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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


histone H3K36me3 reader activity / regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / kinetochore assembly / regulation of signal transduction / mitotic metaphase chromosome alignment / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / nucleosomal DNA binding / telomere organization ...histone H3K36me3 reader activity / regulation of transcription elongation by RNA polymerase II / negative regulation of JNK cascade / kinetochore assembly / regulation of signal transduction / mitotic metaphase chromosome alignment / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / nucleosomal DNA binding / telomere organization / Regulation of PD-L1(CD274) transcription / RNA Polymerase I Promoter Opening / negative regulation of extrinsic apoptotic signaling pathway / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / negative regulation of canonical NF-kappaB signal transduction / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Transcriptional regulation by small RNAs / RNA Polymerase I Promoter Escape / 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 / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / kinetochore / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / chromosome / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / heterochromatin formation / Senescence-Associated Secretory Phenotype (SASP) / double-stranded DNA binding / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / defense response to virus / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA-templated transcription / extracellular exosome / extracellular region / nucleoplasm / zinc ion binding / nucleus
Similarity search - Function
: / : / : / ZMYND11 protein coiled-coil / : / ZMYND11/ZMYD8, MYND zinc finger / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger MYND-type signature. ...: / : / : / ZMYND11 protein coiled-coil / : / ZMYND11/ZMYD8, MYND zinc finger / : / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain profile. / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / SH3 type barrels. / Zinc finger, FYVE/PHD-type / 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 / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Histone-fold / Zinc finger, RING/FYVE/PHD-type / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Histone H3.3 / 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
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
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


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


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

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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