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- PDB-8zxc: NMR solution structures of ASH1L BRD-PHD domain in complex with H... -

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Basic information

Entry
Database: PDB / ID: 8zxc
TitleNMR solution structures of ASH1L BRD-PHD domain in complex with H3K4me2 peptide
Components
  • ASH1L bromodomain and PHD domain
  • Histone H3.3C
KeywordsSTRUCTURAL PROTEIN / ASH1L / Bromodomain / PHD / H3
Function / homology
Function and homology information


nucleosomal DNA binding / euchromatin / structural constituent of chromatin / nucleosome / positive regulation of cell growth / protein heterodimerization activity / nucleoplasm / nucleus
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsZeng, L. / Zhou, M.-M.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31770780 China
CitationJournal: To Be Published
Title: NMR solution structures of ASH1L BRD-PHD domain in complex with H3K4me2 peptide
Authors: Zeng, L. / Zhou, M.-M.
History
DepositionJun 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASH1L bromodomain and PHD domain
B: Histone H3.3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7764
Polymers24,6452
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ASH1L bromodomain and PHD domain


Mass: 23309.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Protein/peptide Histone H3.3C / Histone H3.5


Mass: 1335.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2
#3: 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 modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HN(CA)CB
121isotropic23D HN(COCA)CB
131isotropic13D 1H-15N NOESY
142isotropic13D 1H-13C NOESY aliphatic
152isotropic13D 1H-13C NOESY aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1100 mM sodium phosphate, 2 mM DTT, 50 mM potassium chloride, 90% H2O/10% D2O1_sample90% H2O/10% D2O
solution2100 mM sodium phosphate, 2 mM DTT, 50 mM potassium chloride, 100% D2O2_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMsodium phosphatenatural abundance1
2 mMDTTnatural abundance1
50 mMpotassium chloridenatural abundance1
100 mMsodium phosphatenatural abundance2
2 mMDTTnatural abundance2
50 mMpotassium chloridenatural abundance2
Sample conditionsIonic strength: null Not defined / Label: conditions_1 / pH: 7.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 2
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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