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- PDB-8i60: Crystal structure of GAS41 YEATS domain in complex with histone H... -

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Basic information

Entry
Database: PDB / ID: 8i60
TitleCrystal structure of GAS41 YEATS domain in complex with histone H3K27cr
Components
  • ALA-ARG-KCR-SER-ALA-PRO
  • YEATS domain-containing protein 4
KeywordsPROTEIN BINDING / Histone H3 lysine crotonylation
Function / homology
Function and homology information


modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / lysine-acetylated histone binding / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle ...modification-dependent protein binding / regulation of double-strand break repair / Activation of the TFAP2 (AP-2) family of transcription factors / NuA4 histone acetyltransferase complex / positive regulation of double-strand break repair via homologous recombination / lysine-acetylated histone binding / structural constituent of cytoskeleton / nuclear matrix / nucleosome / mitotic cell cycle / HATs acetylate histones / histone binding / regulation of apoptotic process / nuclear membrane / regulation of cell cycle / chromatin remodeling / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / nucleoplasm / nucleus
Similarity search - Function
YEATS / YEATS superfamily / YEATS family / YEATS domain profile.
Similarity search - Domain/homology
YEATS domain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKonuma, T. / Zhou, M.-M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Mol.Cell / Year: 2023
Title: Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin.
Authors: Liu, N. / Konuma, T. / Sharma, R. / Wang, D. / Zhao, N. / Cao, L. / Ju, Y. / Liu, D. / Wang, S. / Bosch, A. / Sun, Y. / Zhang, S. / Ji, D. / Nagatoishi, S. / Suzuki, N. / Kikuchi, M. / ...Authors: Liu, N. / Konuma, T. / Sharma, R. / Wang, D. / Zhao, N. / Cao, L. / Ju, Y. / Liu, D. / Wang, S. / Bosch, A. / Sun, Y. / Zhang, S. / Ji, D. / Nagatoishi, S. / Suzuki, N. / Kikuchi, M. / Wakamori, M. / Zhao, C. / Ren, C. / Zhou, T.J. / Xu, Y. / Meslamani, J. / Fu, S. / Umehara, T. / Tsumoto, K. / Akashi, S. / Zeng, L. / Roeder, R.G. / Walsh, M.J. / Zhang, Q. / Zhou, M.M.
History
DepositionJan 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: YEATS domain-containing protein 4
D: YEATS domain-containing protein 4
A: ALA-ARG-KCR-SER-ALA-PRO
B: ALA-ARG-KCR-SER-ALA-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7476
Polymers35,5594
Non-polymers1882
Water1,02757
1
C: YEATS domain-containing protein 4
A: ALA-ARG-KCR-SER-ALA-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8753
Polymers17,7792
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: YEATS domain-containing protein 4
B: ALA-ARG-KCR-SER-ALA-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8713
Polymers17,7792
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.980, 91.980, 83.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein YEATS domain-containing protein 4 / Glioma-amplified sequence 41 / Gas41 / NuMA-binding protein 1 / NuBI-1 / NuBI1


Mass: 16479.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YEATS4, GAS41 / Production host: Escherichia coli (E. coli) / References: UniProt: O95619
#2: Protein/peptide ALA-ARG-KCR-SER-ALA-PRO


Mass: 1299.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→61.79 Å / Num. obs: 16481 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 40.4 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 5 / Num. unique obs: 2342 / CC1/2: 0.92

