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- PDB-6v3n: Crystal structure of CDYL2 in complex with H3K27me3 -

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Basic information

Entry
Database: PDB / ID: 6v3n
TitleCrystal structure of CDYL2 in complex with H3K27me3
Components
  • ACE-GLN-LEU-ALA-THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA-THR-TYR-NH2
  • Chromodomain Y-like protein 2
KeywordsGENE REGULATION / chromodomain / epigenetics / Structural Genomics / Structural Genomics Consortium / SGC / PROTEIN BINDING
Function / homology
Function and homology information


histone H3K27me3 reader activity / histone H3K9me2/3 reader activity / : / Chromatin modifying enzymes / 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 / DNA methylation ...histone H3K27me3 reader activity / histone H3K9me2/3 reader activity / : / Chromatin modifying enzymes / 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 / DNA methylation / epigenetic regulation of gene expression / 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 / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / transcription corepressor activity / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane
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. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / Chromo/chromo shadow domain ...: / 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. / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H3.1 / Chromodomain Y-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsQin, S. / Tempel, W. / Arrowsmith, C.H. / Bountra, C. / 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 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: 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
Revision 1.4Oct 22, 2025Group: Derived calculations / Structure summary
Category: audit_author / entity ...audit_author / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature
Item: _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification

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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: Chromodomain Y-like protein 2
C: ACE-GLN-LEU-ALA-THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA-THR-TYR-NH2
D: ACE-GLN-LEU-ALA-THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA-THR-TYR-NH2


Theoretical massNumber of molelcules
Total (without water)18,68316
Polymers18,6834
Non-polymers012
Water00
1
A: Chromodomain Y-like protein 2
C: ACE-GLN-LEU-ALA-THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA-THR-TYR-NH2


Theoretical massNumber of molelcules
Total (without water)9,34212
Polymers9,3422
Non-polymers010
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-11 kcal/mol
Surface area6310 Å2
MethodPISA
2
B: Chromodomain Y-like protein 2
D: ACE-GLN-LEU-ALA-THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA-THR-TYR-NH2


Theoretical massNumber of molelcules
Total (without water)9,3424
Polymers9,3422
Non-polymers02
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-10 kcal/mol
Surface area5920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.792, 60.792, 178.6
Angle α, β, γ (deg.)90, 90, 90
Int Tables number95
Space group name H-MP4322

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Components

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


Mass: 7695.596 Da / Num. of mol.: 2 / Fragment: chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDYL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N8U2
#2: Protein/peptide ACE-GLN-LEU-ALA-THR-LYS-ALA-ALA-ARG-M3L-SER-ALA-PRO-ALA-THR-TYR-NH2


Mass: 1645.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-UNX / UNKNOWN LIGAND


Num. of mol.: 12 / Source method: obtained synthetically
Has ligand of interestY
Has protein modificationY

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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: 4.41 Å3/Da / Density % sol: 72.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.6 M ammonium sulfate, 0.01 M magnesium chloride, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792368 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792368 Å / Relative weight: 1
ReflectionResolution: 2.7→44.65 Å / Num. obs: 9869 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.089 / Net I/σ(I): 26.8
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
2.7-2.8399.8141.09712560.9151.1383
8.96-44.6598.69.80.0313360.9990.03364.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HAE

4hae


Resolution: 2.7→44.65 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.318 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.326 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.244
RfactorNum. reflection% reflectionSelection details
Rfree0.258 673 -RANDOM
Rwork0.24 ---
obs0.241 9823 99.9 %-
Displacement parametersBiso mean: 90.04 Å2
Baniso -1Baniso -2Baniso -3
1--8.2365 Å20 Å20 Å2
2---8.2365 Å20 Å2
3---16.4729 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 12 0 1204
LS refinement shellResolution: 2.7→2.73 Å
RfactorNum. reflection% reflection
Rwork0.2582 --
Rfree-0 -
obs--98.02 %
Refinement TLS params.

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)
11.94631.43782.11872.71810.19188.41850.14311.1940.83381.1940.1508-0.3540.8338-0.354-0.29390.4030.0271-0.069-0.2351-0.0607-0.2265-4.6526-0.7595-11.974
22.69454.47415.47110.11636.34453.22690.2704-0.63540.4628-0.63540.05770.80380.46280.8038-0.32810.2747-0.09010.2631-0.4993-0.0245-0.084211.021719.2065.4126
310.23373.60783.162812.08632.163911.7163-0.14411.09890.5841.09890.40370.65170.5840.6517-0.25960.4230.21610.2058-0.410.07190.090710.092435.17868.0326
404.9175-0.96773.69722.9896.4410.42890.9086-0.48010.90860.1779-0.2457-0.4801-0.2457-0.60680.22820.00580.0089-0.3366-0.0282-0.0839-2.809915.5152-13.2226
50.5382-6.05744.248516.41725.594422.6446-0.0011-0.31040.1005-0.31040.2458-0.78170.1005-0.7817-0.24470.58120.06090.1347-0.40550.0399-0.4124-4.7304-3.4192-8.0845
611.06918.73126.72981.1827-0.46735.9889-0.04380.7902-0.38120.79020.1269-0.0049-0.3812-0.0049-0.08310.62120.16980.1845-0.52360.12430.14086.058138.37267.8343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|2 - 48}
2X-RAY DIFFRACTION2{A|49 - 61}
3X-RAY DIFFRACTION3{B|3 - 48}
4X-RAY DIFFRACTION4{B|49 - 64}
5X-RAY DIFFRACTION5{C|*}
6X-RAY DIFFRACTION6{D|*}

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