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- PDB-3qo2: Structural insights for MPP8 chromodomain interaction with histon... -

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Basic information

Entry
Database: PDB / ID: 3qo2
TitleStructural insights for MPP8 chromodomain interaction with histone H3 lysine 9
Components
  • Histone H3 peptide
  • M-phase phosphoprotein 8
KeywordsDNA BINDING PROTEIN/GENE REGULATION / epigenetics / MPP8 phosphorylation / chromodomain / MPP8-H3K9me modulates the expression of E-cadherin / H3K9 methyl-lysine binding / tri-methyl-lysine / DNA BINDING PROTEIN-GENE REGULATION complex / Histone H3 tail Binding Protein
Function / homology
Function and homology information


positive regulation of DNA methylation-dependent heterochromatin formation / : / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / heterochromatin / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization ...positive regulation of DNA methylation-dependent heterochromatin formation / : / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of gene expression, epigenetic / heterochromatin / Chromatin modifying enzymes / epigenetic regulation of gene expression / methylated histone binding / telomere organization / histone reader activity / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / PRC2 methylates histones and DNA / Defective pyroptosis / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / cilium / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / nucleolus / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Ankyrin repeat ...Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Histone H3 signature 1. / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Histone H3 signature 2. / Ankyrin repeat / Histone H3 / Histone H3/CENP-A / Ankyrin repeat-containing domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Histone H3.1 / M-phase phosphoprotein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsChang, Y. / Horton, J.R. / Bedford, M.T. / Zhang, X. / Cheng, X.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding.
Authors: Chang, Y. / Horton, J.R. / Bedford, M.T. / Zhang, X. / Cheng, X.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: M-phase phosphoprotein 8
P: Histone H3 peptide
B: M-phase phosphoprotein 8
Q: Histone H3 peptide
C: M-phase phosphoprotein 8
R: Histone H3 peptide
D: M-phase phosphoprotein 8
S: Histone H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,07211
Polymers36,8868
Non-polymers1863
Water1,49583
1
A: M-phase phosphoprotein 8
P: Histone H3 peptide


Theoretical massNumber of molelcules
Total (without water)9,2222
Polymers9,2222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-6 kcal/mol
Surface area5620 Å2
MethodPISA
2
B: M-phase phosphoprotein 8
Q: Histone H3 peptide


Theoretical massNumber of molelcules
Total (without water)9,2222
Polymers9,2222
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-5 kcal/mol
Surface area5160 Å2
MethodPISA
3
C: M-phase phosphoprotein 8
R: Histone H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2843
Polymers9,2222
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-6 kcal/mol
Surface area5110 Å2
MethodPISA
4
D: M-phase phosphoprotein 8
S: Histone H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3464
Polymers9,2222
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-3 kcal/mol
Surface area5260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.461, 53.461, 238.792
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
M-phase phosphoprotein 8 / Two hybrid-associated protein 3 with RanBPM / Twa3


Mass: 7613.694 Da / Num. of mol.: 4 / Fragment: unp residues 55-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPHOSPH8, MPP8 / Plasmid: pXC / Production host: Escherichia coli (E. coli) / References: UniProt: Q99549
#2: Protein/peptide
Histone H3 peptide


Mass: 1607.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.31 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 15 % w/v polyethylene glycol PEG400, 30 % w/v PEG 1500 and 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.49→31.94 Å / Num. obs: 13038 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / Biso Wilson estimate: 38.46 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 15.5
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1246 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LWE

3lwe


Resolution: 2.49→31.938 Å / SU ML: 0.33 / σ(F): 0.1 / Phase error: 25.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2895 611 5 %Random
Rwork0.2146 ---
obs0.2182 12215 93.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.134 Å2 / ksol: 0.366 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.0934 Å2-0 Å20 Å2
2---2.0934 Å2-0 Å2
3---4.1868 Å2
Refinement stepCycle: LAST / Resolution: 2.49→31.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 12 83 2428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092410
X-RAY DIFFRACTIONf_angle_d1.0543233
X-RAY DIFFRACTIONf_dihedral_angle_d17.988932
X-RAY DIFFRACTIONf_chiral_restr0.061352
X-RAY DIFFRACTIONf_plane_restr0.003402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.4899-2.74040.34871130.23622592259286
2.7404-3.13660.29471820.20912794279493
3.1366-3.95060.29291270.18782999299997
3.9506-31.94050.26871890.21993219321999

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