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- PDB-4n4i: Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND... -

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Basic information

Entry
Database: PDB / ID: 4n4i
TitleCrystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.3K36me3
Components
  • Peptide from Histone H3.3
  • Zinc finger MYND domain-containing protein 11
KeywordsTRANSCRIPTION / tandem bromodomain-zinc finger-PWWP motif / histone H3.3-specific
Function / homology
Function and homology information


regulation of transcription elongation from RNA polymerase II promoter / negative regulation of JNK cascade / nucleosomal DNA binding / DNA replication-independent chromatin assembly / Inhibition of DNA recombination at telomere / RNA polymerase II core promoter sequence-specific DNA binding / telomere organization / RNA Polymerase I Promoter Opening / DNA methylation / SIRT1 negatively regulates rRNA expression ...regulation of transcription elongation from RNA polymerase II promoter / negative regulation of JNK cascade / nucleosomal DNA binding / DNA replication-independent chromatin assembly / Inhibition of DNA recombination at telomere / RNA polymerase II core promoter sequence-specific DNA binding / telomere organization / RNA Polymerase I Promoter Opening / DNA methylation / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / negative regulation of I-kappaB kinase/NF-kappaB signaling / methylated histone binding / nuclear chromosome / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / negative regulation of extrinsic apoptotic signaling pathway / nucleosome assembly / Pre-NOTCH Transcription and Translation / Meiotic recombination / nucleosome / Activation of anterior HOX genes in hindbrain development during early embryogenesis / transcription corepressor activity / Transcriptional regulation of granulopoiesis / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / double-stranded DNA binding / histone binding / Senescence-Associated Secretory Phenotype (SASP) / defense response to virus / chromosome, telomeric region / positive regulation of cell growth / chromosome / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein heterodimerization activity / Amyloid fiber formation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein-containing complex / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / nucleus
Similarity search - Function
ZMYND8/11, PWWP domain / Zinc finger MYND-type profile. / Zinc finger, MYND-type / Zinc finger MYND-type signature. / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site ...ZMYND8/11, PWWP domain / Zinc finger MYND-type profile. / Zinc finger, MYND-type / Zinc finger MYND-type signature. / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger PHD-type signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / PHD zinc finger / Zinc finger, PHD-type / Histone-fold / Zinc finger, FYVE/PHD-type / Bromodomain-like / Histone Acetyltransferase; Chain A / SH3 type barrels. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Histone H3.3 / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Zinc finger MYND domain-containing protein 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsLi, Y. / Ren, Y. / Li, H.
CitationJournal: Nature / Year: 2014
Title: ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression
Authors: Wen, H. / Li, Y. / Xi, Y. / Jiang, S. / Stratton, S. / Peng, D. / Tanaka, K. / Ren, Y. / Xia, Z. / Wu, J. / Li, B. / Barton, M.C. / Li, W. / Li, H. / Shi, X.
History
DepositionOct 8, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Zinc finger MYND domain-containing protein 11
B: Peptide from Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4295
Polymers32,1632
Non-polymers2673
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-10 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)64.013, 64.013, 122.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Zinc finger MYND domain-containing protein 11 / Adenovirus 5 E1A-binding protein / Protein BS69


Mass: 29503.736 Da / Num. of mol.: 1 / Fragment: UNP residues 154-371 / Mutation: D234A/E236A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BS69, Zmynd11 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R5C8
#2: Protein/peptide Peptide from Histone H3.3 /


Mass: 2659.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243

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Non-polymers , 4 types, 119 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.2 % / Mosaicity: 0.45 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 25% (w/v) polyethylene glycol 4000, 0.1M Tris-HCl, pH 8.3, 0.2M Li2SO4, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2012 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. all: 17984 / Num. obs: 18020 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Rmerge(I) obs: 0.112 / Χ2: 1.646 / Net I/σ(I): 16.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.999-2.0311.90.8288671.3861100
2.03-2.0711.90.7738911.4321100
2.07-2.11120.6018741.3871100
2.11-2.1511.90.5178861.4431100
2.15-2.2120.4088851.4471100
2.2-2.2511.90.3848711.4611100
2.25-2.3111.90.3338901.4951100
2.31-2.3711.90.2728871.5851100
2.37-2.44120.2598841.5321100
2.44-2.5211.80.2078971.5641100
2.52-2.6111.90.1778751.6181100
2.61-2.7111.80.1618871.669199.9
2.71-2.8411.80.1549061.7381100
2.84-2.9911.80.1418951.8231100
2.99-3.1711.60.1349121.9211100
3.17-3.4211.50.1179041.971100
3.42-3.7611.40.0969322.3911100
3.76-4.3110.90.0699291.9941100
4.31-5.4311.50.0639391.6361100
5.43-5010.40.06610311.633198.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N4G
Resolution: 1.999→36.453 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8357 / SU ML: 0.21 / σ(F): 1.36 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 918 5.1 %RANDOM
Rwork0.199 ---
obs0.2011 17984 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.22 Å2 / Biso mean: 35.532 Å2 / Biso min: 12.62 Å2
Refinement stepCycle: LAST / Resolution: 1.999→36.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 13 116 1818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081744
X-RAY DIFFRACTIONf_angle_d1.1792348
X-RAY DIFFRACTIONf_chiral_restr0.085237
X-RAY DIFFRACTIONf_plane_restr0.006300
X-RAY DIFFRACTIONf_dihedral_angle_d16.469650
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9991-2.10450.2641250.23972371249699
2.1045-2.23630.25471280.210823852513100
2.2363-2.40890.25021340.216423792513100
2.4089-2.65130.24781360.215224172553100
2.6513-3.03480.2811450.213124202565100
3.0348-3.82280.2131260.190324642590100
3.8228-36.45870.24321240.184126302754100

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