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- PDB-6v2h: Crystal structure of CDYL2 in complex with H3tK27me3 -

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Basic information

Entry
Database: PDB / ID: 6v2h
TitleCrystal structure of CDYL2 in complex with H3tK27me3
Components
  • Chromodomain Y-like protein 2
  • H3tK27me3
KeywordsGENE REGULATION / histone / chromodomain / Structural Genomics / Structural Genomics Consortium / SGC
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. / 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 / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Histone H3.1 / Chromodomain Y-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDong, C. / Tempel, W. / Walker, J.R. / 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 / Refinement description
Category: citation / citation_author ...citation / citation_author / refine / software
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 / _refine.pdbx_starting_model
Revision 1.2Jul 29, 2020Group: Database references / Derived calculations / Category: citation / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: H3tK27me3
C: Chromodomain Y-like protein 2
D: H3tK27me3
E: Chromodomain Y-like protein 2
F: H3tK27me3
G: Chromodomain Y-like protein 2
H: H3tK27me3
I: Chromodomain Y-like protein 2
J: H3tK27me3
K: Chromodomain Y-like protein 2
L: H3tK27me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,67747
Polymers52,32512
Non-polymers35235
Water00
1
A: Chromodomain Y-like protein 2
B: H3tK27me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7809
Polymers8,7212
Non-polymers597
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-19 kcal/mol
Surface area4410 Å2
MethodPISA
2
C: Chromodomain Y-like protein 2
D: H3tK27me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7804
Polymers8,7212
Non-polymers592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-19 kcal/mol
Surface area4580 Å2
MethodPISA
3
E: Chromodomain Y-like protein 2
F: H3tK27me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,78015
Polymers8,7212
Non-polymers5913
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-19 kcal/mol
Surface area4730 Å2
MethodPISA
4
G: Chromodomain Y-like protein 2
H: H3tK27me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7808
Polymers8,7212
Non-polymers596
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-20 kcal/mol
Surface area4440 Å2
MethodPISA
5
I: Chromodomain Y-like protein 2
J: H3tK27me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7807
Polymers8,7212
Non-polymers595
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-19 kcal/mol
Surface area4590 Å2
MethodPISA
6
K: Chromodomain Y-like protein 2
L: H3tK27me3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7804
Polymers8,7212
Non-polymers592
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-19 kcal/mol
Surface area4350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.750, 210.750, 67.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14A
24I
15A
25K
16C
26E
17C
27G
18C
28I
19C
29K
110E
210G
111E
211I
112E
212K
113G
213I
114G
214K
115I
215K

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEUAA4 - 584 - 58
21GLYGLYLEULEUCC4 - 584 - 58
12GLYGLYLEULEUAA4 - 584 - 58
22GLYGLYLEULEUEE4 - 584 - 58
13GLYGLYLEULEUAA4 - 584 - 58
23GLYGLYLEULEUGG4 - 584 - 58
14GLYGLYLEULEUAA4 - 584 - 58
24GLYGLYLEULEUII4 - 584 - 58
15GLYGLYLEULEUAA4 - 584 - 58
25GLYGLYLEULEUKK4 - 584 - 58
16GLYGLYMETMETCC1 - 601 - 60
26GLYGLYMETMETEE1 - 601 - 60
17GLYGLYLEULEUCC1 - 581 - 58
27GLYGLYLEULEUGG1 - 581 - 58
18GLYGLYLEULEUCC1 - 581 - 58
28GLYGLYLEULEUII1 - 581 - 58
19SERSERHISHISCC3 - 593 - 59
29SERSERHISHISKK3 - 593 - 59
110GLYGLYLEULEUEE1 - 581 - 58
210GLYGLYLEULEUGG1 - 581 - 58
111GLYGLYLEULEUEE1 - 581 - 58
211GLYGLYLEULEUII1 - 581 - 58
112SERSERHISHISEE3 - 593 - 59
212SERSERHISHISKK3 - 593 - 59
113GLYGLYHISHISGG1 - 591 - 59
213GLYGLYHISHISII1 - 591 - 59
114SERSERLEULEUGG3 - 583 - 58
214SERSERLEULEUKK3 - 583 - 58
115SERSERLEULEUII3 - 583 - 58
215SERSERLEULEUKK3 - 583 - 58

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Chromodomain Y-like protein 2 / CDY-like 2 / CDYL2


Mass: 7451.329 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
H3tK27me3


Mass: 1269.536 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 29 / Source method: obtained synthetically
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: 5.49 Å3/Da / Density % sol: 77.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 23% PEG3350, 0.25 M ammonium dihydrogen phosphate, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97957 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 2.6→63.06 Å / Num. obs: 34195 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.045 / Rrim(I) all: 0.109 / Net I/σ(I): 14.8 / Num. measured all: 200420
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.675.90.9971472425150.6580.4521.0951.9100
11.63-63.065.60.05220903740.9960.0240.05741.798.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimless0.5.27data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: an early version of PDB entry 6V41 (CDY1 in complex with a histone peptide)

