolytic process / regulation of aerobic respiration / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / response to hypoxia / Golgi membrane / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA-templated transcription ...granulocyte differentiation / negative regulation of glycolytic process / regulation of aerobic respiration / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / response to hypoxia / Golgi membrane / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / DNA-templated transcription / nucleolus / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Protein CBFA2T3 / CBFA2T family / NHR2-like / NHR2 domain like / TAFH/NHR1 domain superfamily / NHR1 homology to TAF / TAFH/NHR1 domain profile. / TAF homology / TAFH/NHR1 / MYND finger ...Protein CBFA2T3 / CBFA2T family / NHR2-like / NHR2 domain like / 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.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsWilliams, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK115563 United States
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: The role of multivalency in the association of the eight twenty-one protein 2 (ETO2) with the nucleosome remodeling and deacetylase (NuRD) complex.
Authors: Dan-Dukor, G. / Shang, S. / Leighton, G.O. / Travis, C.R. / Schwochert, T.D. / Agrawal, P. / Ajasa, O. / Li, T. / Waters, M.L. / Ginder, G.D. / Williams Jr., D.C.
History
DepositionAug 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GATAD2A-MPPL motif and ETO2 NHR4 domain fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8273
Polymers7,6971
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein GATAD2A-MPPL motif and ETO2 NHR4 domain fusion protein / MTG8-related protein 2 / Myeloid translocation gene on chromosome 16 protein / hMTG16 / Zinc finger ...MTG8-related protein 2 / Myeloid translocation gene on chromosome 16 protein / hMTG16 / Zinc finger MYND domain-containing protein 4


Mass: 7696.501 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBFA2T3, MTG16, MTGR2, ZMYND4 / Production host: Escherichia coli (E. coli) / References: UniProt: O75081
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-13C NOESY aliphatic
131isotropic13D 1H-13C NOESY aromatic
141isotropic13D CBCA(CO)NH
151isotropic13D HN(CA)CB
161isotropic13D HNCO
171isotropic13D HBHA(CO)NH
181isotropic13D 1H-15N NOESY
191isotropic13D C(CO)NH
1101isotropic12D (HB)CB(CGCD)HD
1111isotropic12D (HB)CB(CGCDCE)HE
2122anisotropic13D HNCO JNH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1500 uM [U-100% 13C; U-100% 15N] ETO2-NHR4-MPPLsc, 25 mM BisTris, 100 mM NaCl, 1 mM DTT, 50 uM ZnSO4, 95% H2O/5% D2O13C, 15N ETO2-NHR4-MPPLsc95% H2O/5% D2O
solution2500 uM [U-100% 13C; U-100% 15N] ETO2-NHR4-MPPLsc, 25 mM BisTris, 100 mM NaCl, 1 mM DTT, 50 uM ZnSO4, 5 % PEG:hexonal (C13:E5 r=0.85), 95% H2O/5% D2O13C, 15N ETO2-NHR4-MPPLsc95% H2O/5% D2Oalignment sample
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMETO2-NHR4-MPPLsc[U-100% 13C; U-100% 15N]1
25 mMBisTrisnatural abundance1
100 mMNaClnatural abundance1
1 mMDTTnatural abundance1
50 uMZnSO4natural abundance1
500 uMETO2-NHR4-MPPLsc[U-100% 13C; U-100% 15N]2
25 mMBisTrisnatural abundance2
100 mMNaClnatural abundance2
1 mMDTTnatural abundance2
50 uMZnSO4natural abundance2
5 %PEG:hexonal (C13:E5 r=0.85)natural abundance2
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
1Used for all data collection except alignmentNaCl 100 mM mMcondition_16.81 atm298 K
2Lowered temperature 3 degrees to prevent phase separation of PEG:hexanol liquid crystalline mediaNaCl 100 mM mMcondition_26.81 atm295 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2CCPNchemical shift assignment
X-PLOR NIH3.8Schwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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