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- PDB-7y0i: Solution structures of ASH1L PHD domain in complex with H3K4me2 p... -

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Basic information

Entry
Database: PDB / ID: 7y0i
TitleSolution structures of ASH1L PHD domain in complex with H3K4me2 peptide
Components
  • ALA-ARG-THR-MLY-GLN-THR-ALA-ARG-LYS-SER-THR-GLY-GLY-LYS-ALA
  • Histone-lysine N-methyltransferase ASH1L
KeywordsSTRUCTURAL PROTEIN / ASH1L / PHD domain / H3K4me2 / prostate cancer
Function / homology
Function and homology information


uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / uterus morphogenesis / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / flagellated sperm motility ...uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / uterus morphogenesis / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / flagellated sperm motility / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / histone H3 methyltransferase activity / negative regulation of MAPK cascade / negative regulation of acute inflammatory response / decidualization / single fertilization / bicellular tight junction / post-embryonic development / skeletal system development / PKMTs methylate histone lysines / MAPK cascade / chromosome / methylation / transcription by RNA polymerase II / inflammatory response / chromatin binding / regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Bromo adjacent homology domain ...ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology (BAH) domain / BAH domain profile. / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone-lysine N-methyltransferase ASH1L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsYu, M. / Zeng, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Front Oncol / Year: 2022
Title: Structural insight into ASH1L PHD finger recognizing methylated histone H3K4 and promoting cell growth in prostate cancer.
Authors: Yu, M. / Jia, Y. / Ma, Z. / Ji, D. / Wang, C. / Liang, Y. / Zhang, Q. / Yi, H. / Zeng, L.
History
DepositionJun 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase ASH1L
B: ALA-ARG-THR-MLY-GLN-THR-ALA-ARG-LYS-SER-THR-GLY-GLY-LYS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1704
Polymers8,0392
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1040 Å2
ΔGint-4 kcal/mol
Surface area5110 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histone-lysine N-methyltransferase ASH1L / ASH1-like protein / huASH1 / Absent small and homeotic disks protein 1 homolog / Lysine N-methyltransferase 2H


Mass: 6446.448 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH1L, KIAA1420, KMT2H / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NR48, [histone H3]-lysine36 N-trimethyltransferase, [histone H3]-lysine9 N-methyltransferase
#2: Protein/peptide ALA-ARG-THR-MLY-GLN-THR-ALA-ARG-LYS-SER-THR-GLY-GLY-LYS-ALA


Mass: 1592.843 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HN(CA)CB
121isotropic13D HN(COCA)CB
131isotropic23D 1H-15N NOESY
142isotropic23D 1H-13C NOESY aliphatic
152isotropic23D 1H-13C NOESY aromatic
162isotropic23D 13C-edited 13C/15N-Filtered NOESY aliphatic
172isotropic23D 13C-edited 13C/15N-Filtered NOESY aromatic
181isotropic22D TOCSY
191isotropic22D ROESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution150 mM sodium phosphate, 100 mM sodium chloride, 100 uM ZINC ION, 2.0 mM [U-100% 2H] DTT, 90% H2O/10% D2Osample_190% H2O/10% D2O
solution250 mM sodium phosphate, 100 mM sodium chloride, 100 uM ZINC ION, 2.0 mM [U-100% 2H] DTT, 100% D2Osample_2100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphatenatural abundance1
100 mMsodium chloridenatural abundance1
100 uMZINC IONnatural abundance1
2.0 mMDTT[U-100% 2H]1
50 mMsodium phosphatenatural abundance2
100 mMsodium chloridenatural abundance2
100 uMZINC IONnatural abundance2
2.0 mMDTT[U-100% 2H]2
Sample conditionsIonic strength: null Not defined / Label: condition_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE NEOBrukerAVANCE NEO6001
Bruker AVANCE NEOBrukerAVANCE NEO8002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: DGSA-distance geometry simulated annealing / 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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