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- PDB-7cwh: Structural basis of RACK7 PHD to read a pediatric glioblastoma-as... -

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Basic information

Entry
Database: PDB / ID: 7cwh
TitleStructural basis of RACK7 PHD to read a pediatric glioblastoma-associated histone mutation H3.3G34R
Components
  • Peptide from Histone H3.3
  • Protein kinase C-binding protein 1
KeywordsTRANSCRIPTION / RACK7 / PHD / H3.3G34R
Function / homology
Function and homology information


nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression ...nucleosomal DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / Inhibition of DNA recombination at telomere / telomere organization / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / nucleosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
PRKCBP1, PHD finger / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Histone H3 signature 2. / Zinc finger, PHD-type / PHD zinc finger ...PRKCBP1, PHD finger / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Histone H3 signature 2. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Bromodomain / Bromodomain profile. / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3.3 / Protein kinase C-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLan, W.X. / Li, Z. / Jiao, F.F. / Wang, C.X. / Guo, R. / Cao, C.Y.
CitationJournal: Chin.J.Chem. / Year: 2021
Title: Structural basis of RACK7 PHD domain to read a pediatric glioblastoma‐associated histone mutation H3.3G34R
Authors: Lan, W.X. / Li, Z. / Jiao, F.F. / Wang, C.X. / Guo, R. / Cao, C.Y.
History
DepositionAug 28, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide from Histone H3.3
B: Protein kinase C-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,6014
Polymers8,4712
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area780 Å2
ΔGint2 kcal/mol
Surface area6380 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Peptide from Histone H3.3 /


Mass: 1333.562 Da / Num. of mol.: 1 / Mutation: G34R / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243
#2: Protein Protein kinase C-binding protein 1 / RACK7


Mass: 7137.098 Da / Num. of mol.: 1 / Fragment: PHD-type
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZMYND8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TH12
#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 HNCO
121isotropic13D HN(CA)CB
131isotropic13D HNCA
141isotropic13D CBCA(CO)NH
151isotropic13D 1H-15N TOCSY
161isotropic13D 1H-15N NOESY
172isotropic13D (H)CCH-TOCSY
182isotropic13D 1H-13C NOESY aliphatic
192isotropic13D 1H-13C NOESY aromatic
1101isotropic12D 1H-15N HSQC
1112isotropic12D 1H-13C HSQC
1121isotropic12D filter TOCSY
1131isotropic12D filter NOESY
1141isotropic13D 15N-filter-edit NOESY
1152isotropic13D 13C-filter-edit NOESY
1163isotropic13D HNCO
1173isotropic13D HN(CA)CB
1183isotropic13D CBCA(CO)NH
1193isotropic13D 1H-15N NOESY
1203isotropic13D 1H-15N TOCSY
1213isotropic13D (H)CCH-TOCSY
1223isotropic13D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM [U-13C; U-15N] RACK7 PHD, 1.4 mM H3.3G34R, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DDT, 90% H2O/10% D2O13C_15N_Rack90% H2O/10% D2O
solution20.7 mM [U-13C; U-15N] RACK7 PHD, 1.4 mM H3.3G34R, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DTT, 100% D2O13C_15N_Rack100% D2O
solution31 mM [U-13C; U-15N] G34R, 1.2 mM RACK7 PHD, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DTT, 90% H2O/10% D2O13C_15N_G34R90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMRACK7 PHD[U-13C; U-15N]1
1.4 mMH3.3G34Rnatural abundance1
100 mMsodium chloridenatural abundance1
0.02 % w/vsodium azidenatural abundance1
50 mMsodium phosphatenatural abundance1
2 mMDDT[U-2H]1
0.7 mMRACK7 PHD[U-13C; U-15N]2
1.4 mMH3.3G34Rnatural abundance2
100 mMsodium chloridenatural abundance2
0.02 % w/vsodium azidenatural abundance2
50 mMsodium phosphatenatural abundance2
2 mMDTT[U-2H]2
1 mMG34R[U-13C; U-15N]3
1.2 mMRACK7 PHDnatural abundance3
100 mMsodium chloridenatural abundance3
0.02 % w/vsodium azidenatural abundance3
50 mMsodium phosphatenatural abundance3
2 mMDTT[U-2H]3
Sample conditionsIonic strength: 500 mM / Label: 1 / pH: 7.4 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Agilent DD2 / Manufacturer: Agilent / Model: DD2 / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrungerrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
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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