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- PDB-6ls6: Crystal Structure of YEATS domain of AF9 in complex with H3K9bz p... -

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Basic information

Entry
Database: PDB / ID: 6ls6
TitleCrystal Structure of YEATS domain of AF9 in complex with H3K9bz peptide
Components
  • 2
  • Protein AF-9
KeywordsTRANSCRIPTION / YEATS domain / histone Kbz modification
Function / homology
Function and homology information


modification-dependent protein binding / histone H3K9ac reader activity / histone H3K18ac reader activity / histone H3K27ac reader activity / 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 ...modification-dependent protein binding / histone H3K9ac reader activity / histone H3K18ac reader activity / histone H3K27ac reader activity / 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 / Chromatin modifying enzymes / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / : / RNA Polymerase II Pre-transcription Events / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / transcription elongation factor complex / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / negative regulation of canonical Wnt signaling pathway / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / chromosome / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / histone binding / gene expression / molecular adaptor activity / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...AF-9, ANC1 homology domain / : / ANC1 homology domain (AHD) / : / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Protein AF-9 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLi, H.T. / Ren, X.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31725014, 31871283, 31922016 China
National Basic Research Program of China (973 Program)2016YFA0500700 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins.
Authors: Ren, X. / Zhou, Y. / Xue, Z. / Hao, N. / Li, Y. / Guo, X. / Wang, D. / Shi, X. / Li, H.
History
DepositionJan 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AF-9
B: Protein AF-9
C: 2
D: 2


Theoretical massNumber of molelcules
Total (without water)35,2734
Polymers35,2734
Non-polymers00
Water55831
1
A: Protein AF-9
D: 2


Theoretical massNumber of molelcules
Total (without water)17,6362
Polymers17,6362
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-4 kcal/mol
Surface area8850 Å2
MethodPISA
2
B: Protein AF-9
C: 2


Theoretical massNumber of molelcules
Total (without water)17,6362
Polymers17,6362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-4 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.258, 42.236, 90.253
Angle α, β, γ (deg.)90.000, 96.640, 90.000
Int Tables number5
Space group name H-MC121

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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.: 2 / Fragment: YEATS domain of AF9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42568
#2: Protein/peptide 2


