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- PDB-7x8b: Crystal structure of ENL T1 mutant YEATS domain in complex with h... -

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Basic information

Entry
Database: PDB / ID: 7x8b
TitleCrystal structure of ENL T1 mutant YEATS domain in complex with histone H3 acetylation at K27
Components
  • H3K27ac(24-27) peptide
  • Protein ENL
KeywordsGENE REGULATION / YEATS domain / Complex / histone / Transcription
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 / fibrillar center / chromatin binding / positive regulation of DNA-templated transcription / nucleoplasm / cytosol
Similarity search - Function
YEATS domain / AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, Y. / Peng, B. / Li, H.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91753230 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: Mol.Cell / Year: 2022
Title: Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer.
Authors: Song, L. / Yao, X. / Li, H. / Peng, B. / Boka, A.P. / Liu, Y. / Chen, G. / Liu, Z. / Mathias, K.M. / Xia, L. / Li, Q. / Mir, M. / Li, Y. / Li, H. / Wan, L.
History
DepositionMar 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein ENL
B: H3K27ac(24-27) peptide
C: Protein ENL
D: H3K27ac(24-27) peptide


Theoretical massNumber of molelcules
Total (without water)38,7214
Polymers38,7214
Non-polymers00
Water2,198122
1
A: Protein ENL
B: H3K27ac(24-27) peptide


Theoretical massNumber of molelcules
Total (without water)19,3602
Polymers19,3602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein ENL
D: H3K27ac(24-27) peptide


Theoretical massNumber of molelcules
Total (without water)19,3602
Polymers19,3602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.732, 48.670, 47.654
Angle α, β, γ (deg.)90.000, 101.170, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 18872.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT1, ENL, LTG19, YEATS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03111
#2: Protein/peptide H3K27ac(24-27) peptide


Mass: 487.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20 % (w/v) PEG 4000, 0.1M sodium citrate pH5.6, 20 % (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jul 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 15862 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 25.77 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.045 / Rrim(I) all: 0.102 / Χ2: 2.01 / Net I/σ(I): 15.5 / Num. measured all: 80119
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.345.50.3338010.9320.1550.3681.144100
2.34-2.385.50.3177880.9430.1490.3511.101100
2.38-2.435.40.2947910.9580.1380.3251.11100
2.43-2.485.50.2737750.950.1280.3021.159100
2.48-2.535.40.2497990.9670.1170.2761.13399.9
2.53-2.595.50.2227680.9760.1040.2451.152100
2.59-2.655.30.2188070.9730.1030.2411.281100
2.65-2.735.30.2017910.9730.0970.2231.64100
2.73-2.815.30.1427930.9880.0680.1581.415100
2.81-2.95.20.1357940.9860.0650.151.55199.9
2.9-35.20.1127880.9880.0550.1251.945100
3-3.1250.1017810.9910.050.1132.03499.9
3.12-3.264.90.0888050.9910.0450.12.37100
3.26-3.434.50.0788040.9880.0420.0892.73599.8
3.43-3.654.30.0677710.9940.0360.0763.28698.7
3.65-3.934.60.0637980.9940.0320.0713.27399
3.93-4.334.30.0547920.9950.0290.0623.29499.7
4.33-4.954.70.058060.9970.0240.0553.37799.6
4.95-6.2350.0558110.9960.0260.0613.38299.9
6.23-304.60.0537990.9970.0270.063.41895.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J9S

5j9s


Resolution: 2.3→17.33 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 765 4.82 %
Rwork0.188 15094 -
obs0.1898 15859 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.27 Å2 / Biso mean: 31.5346 Å2 / Biso min: 11.22 Å2
Refinement stepCycle: final / Resolution: 2.3→17.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2497 0 0 122 2619
Biso mean---32.81 -
Num. residues----301
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.470.26521440.2041290696
2.47-2.720.24181630.21063029100
2.72-3.110.2771670.19923002100
3.11-3.910.17651380.181303899
3.91-17.330.22121530.17593119100

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