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- PDB-9pku: Crystal Structure of YEATS domain of human YEATS2 in complex with... -

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Basic information

Entry
Database: PDB / ID: 9pku
TitleCrystal Structure of YEATS domain of human YEATS2 in complex with LS-131 peptide
Components
  • LS-131 peptide
  • YEATS domain-containing protein 2
KeywordsGENE REGULATION / ATAC complex / YEATS2 / chemical probe
Function / homology
Function and homology information


modification-dependent protein binding / ATAC complex / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / histone reader activity / regulation of cell division / regulation of embryonic development / TBP-class protein binding / mitotic spindle / transcription corepressor activity ...modification-dependent protein binding / ATAC complex / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / histone reader activity / regulation of cell division / regulation of embryonic development / TBP-class protein binding / mitotic spindle / transcription corepressor activity / HATs acetylate histones / histone binding / regulation of cell cycle / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
: / Three-helical bundle domain / YEATS / : / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
1-benzofuran-2-carboxylic acid / YEATS domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
Authorsxinyi, Y. / sha, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2242500053 China
CitationJournal: To Be Published
Title: Complex-specific chemical probes for interrogating ATAC histone acetyltransferase complex
Authors: Sha, L.
History
DepositionJul 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YEATS domain-containing protein 2
B: LS-131 peptide
C: YEATS domain-containing protein 2
D: LS-131 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,29717
Polymers33,1304
Non-polymers1,16713
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.399, 51.559, 54.381
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-402-

CL

21C-527-

HOH

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein YEATS domain-containing protein 2


Mass: 16087.455 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS2, KIAA1197
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9ULM3
#2: Protein/peptide LS-131 peptide


Mass: 477.556 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 78 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BZ2 / 1-benzofuran-2-carboxylic acid


Mass: 162.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H6O3 / Source: (synth.) Homo sapiens (human) / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.67 Å3/Da / Density % sol: 66.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 2.0 M Sodium chloride, 0.1 M bis-tris propane pH 7.8
PH range: 7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.88→49.4342 Å / Num. obs: 11011 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.061 / Net I/σ(I): 35.8
Reflection shellResolution: 2.88→2.95 Å / Rmerge(I) obs: 0.299 / Num. unique obs: 494 / CC1/2: 0.976

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.88→49.43 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 1089 9.93 %
Rwork0.2085 --
obs0.213 10967 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.88→49.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 51 65 2435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092427
X-RAY DIFFRACTIONf_angle_d1.093272
X-RAY DIFFRACTIONf_dihedral_angle_d9.856335
X-RAY DIFFRACTIONf_chiral_restr0.067338
X-RAY DIFFRACTIONf_plane_restr0.009409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.88-3.010.3531300.2871191X-RAY DIFFRACTION96
3.01-3.170.41681390.2681198X-RAY DIFFRACTION98
3.17-3.370.33451350.25731223X-RAY DIFFRACTION98
3.37-3.630.31531330.25461243X-RAY DIFFRACTION99
3.63-40.28281360.21821221X-RAY DIFFRACTION99
4-4.570.231420.17681234X-RAY DIFFRACTION99
4.57-5.760.19651370.18481272X-RAY DIFFRACTION100
5.76-49.430.20881370.1931296X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 58.655 Å / Origin y: -2.824 Å / Origin z: 7.3928 Å
111213212223313233
T0.6003 Å20.0562 Å2-0.0348 Å2-0.4838 Å20.0705 Å2--0.4811 Å2
L5.0303 °20.9492 °20.1629 °2-1.3964 °20.1931 °2--1.748 °2
S0.0339 Å °-0.3932 Å °-0.2478 Å °0.2013 Å °-0.0537 Å °0.0334 Å °0.0895 Å °0.232 Å °0.0415 Å °
Refinement TLS groupSelection details: all

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