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- PDB-7e7c: Crystal structure of ENL YEATS domain T1 mutant in complex with h... -

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Basic information

Entry
Database: PDB / ID: 7e7c
TitleCrystal structure of ENL YEATS domain T1 mutant in complex with histone H3 acetylation at K27
Components
  • Histone H3K27ac(24-27) peptide
  • Protein ENL
KeywordsTRANSCRIPTION / YEATS domain / Complex / histone
Function / homology
Function and homology information


RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / lysine-acetylated histone binding / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol
Similarity search - Function
AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
IODIDE ION / Protein ENL
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsLi, Y. / Li, H.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91753203 China
National Natural Science Foundation of China (NSFC)31725014 China
National Natural Science Foundation of China (NSFC)31871283 China
National Natural Science Foundation of China (NSFC)31922016 China
CitationJournal: To Be Published
Title: Crystal structure of ENL YEATS domain T1 mutant in complex with histone H3 acetylation at K27
Authors: Li, Y. / Li, H.
History
DepositionFeb 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ENL
B: Histone H3K27ac(24-27) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7386
Polymers19,3602
Non-polymers3784
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint1 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.635, 118.065, 34.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

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Components

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


Mass: 18872.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q03111
#2: Protein/peptide Histone H3K27ac(24-27) peptide


Mass: 487.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 4000, 0.1M MES pH 6.5, 0.2M Potassium iodide

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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: MAR CCD 130 mm / Detector: CCD / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. obs: 14147 / % possible obs: 98.8 % / Redundancy: 10 % / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.047 / Rrim(I) all: 0.138 / Χ2: 1.551 / Net I/σ(I): 7.2 / Num. measured all: 141761
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.84-1.8712.10.8166590.8760.2440.8520.92799.1
1.87-1.9111.70.7887090.8080.2390.8251.15899.9
1.91-1.9411.90.6486720.9520.1960.6781.45896.7
1.94-1.9811.60.5036940.9410.1540.5271.37899.9
1.98-2.03110.4167040.9580.130.4361.49899.4
2.03-2.0711.20.4156900.9630.130.4351.79497.9
2.07-2.1210.70.3346880.9740.1070.3521.717100
2.12-2.189.90.2986840.9660.0980.3151.87296.2
2.18-2.2510.80.3237040.9680.1020.3392.03699.9
2.25-2.3210.80.2866990.9770.0910.31.96998.7
2.32-2.4110.2446960.9790.0780.2571.85499.6
2.4-2.510.60.2187030.9810.0710.231.80299.2
2.5-2.6110.20.1877180.9880.0620.1971.57299.4
2.61-2.759.50.1757150.9840.0610.1861.60199.9
2.75-2.929.10.1416900.9870.0490.1491.47596.2
2.92-3.159.50.1277240.990.0450.1351.47599.5
3.15-3.468.80.1047270.9930.0390.1121.28499.7
3.46-3.967.70.0917270.9940.0360.0991.17199.6
3.96-4.9970.0827410.9910.0340.0891.30498.1
4.99-506.40.0818030.9920.0350.0881.53998

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5j9s

5j9s


Resolution: 1.84→34.35 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 1411 10 %
Rwork0.2153 12695 -
obs0.2189 14106 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 139.99 Å2 / Biso mean: 33.6941 Å2 / Biso min: 13.47 Å2
Refinement stepCycle: final / Resolution: 1.84→34.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 10 53 1325
Biso mean--59.69 37.06 -
Num. residues----152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.90.30921300.2541166129693
1.9-1.980.27691360.22011230136698
1.98-2.070.25151410.21761264140599
2.07-2.180.27341380.21141238137698
2.18-2.310.27771410.2231268140999
2.31-2.490.30121420.22391274141699
2.49-2.740.27851420.242712911433100
2.74-3.140.28971430.23091275141898
3.14-3.950.25661450.188313081453100
3.96-34.350.19871530.21431381153498

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