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- PDB-4n4h: Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND... -

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Basic information

Entry
Database: PDB / ID: 4n4h
TitleCrystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.1K36me3
Components
  • Peptide from Histone H3.1
  • 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 by RNA polymerase II / Chromatin modifying enzymes / methylated histone binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / DNA methylation ...regulation of transcription elongation by RNA polymerase II / Chromatin modifying enzymes / methylated histone binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / 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) / HDACs deacetylate histones / 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 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / Meiotic recombination / PKMTs methylate histone lysines / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / transcription corepressor activity / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / histone binding / Senescence-Associated Secretory Phenotype (SASP) / double-stranded DNA binding / gene expression / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / protein-containing complex / DNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / nucleus / membrane
Similarity search - Function
: / : / : / 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 ...: / : / : / 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 / Histone H3 signature 1. / Zinc finger, FYVE/PHD-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / SH3 type barrels. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / 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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Histone H3.1 / Zinc finger MYND domain-containing protein 11
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.302 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.name
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 H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1725
Polymers31,9062
Non-polymers2673
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-11 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.358, 64.358, 122.059
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


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: Zmynd11 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8R5C8
#2: Protein/peptide Peptide from Histone H3.1


Mass: 2401.855 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431

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Non-polymers , 4 types, 58 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.: 55 / 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: 1.98 Å3/Da / Density % sol: 37.9 % / 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: 1.0076 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2012 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0076 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 12025 / Num. obs: 11677 / % possible obs: 97.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Biso Wilson estimate: 40.61 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.646 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3411.90.7695671.3861100
2.34-2.3811.70.5285851.4321100
2.38-2.4311.90.4985741.3871100
2.43-2.4811.80.3885991.4431100
2.48-2.5311.90.3545751.4471100
2.53-2.5911.80.3055841.4611100
2.59-2.6611.80.2435811.4951100
2.66-2.7311.80.2155891.5851100
2.73-2.8111.80.1875921.5321100
2.81-2.911.70.1615821.5641100
2.9-311.80.1265941.6181100
3-3.1211.70.1175981.6691100
3.12-3.2611.60.15891.7381100
3.26-3.4411.60.0946041.8231100
3.44-3.6510.50.1014571.921176.9
3.65-3.9310.40.0974541.97173.8
3.93-4.3311.10.0976092.3911100
4.33-4.9510.90.0766231.9941100
4.95-6.2410.70.0566281.6361100
6.24-509.90.0486931.633198.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N4G

4n4g


Resolution: 2.302→36.482 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7803 / SU ML: 0.31 / σ(F): 0 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 868 7.48 %RANDOM
Rwork0.2062 ---
obs0.2105 11605 97.07 %-
all-11955 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.6 Å2 / Biso mean: 40.7597 Å2 / Biso min: 14 Å2
Refinement stepCycle: LAST / Resolution: 2.302→36.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 13 55 1724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031711
X-RAY DIFFRACTIONf_angle_d0.6922304
X-RAY DIFFRACTIONf_chiral_restr0.05232
X-RAY DIFFRACTIONf_plane_restr0.003294
X-RAY DIFFRACTIONf_dihedral_angle_d14.326636
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3024-2.44660.36191540.26491746190099
2.4466-2.63550.27811320.2318001932100
2.6355-2.90060.27451440.21618271971100
2.9006-3.32010.33391430.214418321975100
3.3201-4.1820.24131420.1951551169384
4.182-36.48660.22481530.19231981213499

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