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- PDB-6v41: crystal structure of CDY1 chromodomain bound to H3K9me3 -

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Basic information

Entry
Database: PDB / ID: 6v41
Titlecrystal structure of CDY1 chromodomain bound to H3K9me3
Components
  • Histone H3.1 Peptide
  • Testis-specific chromodomain protein Y 1
KeywordsTRANSFERASE / structural genomics consortium / SGC
Function / homology
Function and homology information


Chromatin modifying enzymes / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity ...Chromatin modifying enzymes / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / : / 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 / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / 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 / transcription corepressor activity / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / 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 / spermatogenesis / 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 subgroup / 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 domain subgroup / 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 / Histone-fold
Similarity search - Domain/homology
Histone H3.1 / Testis-specific chromodomain protein Y 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.603 Å
AuthorsQin, S. / Tempel, W. / Walker, J.R. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium / 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 27, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionDec 25, 2019ID: 6UHG
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Jun 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 1.3Jul 29, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: Testis-specific chromodomain protein Y 1
QQQ: Histone H3.1 Peptide


Theoretical massNumber of molelcules
Total (without water)9,25022
Polymers9,2502
Non-polymers020
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-9 kcal/mol
Surface area5160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.447, 42.447, 37.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Testis-specific chromodomain protein Y 1


Mass: 7642.388 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDY1, CDY1A, CDY1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6F8, histone acetyltransferase
#2: Protein/peptide Histone H3.1 Peptide / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1607.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 20 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.81 Å3/Da / Density % sol: 32.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.4 M sodium citrate, 0.1 M HEPES

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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: Sep 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→23.36 Å / Num. obs: 8814 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 1 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.03 / Net I/σ(I): 43.4
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
8.78-23.3695.75.40.021600.9990.024101.3
1.6-1.6399.16.60.3714380.9140.4035.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4hae

4hae


Resolution: 1.603→23.301 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.971 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.104 / ESU R Free: 0.097
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.215 411 4.674 %
Rwork0.1917 --
all0.193 --
obs-8794 99.955 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.062 Å2
Baniso -1Baniso -2Baniso -3
1-0.253 Å2-0 Å2-0 Å2
2--0.253 Å2-0 Å2
3----0.505 Å2
Refinement stepCycle: LAST / Resolution: 1.603→23.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms586 0 20 20 626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.013624
X-RAY DIFFRACTIONr_bond_other_d0.0020.018525
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.661848
X-RAY DIFFRACTIONr_angle_other_deg1.4911.5941233
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.416578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41724.47438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35115109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.818155
X-RAY DIFFRACTIONr_chiral_restr0.0910.280
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02721
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02128
X-RAY DIFFRACTIONr_nbd_refined0.2820.2129
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.2516
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2285
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2302
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.224
X-RAY DIFFRACTIONr_nbd_other0.2290.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.23
X-RAY DIFFRACTIONr_mcbond_it1.3231.211299
X-RAY DIFFRACTIONr_mcbond_other1.3211.214300
X-RAY DIFFRACTIONr_mcangle_it1.9371.82376
X-RAY DIFFRACTIONr_mcangle_other1.9251.82376
X-RAY DIFFRACTIONr_scbond_it1.7711.375325
X-RAY DIFFRACTIONr_scbond_other1.7691.376326
X-RAY DIFFRACTIONr_scangle_it2.71.991470
X-RAY DIFFRACTIONr_scangle_other2.6981.992471
X-RAY DIFFRACTIONr_lrange_it4.51614.492681
X-RAY DIFFRACTIONr_lrange_other4.45714.198674
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allWRfactor Rwork
1.603-1.6440.209260.1916200.1926460.161
1.644-1.6890.306340.2055830.216170.169
1.689-1.7380.238270.2035840.2046110.164
1.738-1.7910.211270.1935650.1945920.162
1.791-1.850.213440.1855330.1875770.153
1.85-1.9140.23250.2065370.2075620.175
1.914-1.9860.214140.1865090.1875230.161
1.986-2.0660.165270.2035000.25270.179
2.066-2.1570.303250.1854760.1915010.16
2.157-2.2620.149140.1944590.1934730.18
2.262-2.3830.174160.214390.2094550.194
2.383-2.5260.252190.1994080.2014270.182
2.526-2.6980.236220.2273780.2284000.211
2.698-2.9110.244210.2083550.213760.203
2.911-3.1840.20990.1933470.1943560.198
3.184-3.5510.19150.1733050.1743200.183
3.551-4.0850.19170.1552620.1572790.172
4.085-4.9650.172170.1372210.1392380.17
4.965-6.8670.32480.2321850.2361930.257
6.867-23.3010.28840.2511170.2521210.297
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)
13.3228-2.1897-0.20274.18350.65133.7259-0.16460.0167-0.31550.20410.03920.38180.3011-0.10230.12540.0329-0.00770.02190.00450.00120.0776.546515.332224.1641
22.2877-4.97582.236712.8231-3.12213.76030.09730.0279-0.0456-0.2323-0.07410.06690.0633-0.0441-0.02320.01440.03270.00870.1178-0.00550.079913.119710.95518.7142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 62
2X-RAY DIFFRACTION2ALLQQQ1 - 12

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