6v41


Resolution: 2.6→63.14 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.759 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.204
Details: We interpreted strong electron density peaks at the CDYL2 N-termini as octahedrally coordinated nickel, based on our use of nickel ions during affinity chromatography. Coordination bond ...Details: We interpreted strong electron density peaks at the CDYL2 N-termini as octahedrally coordinated nickel, based on our use of nickel ions during affinity chromatography. Coordination bond length restraints are based on queries of the Cambridge Structural Database with MOGUL. COOT was used for interactive model building. Model geometry was monitored with PHENIX.MOLPROBITY.
RfactorNum. reflection% reflection
Rfree0.2366 2234 6.5 %
Rwork0.2173 --
obs0.2185 31961 99.97 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 135.65 Å2 / Biso mean: 58.187 Å2 / Biso min: 25.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0.3 Å20 Å2
2---0.6 Å20 Å2
3---1.94 Å2
Refinement stepCycle: final / Resolution: 2.6→63.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 35 0 3357
Biso mean--46.08 --
Num. residues----408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193442
X-RAY DIFFRACTIONr_bond_other_d0.0020.023066
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9374647
X-RAY DIFFRACTIONr_angle_other_deg0.91137026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3945398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6723.556180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70315534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5221523
X-RAY DIFFRACTIONr_chiral_restr0.0790.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A34620.04
12C34620.04
21A34040.06
22E34040.06
31A34940.02
32G34940.02
41A34060.04
42I34060.04
51A34700.04
52K34700.04
61C36520.04
62E36520.04
71C35580.05
72G35580.05
81C35720.02
82I35720.02
91C34940.06
92K34940.06
101E34920.06
102G34920.06
111E35360.03
112I35360.03
121E34300.06
122K34300.06
131G35340.05
132I35340.05
141G35100.04
142K35100.04
151I34320.05
152K34320.05
LS refinement shellResolution: 2.6→2.668 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 162 -
Rwork0.34 2349 -
all-2511 -
obs--100 %
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)
16.79770.60551.07537.2676-0.91552.97670.0888-0.27890.04390.3712-0.0627-0.8726-0.070.5655-0.02610.2308-0.1480.04360.33140.02880.289859.326180.612642.3178
23.37360.85551.02018.71481.22713.50550.0004-0.11070.04860.56880.14110.0785-0.197-0.2147-0.14150.1655-0.08470.05330.26160.00580.215251.477978.284144.774
35.37210.78012.07233.9092-2.60916.17590.0985-0.0091-0.2119-0.1268-0.2692-0.46720.36760.35710.17070.2654-0.1840.18970.30460.00840.515567.212893.240127.0242
47.24930.27292.35644.66332.36923.7530.36260.61710.03110.1329-0.1332-0.11910.48020.0815-0.22930.2737-0.11150.11640.33810.09550.294572.051797.169720.7846
56.19541.7775-1.54752.6941.82094.08910.03050.22320.1716-0.12030.13180.1049-0.2044-0.0707-0.16230.1017-0.00260.00090.08390.01360.0335.306967.587242.8763
63.22344.2447-0.13555.8271-1.49768.6450.024-0.01680.34950.2237-0.16770.3995-1.10840.14310.14370.1732-0.05570.00780.35540.08640.106741.582474.086142.8903
72.52751.30071.25686.2821.86838.5286-0.02070.17830.297-0.33160.12540.239-0.2105-0.1884-0.10470.1665-0.0522-0.02020.11230.05230.072935.237277.543916.4557
87.02320.4481-0.00639.4062-1.83253.7155-0.0749-0.26470.59410.26380.21230.577-0.3318-0.421-0.13730.2501-0.02680.01130.126-0.06040.145134.026583.838621.429
95.6261.12381.60386.43632.94623.23840.057-0.36960.65780.21020.09290.2434-0.5047-0.0311-0.14990.2839-0.0520.10750.1362-0.11620.409342.84199.711529.7278
106.7789-2.27081.65148.4254-1.10375.7714-0.0029-0.7530.09330.40580.28290.3854-0.0952-0.3911-0.280.2766-0.06440.01790.1463-0.08820.273739.248292.080127.7084
117.5768-2.8013-0.22635.63281.31695.2655-0.11990.1106-0.0882-0.0793-0.0661-0.3505-0.11990.3020.18590.5117-0.06950.01650.1366-0.20190.611654.8601116.043336.4605
124.5550.1557-0.12660.19130.15113.6205-0.2330.21790.3759-0.18190.06510.0597-0.2660.24010.16780.45350.0258-0.02780.125-0.09430.406353.4835124.365438.2994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 101
2X-RAY DIFFRACTION2B21 - 29
3X-RAY DIFFRACTION3C1 - 101
4X-RAY DIFFRACTION4D21 - 29
5X-RAY DIFFRACTION5E1 - 101
6X-RAY DIFFRACTION6F21 - 29
7X-RAY DIFFRACTION7G1 - 101
8X-RAY DIFFRACTION8H21 - 30
9X-RAY DIFFRACTION9I1 - 101
10X-RAY DIFFRACTION10J21 - 29
11X-RAY DIFFRACTION11K1 - 101
12X-RAY DIFFRACTION12L21 - 29

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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