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

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Basic information

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


response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / DNA replication-dependent chromatin disassembly / response to sorbitol / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / natural killer cell differentiation / internal peptidyl-lysine acetylation ...response to hydroxyurea / response to actinomycin D / response to dithiothreitol / response to anisomycin / DNA replication-dependent chromatin disassembly / response to sorbitol / positive regulation of hematopoietic stem cell proliferation / regulation of DNA biosynthetic process / natural killer cell differentiation / internal peptidyl-lysine acetylation / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / regulation of nucleotide-excision repair / stress-activated protein kinase signaling cascade / histone H3-K14 acetyltransferase complex / positive regulation of DNA-templated transcription, elongation / regulation of DNA-templated DNA replication initiation / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / erythrocyte maturation / histone acetyltransferase activity / regulation of DNA replication / site of DNA damage / response to immobilization stress / DNA replication origin binding / histone acetyltransferase complex / chromosome, centromeric region / response to electrical stimulus / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / transcription initiation-coupled chromatin remodeling / positive regulation of erythrocyte differentiation / histone reader activity / positive regulation of DNA replication / transcription coregulator activity / regulation of cell growth / positive regulation of protein localization to nucleus / HATs acetylate histones / chromosome / perikaryon / histone binding / DNA replication / regulation of cell cycle / nuclear speck / chromatin remodeling / DNA repair / dendrite / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / zinc ion binding / nucleoplasm / nucleus / 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. ...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 (BrD) profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-JAV / Histone acetyltransferase KAT7 / Bromodomain-containing protein 1 / BRD1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.139 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
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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)39,3666
Polymers38,7162
Non-polymers6504
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-18 kcal/mol
Surface area14440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.543, 111.543, 73.702
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein , 2 types, 2 molecules AB

#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

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Non-polymers , 4 types, 161 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-JAV / 4-fluoro-N'-[(3-hydroxyphenyl)sulfonyl]-5-methyl[1,1'-biphenyl]-3-carbohydrazide


Mass: 400.423 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C20H17FN2O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystals were grown at 20 C in sitting drop plates in drops of 200 nL crystallant and 200 nL protein. The protein was at 2.5 mg/mL and the reservoir was 20% PEG 3350 with 244 mM diammonium tartrate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.14→58.6 Å / Num. obs: 18887 / % possible obs: 100 % / Redundancy: 5.3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.095 / Net I/σ(I): 5.7
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.292 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1486 / CC1/2: 0.583 / Rpim(I) all: 0.614 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.139→58.595 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 841 4.47 %
Rwork0.1949 --
obs0.1967 18829 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.139→58.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 41 157 2541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042454
X-RAY DIFFRACTIONf_angle_d0.7333311
X-RAY DIFFRACTIONf_dihedral_angle_d5.6012008
X-RAY DIFFRACTIONf_chiral_restr0.046352
X-RAY DIFFRACTIONf_plane_restr0.005407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1393-2.27340.31911470.28242974X-RAY DIFFRACTION99
2.2734-2.44890.32951670.25882964X-RAY DIFFRACTION100
2.4489-2.69530.26211260.22873009X-RAY DIFFRACTION100
2.6953-3.08540.27671570.2012985X-RAY DIFFRACTION100
3.0854-3.88710.22891100.16243041X-RAY DIFFRACTION100
3.8871-58.61680.16771340.16663015X-RAY DIFFRACTION100
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)
11.2789-0.74961.47372.13010.08492.2261-0.046-0.09640.3677-0.0104-0.1544-0.2174-0.61150.10980.12650.33410.03-0.01840.20570.030.293829.5243206.6689-81.5816
22.45760.5614-0.48362.0555-0.34722.04640.27930.34040.43140.3549-0.2762-0.0636-0.6923-0.15640.13020.38510.08520.04620.29010.09580.336921.804210.6677-89.248
30.9798-0.41730.17582.0135-0.04751.62670.08220.2156-0.08330.0251-0.05440.2163-0.087-0.41770.00210.14120.00380.00650.2524-0.00220.184318.4923193.0166-88.9788
40.95340.21280.12092.5471-0.22453.10540.0411-0.01430.09220.05790.08810.0897-0.132-0.1408-0.09040.14860.02060.0060.16940.01840.199224.9878192.9297-85.8116
51.37110.0188-0.32441.7998-0.47813.1583-0.0283-0.0557-0.01760.0651-0.0071-0.08260.109-0.0758-0.00750.1527-0.02720.00140.17010.00970.217228.7939188.1769-81.3801
62.46210.1641-0.2462.00950.14452.37360.11570.026-0.1710.1908-0.1050.14090.3547-0.13840.03020.2418-0.0351-0.00090.1960.01270.223126.8674180.7272-79.8855
72.273-0.9156-0.19053.1323-0.34891.5008-0.2212-0.2874-0.4420.26130.11730.26580.515-0.1024-0.06920.4723-0.01810.06730.20560.0790.316429.2537173.4269-70.1363
80.97860.68210.87551.6917-0.98212.8285-0.1443-0.4418-0.32871.11420.2003-0.52420.28350.8882-0.03410.710.2288-0.12030.45780.07930.388138.723169.0532-64.5771
91.1338-1.15410.3441.2588-0.65690.6568-0.164-0.3449-0.06940.79810.22540.69430.7824-0.16110.00870.676-0.08490.17380.5083-0.00140.408319.0392178.2858-69.8253
103.13150.21540.21111.2946-0.41460.44670.3158-0.309-0.61160.44830.2514-0.96110.21910.8228-0.16550.8870.04410.16570.9490.24311.229345.3806166.6958-73.2448
110.98820.1174-0.16350.91030.02892.5135-0.1867-0.3661-0.19650.30740.1327-0.60760.0889-0.0930.01840.82640.10680.02220.39370.18140.601735.4238161.092-67.0136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 335 through 356 )
2X-RAY DIFFRACTION2chain 'A' and (resid 357 through 387 )
3X-RAY DIFFRACTION3chain 'A' and (resid 388 through 427 )
4X-RAY DIFFRACTION4chain 'A' and (resid 428 through 463 )
5X-RAY DIFFRACTION5chain 'A' and (resid 464 through 485 )
6X-RAY DIFFRACTION6chain 'A' and (resid 486 through 512 )
7X-RAY DIFFRACTION7chain 'A' and (resid 513 through 551 )
8X-RAY DIFFRACTION8chain 'A' and (resid 552 through 577 )
9X-RAY DIFFRACTION9chain 'A' and (resid 578 through 607 )
10X-RAY DIFFRACTION10chain 'B' and (resid 38 through 52 )
11X-RAY DIFFRACTION11chain 'B' and (resid 53 through 61 )

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