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- PDB-3r93: Crystal structure of the chromo domain of M-phase phosphoprotein ... -

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Basic information

Entry
Database: PDB / ID: 3r93
TitleCrystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3 peptide
Components
  • H3K9Me3 peptide
  • M-phase phosphoprotein 8
KeywordsCELL CYCLE / epigenetics / M-phase / chromodomain / Structural Genomics / Structural Genomics Consortium / SGC
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 / methylated histone binding / histone reader activity / RNA Polymerase I Promoter Opening ...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 / methylated histone binding / 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 / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / nucleolus / DNA binding / extracellular exosome / extracellular region / nucleoplasm / 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) / Ankyrin repeat profile. / Histone H3 signature 1. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Histone H3 signature 2. / 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 H3.2 / M-phase phosphoprotein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.057 Å
AuthorsLi, J. / Li, Z. / Ruan, J. / Xu, C. / Tong, Y. / Pan, P.W. / Tempel, W. / Crombet, L. / Min, J. / Zang, J. / Structural Genomics Consortium (SGC)
CitationJournal: Plos One / Year: 2011
Title: Structural basis for specific binding of human MPP8 chromodomain to histone H3 methylated at lysine 9.
Authors: Li, J. / Li, Z. / Ruan, J. / Xu, C. / Tong, Y. / Pan, P.W. / Tempel, W. / Crombet, L. / Min, J. / Zang, J.
History
DepositionMar 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Mar 21, 2012Group: Database references
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M-phase phosphoprotein 8
B: M-phase phosphoprotein 8
C: M-phase phosphoprotein 8
D: M-phase phosphoprotein 8
E: H3K9Me3 peptide
F: H3K9Me3 peptide
G: H3K9Me3 peptide
H: H3K9Me3 peptide


Theoretical massNumber of molelcules
Total (without water)35,80911
Polymers35,8098
Non-polymers03
Water1,63991
1
A: M-phase phosphoprotein 8
E: H3K9Me3 peptide


Theoretical massNumber of molelcules
Total (without water)8,9523
Polymers8,9522
Non-polymers01
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-8 kcal/mol
Surface area4870 Å2
MethodPISA
2
B: M-phase phosphoprotein 8
F: H3K9Me3 peptide


Theoretical massNumber of molelcules
Total (without water)8,9522
Polymers8,9522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-8 kcal/mol
Surface area5120 Å2
MethodPISA
3
C: M-phase phosphoprotein 8
G: H3K9Me3 peptide


Theoretical massNumber of molelcules
Total (without water)8,9523
Polymers8,9522
Non-polymers01
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-7 kcal/mol
Surface area4850 Å2
MethodPISA
4
D: M-phase phosphoprotein 8
H: H3K9Me3 peptide


Theoretical massNumber of molelcules
Total (without water)8,9523
Polymers8,9522
Non-polymers01
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-7 kcal/mol
Surface area5020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.148, 74.005, 72.609
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY INFORMATION FOR THE STRUCTURE IS UNKNOWN.

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Components

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


Mass: 7344.350 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MPHOSPH8, MPP8 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q99549
#2: Protein/peptide
H3K9Me3 peptide


Mass: 1607.877 Da / Num. of mol.: 4 / Source method: obtained synthetically / References: UniProt: Q71DI3*PLUS
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 35% PEG2000-MME, 8-fold excess of H3K9Me3, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 24361 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.072 / Χ2: 1.824 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.1250.73523401.706197.6
2.12-2.216.10.65823901.752199.9
2.21-2.3170.62924091.7931100
2.31-2.437.20.50423861.7871100
2.43-2.587.20.31924351.7811100
2.58-2.787.20.18924291.8111100
2.78-3.067.20.10324311.7991100
3.06-3.517.10.05524511.861100
3.51-4.4270.04224822.1861100
4.42-506.60.0326081.709199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3LWE