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→61.79 Å / SU ML: 0.3514 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2911 833 5.07 %
Rwork0.2561 15596 -
obs0.2579 16429 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.87 Å2
Refinement stepCycle: LAST / Resolution: 2.3→61.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 11 57 1859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841847
X-RAY DIFFRACTIONf_angle_d1.20172518
X-RAY DIFFRACTIONf_chiral_restr0.0585281
X-RAY DIFFRACTIONf_plane_restr0.008322
X-RAY DIFFRACTIONf_dihedral_angle_d14.2964264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.35431180.31712546X-RAY DIFFRACTION99.59
2.44-2.630.34821470.32542537X-RAY DIFFRACTION99.96
2.63-2.90.38091380.30882556X-RAY DIFFRACTION99.93
2.9-3.320.30131440.27512576X-RAY DIFFRACTION100
3.32-4.180.29831440.22412620X-RAY DIFFRACTION99.96
4.18-61.790.22991420.23122761X-RAY DIFFRACTION99.97
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)
12.954052369563.466761642541.879049445695.95421931593.73990113393.976808076620.203444657261-0.0728467495041-0.5547389730960.0174409118010.23865970508-0.594837191857-0.372201834672-0.16393380211-0.4040577540410.2614417345880.07974076697840.0426505066340.3109749755650.1023288014490.316145948088.052927709232.673222996310.3130110295
29.434572447154.279334811466.149973231282.640071349743.595694182725.92905629827-1.03469986036-0.435816268777-2.295631600020.380647611024-0.871888394070.2711612797480.629812119715-0.01227683013311.506876614210.502224130792-0.1693089370460.1686059452430.473993626761-0.04865726722260.870736421098-15.33332411329.5764179915311.8630934663
33.79382493181-1.91712753515-1.008403448722.935010133831.850310075014.973929106780.3154117286860.1159334702360.1759363638510.4465794555720.244117518462-0.7558607362310.4083454737880.275947027526-0.4542539919810.2793717163540.0256882591673-0.0725703029480.197297219672-0.008491050783240.3955230913295.9972125061724.806097434913.0746951248
40.5214943521151.83535509424-0.1535175557456.71152990860.2059012717892.251131178-0.00611540626536-0.639921160080.3054134987470.2619681256650.12231076811.017203422780.485391787324-0.662993088193-0.1014903248560.424926203067-0.1154354167860.1377453329970.853559885508-0.03145695900590.345805284005-11.541558829623.270419232220.044282893
51.58430228301-0.0488506525997-0.05260720216876.018338820241.612610666813.048768184320.00409413387067-0.0663347246841-0.1043276224740.8395611297440.0499513118944-0.5401094824930.159160544726-0.418480588727-0.0459452616290.355580318199-0.0289175042282-0.03493008421210.3125531812070.08731946398860.324908007884-1.9501759652524.429578311816.3708403389
63.185337670.06134185400811.053096090091.605666693690.1946997871892.2424018474-0.0665958889312-0.5477410270770.529595415330.3290059077710.250935110988-0.213932512636-0.6775341781480.07570226711450.007795734199660.428526072950.0384199172824-0.003980535732620.1849618121170.04779355757210.2684577103463.5755797217435.559361643616.9376449869
74.981093639382.601358807520.7964790236783.206749558860.2385298212324.13496430129-0.08367062625160.9283411905730.827721506683-0.8461120123070.2939261937560.305395741977-0.595550093093-0.43322483081-0.1385092911060.3354389917920.09531440460090.1719402402060.4811854015460.08935331894310.5159699190420.41532240373326.64308341924.71435409463
80.32139027635-0.515537224708-0.9420621162580.8264386136411.50244619132.737816883720.340825672801-0.318346207645-0.268688882583-0.7637695001130.4577532361820.696569736422-0.15359541732-0.640503236360.7546528097061.02852137828-0.0165331732311-0.2123948614640.5991194306450.4145526799640.60370100394624.87642.24617.921
92.94227819694-1.26391581026-1.091206731262.742266817650.2877788243.614771636920.059358204440.308448813883-0.1768112648740.2171570045550.5779719339390.1856489085330.1091778438470.95474759817-0.1801923353880.317163995435-0.005461481885990.05974168496540.417508414264-0.2090174748930.31478482482511.293515561423.3945660386-6.0134286216
101.808179344-0.4960427720270.1551573008970.546978952011.516721019486.034840232770.835125889594-0.6336641790630.868164182749-0.2109734930090.440819579307-0.9220186448410.01593251394431.19927838102-0.2638270514130.962154577962-0.475770918470.2562090246270.79221341505-0.1630985329590.66317266608115.59390895136.6821586734-7.4374861748
113.43684545604-0.703946112128-1.379917295157.921234354573.41618315548.008419453360.1848959249860.4715436000760.210231126539-1.10071707273-0.2042188705320.543197184237-1.254259174410.655198767526-0.009576609060910.496972117654-0.0108516711315-0.04239405130830.4736261586610.00653057329180.2954228078089.8156949943225.5883040726-15.0129741075
122.804273006590.3706715777591.171896257113.24519479459-1.230028867681.07455315711-0.04847168329930.0123089071157-0.3643407801550.7776253070920.111922854148-0.1420177014440.141144085143-0.230601329648-0.0158758392060.4032452947780.1101575556510.006364153692990.416861616906-0.112842625370.4535961166612.57059634767.70192591104-6.41861496128
130.2967080499120.26828883643-0.3608892350335.97418529472-1.454627879690.667187828064-0.0480429997190.0888123402164-0.7834006083271.355315554830.00859892626369-1.640313885450.1367093490730.785064977725-0.2226678744920.4236597672440.1702347266060.01649968391451.03714190039-0.2760733499170.38390609599724.50727.046-6.844
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 14 through 33 )CA14 - 331 - 20
22chain 'C' and (resid 34 through 44 )CA34 - 4421 - 29
33chain 'C' and (resid 45 through 69 )CA45 - 6930 - 54
44chain 'C' and (resid 70 through 77 )CA70 - 7755 - 62
55chain 'C' and (resid 78 through 104 )CA78 - 10463 - 89
66chain 'C' and (resid 105 through 117 )CA105 - 11790 - 102
77chain 'C' and (resid 118 through 146 )CA118 - 146103 - 124
88chain 'C' and (resid 147 through 149 )CA - B147 - 301125
99chain 'D' and (resid 23 through 58 )DC23 - 581 - 28
1010chain 'D' and (resid 59 through 69 )DC59 - 6929 - 39
1111chain 'D' and (resid 70 through 123 )DC70 - 12340 - 84
1212chain 'D' and (resid 124 through 137 )DC124 - 13785 - 98
1313chain 'D' and (resid 138 through 143 )DC - D138 - 30199

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