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- PDB-5jjz: Chromo domain of human Chromodomain Protein, Y-Like 2 -

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Basic information

Entry
Database: PDB / ID: 5jjz
TitleChromo domain of human Chromodomain Protein, Y-Like 2
Components
  • Chromodomain Y-like protein 2
  • LYS-LYS-LYS-ALA-ARG-MLY-SER-ALA-GLY-ALA-ALA-LYS-TYR
KeywordsPROTEIN BINDING / CDYL2 / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / heterochromatin / nucleosomal DNA binding / methylated histone binding / chromatin DNA binding / histone deacetylase binding / structural constituent of chromatin ...negative regulation of DNA recombination / Apoptosis induced DNA fragmentation / chromosome condensation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / heterochromatin / nucleosomal DNA binding / methylated histone binding / chromatin DNA binding / histone deacetylase binding / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / double-stranded DNA binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleus
Similarity search - Function
Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Chromo domain, conserved site / Chromo domain signature. / Enoyl-CoA hydratase, C-terminal / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain ...Linker histone H1/H5 / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Chromo domain, conserved site / Chromo domain signature. / Enoyl-CoA hydratase, C-terminal / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / ClpP/crotonase-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Histone H1.4 / Chromodomain Y-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsDONG, A. / DOMBROVSKI, L. / LOPPNAU, P. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / MIN, J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: The crystal structure of CDYL2 domain of human CDYL2 protein
Authors: WU, H. / DONG, A. / ZENG, H. / ELBAKKOURI, M. / BARSYTE, D. / VEDADI, M. / TATLOCK, J. / OWEN, D. / BUNNAGE, M. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J.
History
DepositionApr 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromodomain Y-like protein 2
B: LYS-LYS-LYS-ALA-ARG-MLY-SER-ALA-GLY-ALA-ALA-LYS-TYR


Theoretical massNumber of molelcules
Total (without water)11,5492
Polymers11,5492
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-4 kcal/mol
Surface area4780 Å2
MethodPISA
2
A: Chromodomain Y-like protein 2
B: LYS-LYS-LYS-ALA-ARG-MLY-SER-ALA-GLY-ALA-ALA-LYS-TYR

A: Chromodomain Y-like protein 2
B: LYS-LYS-LYS-ALA-ARG-MLY-SER-ALA-GLY-ALA-ALA-LYS-TYR


Theoretical massNumber of molelcules
Total (without water)23,0984
Polymers23,0984
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area2400 Å2
ΔGint-18 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.962, 57.962, 98.824
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Chromodomain Y-like protein 2 / CDY-like 2


Mass: 10109.275 Da / Num. of mol.: 1 / Fragment: UNP residues 2-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDYL2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)V2RpRARE / References: UniProt: Q8N8U2
#2: Protein/peptide LYS-LYS-LYS-ALA-ARG-MLY-SER-ALA-GLY-ALA-ALA-LYS-TYR


Mass: 1439.769 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: sequence from Human histone H1K26me(21-33) / Source: (synth.) Homo sapiens (human) / References: UniProt: P10412*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M K/Na tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 7130 / % possible obs: 99.6 % / Redundancy: 21.5 % / Rmerge(I) obs: 0.051 / Χ2: 1.413 / Net I/av σ(I): 84.631 / Net I/σ(I): 15.5 / Num. measured all: 153213
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.0316.50.845198.8
2.03-2.0718.70.779199.4
2.07-2.11210.65199.7
2.11-2.1522.80.4951100
2.15-2.222.60.421100
2.2-2.25230.3391100
2.25-2.31230.311100
2.31-2.3723.10.2231100
2.37-2.4422.80.1841100
2.44-2.5222.80.1451100
2.52-2.61230.1151100
2.61-2.7122.60.1061100
2.71-2.8422.70.0821100
2.84-2.9922.40.061100
2.99-3.1722.30.051100
3.17-3.4222.10.0441100
3.42-3.7621.40.0431100
3.76-4.3120.70.0431100
4.31-5.4319.80.0371100
5.43-5017.40.03195.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation35.22 Å2.44 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREP11.0.05phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HAE

4hae


Resolution: 2→50.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 9.096 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. Authors state: density only supports (with clashes) 4 of supposedly 13 peptide residues. Direction of peptide main ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED. Authors state: density only supports (with clashes) 4 of supposedly 13 peptide residues. Direction of peptide main chain opposite of what is seen in 3R93,3SVM (MPP8). Peptide segment of only 4 length and lack of plausible main chain interactions with host chromodomain weakens the evidence for novel binding mode. Nevertheless, a reasonable hypothesis for future studies.
RfactorNum. reflection% reflectionSelection details
Rfree0.2601 390 5.5 %RANDOM
Rwork0.2298 ---
obs0.2315 6702 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.13 Å2 / Biso mean: 50.308 Å2 / Biso min: 34.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å2-0.62 Å20 Å2
2---1.25 Å20 Å2
3---4.04 Å2
Refinement stepCycle: final / Resolution: 2→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms516 0 0 17 533
Biso mean---50.93 -
Num. residues----63
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019530
X-RAY DIFFRACTIONr_bond_other_d0.0020.02463
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.925714
X-RAY DIFFRACTIONr_angle_other_deg0.89631063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.642561
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.15323.79329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3481583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.672153
X-RAY DIFFRACTIONr_chiral_restr0.0960.269
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02134
X-RAY DIFFRACTIONr_mcbond_it1.5363.471248
X-RAY DIFFRACTIONr_mcbond_other1.5333.487249
X-RAY DIFFRACTIONr_mcangle_it2.3795.172307
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 26 -
Rwork0.32 471 -
all-497 -
obs--99.2 %
Refinement TLS params.Method: refined / Origin x: 2.5391 Å / Origin y: -22.3033 Å / Origin z: -3.6285 Å
111213212223313233
T0.0762 Å2-0.0246 Å2-0.0838 Å2-0.1183 Å20.0206 Å2--0.1265 Å2
L3.9167 °20.8926 °20.9617 °2-4.7603 °20.8982 °2--3.3627 °2
S-0.0024 Å °0.0793 Å °-0.3261 Å °-0.1428 Å °0.1638 Å °0.0683 Å °0.1855 Å °0.0349 Å °-0.1614 Å °

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