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- PDB-9ehi: Crystal structure of ENL YEATS in complex with histone H3 methacr... -

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Basic information

Entry
Database: PDB / ID: 9ehi
TitleCrystal structure of ENL YEATS in complex with histone H3 methacrylated at K18
Components
  • Histone H3.1
  • Protein ENL
KeywordsTRANSCRIPTION / ENL / YEATS / PTM / methacrylation / acetylation / bromodomain
Function / homology
Function and homology information


Chromatin modifying enzymes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / 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 ...Chromatin modifying enzymes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / 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) / epigenetic regulation of gene expression / HCMV Late Events / SIRT1 negatively regulates rRNA expression / transcription elongation factor complex / 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 / fibrillar center / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / 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 / Estrogen-dependent gene expression / gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / 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 / Protein ENL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBecht, D.C. / Selvam, K. / Kutateladze, T.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: The YEATS domain is a selective reader of histone methacrylation.
Authors: Becht, D.C. / Song, J. / Selvam, K. / Yin, K. / Bai, W. / Zhao, Y. / Wu, R. / Zheng, Y.G. / Kutateladze, T.G.
History
DepositionNov 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 16, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ENL
B: Protein ENL
C: Protein ENL
D: Protein ENL
E: Protein ENL
F: Protein ENL
G: Protein ENL
H: Protein ENL
I: Protein ENL
J: Protein ENL
K: Protein ENL
L: Protein ENL
M: Protein ENL
N: Protein ENL
O: Protein ENL
P: Protein ENL
Q: Histone H3.1
R: Histone H3.1
S: Histone H3.1
T: Histone H3.1
U: Histone H3.1
V: Histone H3.1
W: Histone H3.1
X: Histone H3.1
Y: Histone H3.1
Z: Histone H3.1
a: Histone H3.1
b: Histone H3.1
c: Histone H3.1
d: Histone H3.1
e: Histone H3.1
f: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,79737
Polymers287,82132
Non-polymers9765
Water6,449358
1
A: Protein ENL
Q: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein ENL
R: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1843
Polymers17,9892
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein ENL
S: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1843
Polymers17,9892
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein ENL
T: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Protein ENL
U: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Protein ENL
V: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Protein ENL
W: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Protein ENL
X: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Protein ENL
Y: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1843
Polymers17,9892
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Protein ENL
Z: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Protein ENL
a: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Protein ENL
b: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: Protein ENL
c: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: Protein ENL
d: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1843
Polymers17,9892
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: Protein ENL
e: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)17,9892
Polymers17,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: Protein ENL
f: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1843
Polymers17,9892
Non-polymers1951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.463, 98.413, 118.449
Angle α, β, γ (deg.)87.59, 90.00, 90.02
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein ENL / YEATS domain-containing protein 1


Mass: 17136.793 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03111
#2: Protein/peptide
Histone H3.1 / 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: 852.013 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES monohydrate, pH 6.0, 20% (v/v) Jeffamine M600, pH 7.0
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.6→39.45 Å / Num. obs: 72529 / % possible obs: 97.8 % / Redundancy: 3.1 % / CC1/2: 0.971 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.115 / Rrim(I) all: 0.205 / Χ2: 1.49 / Net I/σ(I): 9.8 / Num. measured all: 221400
Reflection shellResolution: 2.6→2.66 Å / % possible obs: 97.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.576 / Num. measured all: 13756 / Num. unique obs: 4523 / CC1/2: 0.675 / Rpim(I) all: 0.39 / Rrim(I) all: 0.698 / Χ2: 0.97 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→37.18 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.881 / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26653 3588 4.9 %RANDOM
Rwork0.21947 ---
obs0.22173 68933 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.374 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å2-0.19 Å20.73 Å2
2---0.22 Å20.85 Å2
3----1.07 Å2
Refinement stepCycle: 1 / Resolution: 2.6→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19542 0 60 358 19960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01220269
X-RAY DIFFRACTIONr_bond_other_d0.0010.01619331
X-RAY DIFFRACTIONr_angle_refined_deg1.411.88427405
X-RAY DIFFRACTIONr_angle_other_deg1.4931.78244597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25952324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.1045224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.435103469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.22848
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0223734
X-RAY DIFFRACTIONr_gen_planes_other0.0140.024958
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8023.6319418
X-RAY DIFFRACTIONr_mcbond_other2.8023.6319418
X-RAY DIFFRACTIONr_mcangle_it4.636.50811728
X-RAY DIFFRACTIONr_mcangle_other4.636.50811729
X-RAY DIFFRACTIONr_scbond_it3.1183.94610851
X-RAY DIFFRACTIONr_scbond_other3.1143.94410849
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2367.10415662
X-RAY DIFFRACTIONr_long_range_B_refined8.25144.3920239
X-RAY DIFFRACTIONr_long_range_B_other8.25244.3920240
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 268 -
Rwork0.302 5081 -
obs--96.97 %

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