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- PDB-6v2d: Crystal Structure of chromodomain of CDYL2 in complex with inhibi... -

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Basic information

Entry
Database: PDB / ID: 6v2d
TitleCrystal Structure of chromodomain of CDYL2 in complex with inhibitor UNC3866
Components
  • Chromodomain Y-like protein 2
  • UNC3866
KeywordsGENE REGULATION / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3K27me3 reader activity / histone H3K9me2/3 reader activity / : / transcription corepressor activity / nucleus
Similarity search - Function
: / Chromo domain, conserved site / Enoyl-CoA hydratase, C-terminal / Chromo domain signature. / 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 domain, conserved site / Enoyl-CoA hydratase, C-terminal / Chromo domain signature. / 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) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
UNC3866 / Chromodomain Y-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Cell Chem Biol / Year: 2020
Title: Structural Basis for the Binding Selectivity of Human CDY Chromodomains.
Authors: Dong, C. / Liu, Y. / Lyu, T.J. / Beldar, S. / Lamb, K.N. / Tempel, W. / Li, Y. / Li, Z. / James, L.I. / Qin, S. / Wang, Y. / Min, J.
History
DepositionNov 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Chromodomain Y-like protein 2
E: Chromodomain Y-like protein 2
G: Chromodomain Y-like protein 2
I: Chromodomain Y-like protein 2
K: Chromodomain Y-like protein 2
J: UNC3866
L: UNC3866
B: UNC3866
D: UNC3866
F: UNC3866
H: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,44840
Polymers50,94412
Non-polymers50428
Water2,702150
1
A: Chromodomain Y-like protein 2
B: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,63510
Polymers8,4912
Non-polymers1448
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7 kcal/mol
Surface area4410 Å2
MethodPISA
2
C: Chromodomain Y-like protein 2
D: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5817
Polymers8,4912
Non-polymers905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-7 kcal/mol
Surface area5230 Å2
MethodPISA
3
E: Chromodomain Y-like protein 2
F: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5093
Polymers8,4912
Non-polymers181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-7 kcal/mol
Surface area4320 Å2
MethodPISA
4
G: Chromodomain Y-like protein 2
H: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5998
Polymers8,4912
Non-polymers1086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7 kcal/mol
Surface area5090 Å2
MethodPISA
5
I: Chromodomain Y-like protein 2
J: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5998
Polymers8,4912
Non-polymers1086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-7 kcal/mol
Surface area4440 Å2
MethodPISA
6
K: Chromodomain Y-like protein 2
L: UNC3866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,5274
Polymers8,4912
Non-polymers362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-6 kcal/mol
Surface area4050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.979, 83.835, 115.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
Chromodomain Y-like protein 2 / CDY-like 2 / cdyl2


Mass: 7695.596 Da / Num. of mol.: 6 / Fragment: Chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDYL2 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -V2R-pRARE2 / References: UniProt: Q8N8U2
#2: Protein/peptide
UNC3866


Type: Oligopeptide / Class: Inhibitor / Mass: 795.020 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UNC3866
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% P3350, 0.2M ammonium acetate, 0.1M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→38.43 Å / Num. obs: 28615 / % possible obs: 92.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 25.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.116 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
8.93-38.43995.80.0234130.9990.02654.7
2-2.0597.76.50.88221760.7280.9562

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: preliminary coordinates of PDB entries 5EPJ and 5EPK

5epj

5epk


Resolution: 2.1→38.05 Å / SU ML: 0.259 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 27.1204
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2682 1203 4.93 %thin shells (sftools)
Rwork0.2118 23174 --
obs0.2146 24377 91.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.65 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 28 150 3448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01013409
X-RAY DIFFRACTIONf_angle_d1.04984606
X-RAY DIFFRACTIONf_chiral_restr0.0619431
X-RAY DIFFRACTIONf_plane_restr0.0058589
X-RAY DIFFRACTIONf_dihedral_angle_d20.87731243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.30731740.23752731X-RAY DIFFRACTION99.97
2.18-2.2800.27151118X-RAY DIFFRACTION38.46
2.28-2.40.31131620.24482783X-RAY DIFFRACTION99.73
2.4-2.550.31271660.24092767X-RAY DIFFRACTION99.83
2.55-2.750.34241350.24782793X-RAY DIFFRACTION100
2.75-3.030.34271580.24342803X-RAY DIFFRACTION99.93
3.03-3.470.27021310.21672843X-RAY DIFFRACTION99.93
3.47-4.370.20341260.17462325X-RAY DIFFRACTION81.35
4.37-38.050.2131510.17813011X-RAY DIFFRACTION99.87

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