Mass: 1025.160 Da / Num. of mol.: 2 / Fragment: histone H3 peptide / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.33 Å3/Da / Density % sol: 47.29 % / Mosaicity: 0.706 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5??200 mM lithium sulfate, 25% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2018 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.196→50 Å / Num. obs: 16939 / % possible obs: 96.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.075 / Rrim(I) all: 0.159 / Χ2: 1.352 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.30.4228080.9230.2490.4920.61594
2.24-2.283.40.4428380.920.2590.5150.66996.9
2.28-2.323.50.4188300.9190.2490.4890.62996.6
2.32-2.373.60.4238900.9280.2470.4920.66798.3
2.37-2.423.60.378150.9260.2180.4310.7398.3
2.42-2.483.50.3438390.9270.2060.4020.77296.7
2.48-2.543.40.3267860.940.2020.3870.77190.2
2.54-2.613.90.38680.9590.1710.3470.77398.6
2.61-2.693.80.2688720.9620.1530.310.95599.2
2.69-2.773.90.2438600.9730.1380.2810.94498.9
2.77-2.873.80.1858600.9840.1070.2151.22999.4
2.87-2.993.80.1658600.9840.0950.1911.23197.6
2.99-3.123.80.1858620.9830.1030.2121.32598.2
3.12-3.294.80.2488500.9830.1220.2781.37498
3.29-3.494.50.2028480.9830.1050.231.69797.1
3.49-3.764.30.1567810.9880.0830.1781.70788.5
3.76-4.144.70.1398690.990.0730.1581.83197.1
4.14-4.744.40.0958460.9940.0520.1092.28496.6
4.74-5.974.40.0928890.990.0510.1062.2998.3
5.97-504.50.0778680.9920.040.0882.82793.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14rc3_3206refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 2.2→44.824 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2718 1238 7.34 %
Rwork0.2268 15636 -
obs0.2301 16874 96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.97 Å2 / Biso mean: 55.5557 Å2 / Biso min: 25.81 Å2
Refinement stepCycle: final / Resolution: 2.2→44.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 0 31 2479
Biso mean---46.22 -
Num. residues----292
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.28350.35811410.3185165393
2.2835-2.38750.3861370.3168174297
2.3875-2.51330.39551150.296170794
2.5133-2.67080.36081390.2784175498
2.6708-2.8770.3231510.2789176599
2.877-3.16640.29741380.2456175097
3.1664-3.62440.27121380.2123171995
3.6244-4.56570.20741370.1815175295
4.5657-44.8240.22231420.1975179496
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6386-0.2572-0.29320.1905-0.0190.319-0.1649-0.24110.15660.13130.2201-0.1772-0.4411-0.416-0.00030.51810.0634-0.02560.4095-0.01070.37272.53637.342928.2729
20.61360.4934-0.41810.4758-0.36060.3911-0.3917-0.2018-0.07920.97090.26370.0164-0.6328-0.1867-0.00050.61710.0512-0.00020.3104-0.00210.3266.7126-0.629642.8405
30.86050.2744-0.47251.31440.28440.78840.12450.0978-0.0194-0.124-0.11460.19160.2921-0.2551-00.34390.0067-0.01990.2669-0.0160.3544-1.3388-5.235235.4116
40.2763-0.0949-0.44481.00260.4050.7497-0.03870.42260.0764-0.0795-0.0214-0.0912-0.25780.1346-00.34970.05240.03630.31130.02350.35223.61393.59429.8079
50.152-0.18730.02430.24320.04220.6201-0.19470.2090.0463-0.04830.20970.08220.90590.27690.01210.633-0.02350.00790.6564-0.10710.48598.9752-20.6849-3.7423
60.92970.2167-0.31880.6024-0.52740.47690.18080.15970.22750.2158-0.1597-0.1832-0.07790.2611-0.03680.35520.1295-0.01450.5583-0.18230.442717.285-11.567814.4836
70.88280.4098-0.1390.66590.41250.4570.03280.23340.19-0.20910.3518-0.1241-0.47240.23880.00050.40970.03090.04060.5952-0.11590.390713.6981-7.34552.4846
80.22840.2957-0.16571.1499-0.00540.2361-0.09830.0455-0.0842-0.23950.0492-0.06710.4804-0.74070.00160.62370.0767-0.0890.5368-0.09440.43517.5022-12.24934.2378
90.0016-0.00790.03020.0045-0.0170.0542-0.39840.1617-0.1715-0.01810.3509-0.02610.5814-0.56720.00010.8003-0.10830.00410.6594-0.09850.47416.2517-20.1790.0993
100.1501-0.0586-0.09280.232-0.04530.0862-0.05680.5903-0.26-1.01570.5427-0.20580.71190.47110.00180.6872-0.1271-0.00970.7101-0.17630.49412.0347-19.1763-18.4964
110.2037-0.01670.08710.2428-0.21730.2049-0.0492-0.2682-0.05820.11420.2493-0.0496-0.3186-0.60870.00150.62090.0756-0.05420.5001-0.03970.49124.3647-9.022219.6854
120.3115-0.0477-0.31741.0618-0.71380.8764-0.21790.16-0.05780.0944-0.1734-0.4189-0.17280.0367-0.46680.19110.0333-0.05290.4371-0.00570.641517.9505-12.137.0388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 22 )A4 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 50 )A23 - 50
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 99 )A51 - 99
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 141 )A100 - 141
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 22 )B4 - 22
6X-RAY DIFFRACTION6chain 'B' and (resid 23 through 44 )B23 - 44
7X-RAY DIFFRACTION7chain 'B' and (resid 45 through 92 )B45 - 92
8X-RAY DIFFRACTION8chain 'B' and (resid 93 through 116 )B93 - 116
9X-RAY DIFFRACTION9chain 'B' and (resid 117 through 128 )B117 - 128
10X-RAY DIFFRACTION10chain 'B' and (resid 129 through 141 )B129 - 141
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 10 )C3 - 10
12X-RAY DIFFRACTION12chain 'D' and (resid 3 through 10 )D3 - 10

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