3lwe


Resolution: 2.057→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.214 / Occupancy max: 1 / Occupancy min: 1 / SU B: 12.486 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. The programs BUCCANEER, COOT were used as well as the MOLPROBITY server.
RfactorNum. reflection% reflectionSelection details
Rfree0.2732 1237 5.103 %THIN SHELLS (SFTOOLS)
Rwork0.2198 ---
obs0.222 24241 99.161 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso max: 102.11 Å2 / Biso mean: 40.273 Å2 / Biso min: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.828 Å20 Å20 Å2
2--0.903 Å20 Å2
3---1.925 Å2
Refinement stepCycle: LAST / Resolution: 2.057→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 3 91 2272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222210
X-RAY DIFFRACTIONr_bond_other_d0.0010.021478
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9682980
X-RAY DIFFRACTIONr_angle_other_deg0.80333616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14824.78392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57315373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2821510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_mcbond_it0.5791.51391
X-RAY DIFFRACTIONr_mcbond_other0.1381.5574
X-RAY DIFFRACTIONr_mcangle_it1.14222196
X-RAY DIFFRACTIONr_scbond_it2.0193819
X-RAY DIFFRACTIONr_scangle_it3.2384.5784
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.057-2.1100.3161645176393.307
2.11-2.1680.3191680.2771573174999.543
2.168-2.2300.2441658166699.52
2.23-2.2980.3041450.2481481162799.939
2.298-2.37300.2531592159999.562
2.373-2.4560.2571400.2371387153399.609
2.456-2.5480.2561220.2181351147699.797
2.548-2.65100.2281429143599.582
2.651-2.7680.2841150.2141252137099.781
2.768-2.9020.255990.2191225132799.774
2.902-3.0580.241840.2271160124799.759
3.058-3.24100.231198120299.667
3.241-3.4620.287640.2261060112999.557
3.462-3.7350.249600.211988105499.431
3.735-4.0850.29500.19593198399.797
4.085-4.5570.306420.17884389099.438
4.557-5.2420.256790.16671779999.625
5.242-6.3710.207240.2465968899.273
6.371-8.8140.334280.24852155099.818
8.814-300.334170.2333435997.772
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.3645-1.01060.68834.7554-1.24994.1926-0.0851-0.70860.58640.3101-0.0024-0.0706-0.36190.06640.08750.1617-0.01290.0120.116-0.09240.25537.641623.121913.7621
27.2610.2408-0.92376.79712.23775.09240.043-0.7127-0.41470.41890.0339-0.45060.21460.1465-0.07690.11820.011-0.05390.20030.06470.0849-28.21428.930916.1108
36.29010.60152.76453.8661.36864.175-0.04020.0310.52980.0724-0.14520.0557-0.1993-0.04380.18540.09370.00160.06130.027-0.00360.2594-8.296223.7773-1.0496
46.3348-1.10840.29766.7067-2.56477.04670.0236-0.45490.23730.44170.18730.3608-0.2768-0.3277-0.21090.21940.05210.03860.4412-0.00350.0646-7.73077.795329.6997
512.2695.8094-3.18478.4499-3.5286.6965-0.0158-1.8250.7268-0.0803-0.6403-0.2628-0.2706-0.01670.65610.26790.0965-0.06390.4094-0.14460.23585.643218.141822.0438
612.84242.9111.91576.52693.402416.58040.3221-0.5702-0.8140.5294-0.0128-0.52670.8159-0.0988-0.30930.19560.0672-0.0270.19640.07770.2996-29.573320.171213.0099
721.592-16.6-0.028720.78851.07452.93410.06450.99340.49750.0965-0.43430.1042-0.18140.44170.36980.0986-0.0660.01130.17220.05310.1914-5.635118.7831-9.5567
824.22971.4668-17.92245.987-1.133417.48790.2208-0.57711.17640.45910.1264-0.1679-0.7145-0.0996-0.34720.28490.1249-0.04670.3819-0.03560.2264-5.769416.656724.9892
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 114
2X-RAY DIFFRACTION2B57 - 114
3X-RAY DIFFRACTION3C57 - 114
4X-RAY DIFFRACTION4D56 - 114
5X-RAY DIFFRACTION5E4 - 15
6X-RAY DIFFRACTION6F2 - 15
7X-RAY DIFFRACTION7G4 - 15
8X-RAY DIFFRACTION8H4 - 15

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