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- PDB-6l5z: Crystal strucutre of AF9 YEATS domain in complex with a cyclopept... -

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Basic information

Entry
Database: PDB / ID: 6l5z
TitleCrystal strucutre of AF9 YEATS domain in complex with a cyclopeptide inhibitor
Components
  • Protein AF-9
  • SC0-ALO-ALA-SC3-SC4-NH2
KeywordsTRANSCRIPTION / YEATS domain / Complex / Cyclopeptide inhibitor /
Function / homology
Function and homology information


modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events ...modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / negative regulation of canonical Wnt signaling pathway / lysine-acetylated histone binding / gene expression / chromosome / histone binding / molecular adaptor activity / chromatin binding / positive regulation of DNA-templated transcription / DNA binding / extracellular exosome / nucleoplasm / nucleus / 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
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsLi, Y. / Chen, G. / Li, H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91753203 China
National Natural Science Foundation of China (NSFC)31922016 China
National Natural Science Foundation of China (NSFC)31871283 China
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Selective Targeting of AF9 YEATS Domain by Cyclopeptide Inhibitors with Preorganized Conformation.
Authors: Jiang, Y. / Chen, G. / Li, X.M. / Liu, S. / Tian, G. / Li, Y. / Li, X. / Li, H. / Li, X.D.
History
DepositionOct 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AF-9
C: SC0-ALO-ALA-SC3-SC4-NH2


Theoretical massNumber of molelcules
Total (without water)17,4262
Polymers17,4262
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.240, 106.240, 45.492
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein AF-9 / ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated ...ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated to chromosome 3 protein / YEATS domain-containing protein 3


Mass: 16611.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Production host: Escherichia coli (E. coli) / References: UniProt: P42568
#2: Protein/peptide SC0-ALO-ALA-SC3-SC4-NH2 / Cyclopeptide inhibitor


Mass: 814.909 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.21 Å3/Da / Density % sol: 70.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v)PEG 3350,0.2M Ammonium Nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 5816 / % possible obs: 99.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.033 / Rrim(I) all: 0.103 / Χ2: 0.628 / Net I/σ(I): 6.4 / Num. measured all: 56564
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.05-3.19.60.82770.8990.2690.8440.425100
3.1-3.169.40.662800.9220.2240.6970.421100
3.16-3.2290.5872970.9340.2090.6240.45100
3.22-3.298.70.442880.9560.1590.4690.46199.7
3.29-3.3610.10.3612730.9730.1180.380.433100
3.36-3.4310.40.2762900.9840.0890.290.462100
3.43-3.5210.30.2092910.9880.0670.220.515100
3.52-3.6210.60.182790.990.0580.190.581100
3.62-3.7210.30.1442880.9950.0470.1510.582100
3.72-3.8410.20.142990.9950.0460.1470.624100
3.84-3.9810.20.1212780.9950.0390.1270.667100
3.98-4.149.90.1012990.9950.0330.1060.714100
4.14-4.339.70.0842870.9970.0280.0890.861100
4.33-4.569.40.0782930.9960.0270.0830.69699.3
4.56-4.848.20.0672860.9970.0250.0720.74199.3
4.84-5.21100.0682910.9980.0220.0720.807100
5.21-5.7410.20.073060.9970.0230.0740.681100
5.74-6.5710.10.0662900.9980.0220.0690.755100
6.57-8.279.60.0593040.9980.020.0630.811100
8.27-508.70.0493200.9970.0180.0520.84198.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 3.05→40.78 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 620 10.68 %
Rwork0.1904 5183 -
obs0.1937 5803 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.79 Å2 / Biso mean: 77.0601 Å2 / Biso min: 39.31 Å2
Refinement stepCycle: final / Resolution: 3.05→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1145 0 58 4 1207
Biso mean--70.52 66.05 -
Num. residues----137
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.05-3.360.33221350.26412801415
3.36-3.840.28251410.222113031444
3.84-4.840.21151660.171512741440
4.84-40.780.18451780.171613261504

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