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- PDB-6mak: HBO1 is required for the maintenance of leukaemia stem cells -

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Basic information

Entry
Database: PDB / ID: 6mak
TitleHBO1 is required for the maintenance of leukaemia stem cells
Components
  • BRD1 protein
  • Histone acetyltransferase KAT7
Keywordsantitumor protein/transferase / MYST domain / cancer inhibitor / ANTITUMOR PROTEIN / antitumor protein-transferase complex
Function / homology
Function and homology information


histone H3K4 acetyltransferase activity / response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / response to sorbitol / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / histone H3K23 acetyltransferase activity / histone H4K12 acetyltransferase activity ...histone H3K4 acetyltransferase activity / response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / response to sorbitol / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / histone H3K23 acetyltransferase activity / histone H4K12 acetyltransferase activity / DNA replication-dependent chromatin disassembly / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / natural killer cell differentiation / histone H4 acetyltransferase activity / internal peptidyl-lysine acetylation / histone H3 acetyltransferase activity / regulation of nucleotide-excision repair / stress-activated protein kinase signaling cascade / positive regulation of DNA-templated transcription, elongation / histone H3-K14 acetyltransferase complex / regulation of DNA-templated DNA replication initiation / regulation of developmental process / regulation of hemopoiesis / MOZ/MORF histone acetyltransferase complex / regulation of DNA replication / erythrocyte maturation / site of DNA damage / DNA replication origin binding / chromosome, centromeric region / response to immobilization stress / histone acetyltransferase complex / response to electrical stimulus / histone acetyltransferase activity / histone acetyltransferase / transcription initiation-coupled chromatin remodeling / Regulation of TP53 Activity through Acetylation / histone reader activity / positive regulation of erythrocyte differentiation / positive regulation of DNA replication / regulation of cell growth / transcription coregulator activity / positive regulation of protein localization to nucleus / chromosome / HATs acetylate histones / histone binding / perikaryon / DNA replication / regulation of cell cycle / nuclear speck / chromatin remodeling / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / dendrite / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / BRPF2, ePHD domain ...Zinc finger, C2H2C-type superfamily / Zinc finger, C2HC type / Zinc finger, C2H2C-type / Zinc finger CCHHC-type profile. / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / BRPF2, ePHD domain / BRPF2, PHD domain / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Acyl-CoA N-acyltransferase / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ACETYL COENZYME *A / Histone acetyltransferase KAT7 / Bromodomain-containing protein 1 / BRD1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsRen, B. / Peat, T.S. / Monahan, B. / Dawson, M. / Street, I.
CitationJournal: Nature / Year: 2020
Title: HBO1 is required for the maintenance of leukaemia stem cells.
Authors: MacPherson, L. / Anokye, J. / Yeung, M.M. / Lam, E.Y.N. / Chan, Y.C. / Weng, C.F. / Yeh, P. / Knezevic, K. / Butler, M.S. / Hoegl, A. / Chan, K.L. / Burr, M.L. / Gearing, L.J. / Willson, T. ...Authors: MacPherson, L. / Anokye, J. / Yeung, M.M. / Lam, E.Y.N. / Chan, Y.C. / Weng, C.F. / Yeh, P. / Knezevic, K. / Butler, M.S. / Hoegl, A. / Chan, K.L. / Burr, M.L. / Gearing, L.J. / Willson, T. / Liu, J. / Choi, J. / Yang, Y. / Bilardi, R.A. / Falk, H. / Nguyen, N. / Stupple, P.A. / Peat, T.S. / Zhang, M. / de Silva, M. / Carrasco-Pozo, C. / Avery, V.M. / Khoo, P.S. / Dolezal, O. / Dennis, M.L. / Nuttall, S. / Surjadi, R. / Newman, J. / Ren, B. / Leaver, D.J. / Sun, Y. / Baell, J.B. / Dovey, O. / Vassiliou, G.S. / Grebien, F. / Dawson, S.J. / Street, I.P. / Monahan, B.J. / Burns, C.J. / Choudhary, C. / Blewitt, M.E. / Voss, A.K. / Thomas, T. / Dawson, M.A.
History
DepositionAug 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT7
B: BRD1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5914
Polymers38,7162
Non-polymers8752
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-21 kcal/mol
Surface area15410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.628, 39.026, 107.765
Angle α, β, γ (deg.)90.00, 99.59, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-103-

HOH

21B-104-

HOH

31B-105-

HOH

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Components

#1: Protein Histone acetyltransferase KAT7 / Histone acetyltransferase binding to ORC1 / Lysine acetyltransferase 7 / MOZ / YBF2/SAS3 / SAS2 and ...Histone acetyltransferase binding to ORC1 / Lysine acetyltransferase 7 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 2 / MYST-2


Mass: 32872.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT7, HBO1, HBOa, MYST2 / Production host: unidentified baculovirus / References: UniProt: O95251, histone acetyltransferase
#2: Protein BRD1 protein


Mass: 5843.446 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD1 / Production host: unidentified baculovirus / References: UniProt: Q86X06, UniProt: O95696*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 2.5 mg/mL was added in equal volume ratio with reservoir, 200 nL plus 200 nL. The reservoir consisted of 22% PEG MME 2000 plus 57 mM diammonium tartrate. Plates were stored at 20 C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953736 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953736 Å / Relative weight: 1
ReflectionResolution: 2.13→43.2 Å / Num. obs: 19938 / % possible obs: 98 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Net I/σ(I): 13.1
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1558 / CC1/2: 0.882 / Rpim(I) all: 0.31 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→43.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.93 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.21 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26434 972 4.9 %RANDOM
Rwork0.21366 ---
obs0.21629 18965 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 59.159 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å20 Å2-2.54 Å2
2--6.28 Å20 Å2
3----2.77 Å2
Refinement stepCycle: 1 / Resolution: 2.13→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 52 24 2512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0142546
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172315
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.6883441
X-RAY DIFFRACTIONr_angle_other_deg0.7781.6615419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4322.033123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35515459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3061514
X-RAY DIFFRACTIONr_chiral_restr0.0570.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022757
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02485
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8315.8821195
X-RAY DIFFRACTIONr_mcbond_other3.8245.881193
X-RAY DIFFRACTIONr_mcangle_it5.4668.8131489
X-RAY DIFFRACTIONr_mcangle_other5.4648.8161490
X-RAY DIFFRACTIONr_scbond_it4.0496.3131350
X-RAY DIFFRACTIONr_scbond_other4.0476.3141351
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1869.2931953
X-RAY DIFFRACTIONr_long_range_B_refined9.5499871
X-RAY DIFFRACTIONr_long_range_B_other9.5499870
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.131→2.187 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 60 -
Rwork0.338 1332 -
obs--93.17 %

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