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- PDB-7e74: Crystal structure of ENL YEATS domain T3 mutant in complex with h... -

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Basic information

Entry
Database: PDB / ID: 7.0E+74
TitleCrystal structure of ENL YEATS domain T3 mutant in complex with histone H3 acetylation at K27
Components
  • ALA-ALA-ARG-ALY
  • 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 / 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 superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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: 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
DepositionFeb 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Protein ENL
B: Protein ENL
C: Protein ENL
D: Protein ENL
E: ALA-ALA-ARG-ALY
F: ALA-ALA-ARG-ALY
G: ALA-ALA-ARG-ALY
H: ALA-ALA-ARG-ALY


Theoretical massNumber of molelcules
Total (without water)75,2638
Polymers75,2638
Non-polymers00
Water1267
1
A: Protein ENL
E: ALA-ALA-ARG-ALY


Theoretical massNumber of molelcules
Total (without water)18,8162
Polymers18,8162
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein ENL
H: ALA-ALA-ARG-ALY


Theoretical massNumber of molelcules
Total (without water)18,8162
Polymers18,8162
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein ENL
G: ALA-ALA-ARG-ALY


Theoretical massNumber of molelcules
Total (without water)18,8162
Polymers18,8162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein ENL
F: ALA-ALA-ARG-ALY


Theoretical massNumber of molelcules
Total (without water)18,8162
Polymers18,8162
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.789, 91.309, 165.823
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18328.127 Da / Num. of mol.: 4 / Mutation: N111K
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
ALA-ALA-ARG-ALY


Mass: 487.573 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.16 Å3/Da / Density % sol: 70.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2M sodium formate, 0.1M sodium acetate trihydrate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 28625 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.068 / Rrim(I) all: 0.248 / Χ2: 0.419 / Net I/σ(I): 1.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.91-2.9613.40.95514300.8630.2690.9920.381100
2.96-3.0113.30.87413940.8680.2480.9090.392100
3.01-3.0713.10.78313990.8860.2240.8150.394100
3.07-3.1312.70.66114120.9110.1930.690.405100
3.13-3.212.10.5714080.9420.1710.5960.408100
3.2-3.28130.50114200.9550.1440.5220.422100
3.28-3.3612.70.42613880.9690.1240.4440.413100
3.36-3.4513.80.38814360.9730.1070.4030.419100
3.45-3.55140.31213950.9790.0860.3240.424100
3.55-3.67140.26514190.9840.0730.2750.433100
3.67-3.813.70.24814190.9870.0690.2570.437100
3.8-3.9513.80.22714270.9890.0630.2360.436100
3.95-4.1313.50.20714250.990.0580.2160.437100
4.13-4.3513.20.17914140.9920.0510.1870.454100
4.35-4.62120.15114480.9920.0450.1570.432100
4.62-4.9712.40.13914170.9940.0410.1450.412100
4.97-5.4713.50.15914570.9940.0450.1650.418100
5.47-6.2713.60.16614520.9940.0460.1730.425100
6.27-7.8912.70.15914850.9940.0460.1650.407100
7.89-5011.80.09515800.9970.0280.0990.42399.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5j9s


Resolution: 2.9→45.97 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 1410 4.95 %
Rwork0.2083 27071 -
obs0.2103 28481 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.21 Å2 / Biso mean: 45.843 Å2 / Biso min: 20.32 Å2
Refinement stepCycle: final / Resolution: 2.9→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 53 7 4757
Biso mean--52.32 33.07 -
Num. residues----557
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-30.37041340.336255295
3-3.120.31361250.27612667100
3.12-3.260.30591390.23662707100
3.26-3.430.28681340.2412700100
3.43-3.650.27721490.24632688100
3.65-3.930.23321460.1992701100
3.93-4.320.23621560.18432703100
4.32-4.950.22111450.15942733100
4.95-6.230.20951550.18142747100
6.23-100.19921270.1946287398

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