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- PDB-2ndf: Solution NMR structures of AF9 yeats domain in complex with histo... -

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Basic information

Entry
Database: PDB / ID: 2ndf
TitleSolution NMR structures of AF9 yeats domain in complex with histon H3 acetylation at K18
Components
  • Histone H3 peptide
  • Protein AF-9
KeywordsTRANSCRIPTION / Histone / crotonylation
Function / homology
Function and homology information


modification-dependent protein binding / histone H3K9ac reader activity / histone H3K18ac reader activity / histone H3K27ac reader activity / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation ...modification-dependent protein binding / histone H3K9ac reader activity / histone H3K18ac reader activity / histone H3K27ac reader activity / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / Chromatin modifying enzymes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / : / RNA Polymerase II Pre-transcription Events / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / transcription elongation factor complex / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / negative regulation of canonical Wnt signaling pathway / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / histone binding / gene expression / molecular adaptor activity / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
YEATS domain / AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. ...YEATS domain / AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein AF-9 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsZeng, L. / Zhou, M.
CitationJournal: Structure / Year: 2016
Title: Structural Insights into Histone Crotonyl-Lysine Recognition by the AF9 YEATS Domain.
Authors: Zhang, Q. / Zeng, L. / Zhao, C. / Ju, Y. / Konuma, T. / Zhou, M.M.
History
DepositionMay 19, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Oct 30, 2024Group: Database references / Structure summary
Category: database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein AF-9
B: Histone H3 peptide


Theoretical massNumber of molelcules
Total (without water)17,9822
Polymers17,9822
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein AF-9 / ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated ...ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated to chromosome 3 protein / YEATS domain-containing protein 3


Mass: 16611.160 Da / Num. of mol.: 1 / Fragment: YEATS domain residues 1-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Production host: Escherichia coli (E. coli) / Strain (production host): RIL strain cells / References: UniProt: P42568
#2: Protein/peptide Histone H3 peptide


Mass: 1370.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: P68431*PLUS
Has protein modificationY

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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 HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D 1H-15N NOESY
1613D 1H-15N TOCSY
1723D 1H-13C NOESY aliphatic
1823D 1H-13C NOESY aromatic
1923D filtered 1H-13C NOESY aliphatic
11023D filtered 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM sodium phosphate, 500 mM sodium chloride, 2 mM EDTA, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O90% H2O/10% D2O
210 mM sodium phosphate, 500 mM sodium chloride, 2 mM EDTA, 2 mM [U-100% 2H] DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphate-11
500 mMsodium chloride-21
2 mMEDTA-31
2 mMDTT-4[U-100% 2H]1
10 mMsodium phosphate-52
500 mMsodium chloride-62
2 mMEDTA-72
2 mMDTT-8[U-100% 2H]2
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002
Bruker AvanceBrukerAVANCE6003
Bruker AvanceBrukerAVANCE5004

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
NMRPipe7.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipe7.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift calculation
NMRView5.04 C-versionJohnson, One Moon Scientificpeak picking
NMRView5.04 C-versionJohnson, One Moon Scientificchemical shift assignment
NMRView5.04 C-versionJohnson, One Moon Scientificdata analysis
TALOStalosn, talosplusCornilescu, Delaglio and Baxrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospincollection
RefinementMethod: distance geometry, simulated annealing, torsion angle dynamics
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: 20

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