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- PDB-5b76: Crystal structure of MOZ double PHD finger domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 5b76
TitleCrystal structure of MOZ double PHD finger domain in complex with histone H3 crotonylation at K14
Components
  • Histone H3
  • Histone acetyltransferase KAT6A
KeywordsTRANSFERASE / double PHD finger
Function / homology
Function and homology information


histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis ...histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / protein acetylation / acetyltransferase activity / chromosome organization / histone acetyltransferase activity / histone acetyltransferase / Regulation of TP53 Activity through Acetylation / regulation of signal transduction by p53 class mediator / transcription coregulator activity / PML body / structural constituent of chromatin / cellular senescence / nucleosome / nucleosome assembly / HATs acetylate histones / DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain 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. / Linker histone H1/H5, domain H15 ...: / SAM domain-containing protein 1, WH domain / SAMD1-like winged helix (WH) domain 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. / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / PHD-finger / 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 / 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 / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3 / Histone acetyltransferase KAT6A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 Å
AuthorsLi, H. / Xiong, X.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2
Authors: Xiong, X. / Panchenko, T. / Yang, S. / Zhao, S. / Yan, P. / Zhang, W. / Xie, W. / Li, Y. / Zhao, Y. / Allis, C.D. / Li, H.
History
DepositionJun 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Nov 8, 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 / 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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT6A
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1809
Polymers17,6302
Non-polymers5507
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-40 kcal/mol
Surface area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.120, 47.633, 76.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone acetyltransferase KAT6A / MOZ


Mass: 14930.603 Da / Num. of mol.: 1 / Fragment: UNP residues 194-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MOZ / Production host: Escherichia coli (E. coli) / References: UniProt: Q92794, histone acetyltransferase
#2: Protein/peptide Histone H3


Mass: 2699.164 Da / Num. of mol.: 1 / Fragment: UNP residues 2-26 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: K7EMV3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: polyethylene glycol 4000, lithium sulfate, Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97893 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.65→24.1 Å / Num. obs: 21315 / % possible obs: 99.5 % / Redundancy: 8.6 % / Net I/σ(I): 44.2
Reflection shellResolution: 1.65→1.68 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data processing
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LLB

4llb


Resolution: 1.653→24.06 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.04
RfactorNum. reflection% reflection
Rfree0.2365 1092 5.12 %
Rwork0.1866 --
obs0.189 21315 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.653→24.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 19 180 1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031154
X-RAY DIFFRACTIONf_angle_d0.6281550
X-RAY DIFFRACTIONf_dihedral_angle_d12.849725
X-RAY DIFFRACTIONf_chiral_restr0.042163
X-RAY DIFFRACTIONf_plane_restr0.004203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6532-1.72840.25821190.21222500X-RAY DIFFRACTION99
1.7284-1.81950.22151310.20162497X-RAY DIFFRACTION100
1.8195-1.93340.33111300.27432473X-RAY DIFFRACTION98
1.9334-2.08270.23051490.20492503X-RAY DIFFRACTION99
2.0827-2.29210.27571550.23322429X-RAY DIFFRACTION97
2.2921-2.62340.20421390.17772551X-RAY DIFFRACTION100
2.6234-3.30390.20871390.18152580X-RAY DIFFRACTION100
3.3039-24.06250.2351300.15752690X-RAY DIFFRACTION99
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)
11.9607-0.7329-2.20711.47251.65653.2420.1046-1.1445-0.2170.9845-0.0134-0.74560.66681.02450.10630.6045-0.0621-0.13510.55210.07320.49266.5227-6.4444-5.862
20.22360.00410.21810.1256-0.1690.1684-0.00910.0220.01910.01430.14980.15820.1112-0.18060.00020.26580.0108-0.03930.1743-0.00730.2234-1.52177.0862-20.3966
30.7224-0.0481-0.17430.3417-0.2450.36150.07970.0762-0.0071-0.4616-0.1408-0.10910.27090.1543-0.0120.43040.06160.0120.22770.01240.19045.21429.8661-27.6896
40.1676-0.03190.21270.3841-0.21570.2526-0.03770.0366-0.1085-0.148-0.1094-0.13210.1035-0.0433-0.00010.21750.0219-0.01140.17930.0070.22825.45118.521-16.852
50.6708-0.16720.95910.9871-0.47851.56760.1415-0.12580.1007-0.0552-0.0893-0.09180.18940.16980.00020.21070.0373-0.00940.194-0.02030.27029.55644.3393-12.0064
60.5635-0.01240.31690.1639-0.11180.54530.0551-0.47130.15150.2535-0.12130.1054-0.0524-0.4792-00.25910.02450.00450.3879-0.04620.27545.24967.7712.9947
70.77630.40860.550.23670.1810.43730.0357-0.1323-0.06380.1584-0.0718-0.11120.17170.097-00.20090.0036-0.02630.2731-0.00260.219414.1597.7519-0.038
80.5217-0.05970.26290.3582-0.11230.1485-0.1319-0.17-0.05190.1836-0.06790.0902-0.19660.6075-0.00050.289-0.0393-0.00420.33450.03290.243219.526214.0293-0.6067
90.35070.2259-0.21140.1498-0.1140.1540.5681-0.2222-0.2022-0.1583-0.3594-0.14980.0471.52250.02310.28470.0664-0.05520.51420.01630.328221.86931.8841-2.1937
100.24460.01820.10080.24680.05990.2049-0.1422-0.28770.5956-0.0526-0.27540.1154-0.4402-0.3607-0.00070.31830.0245-0.05630.2581-0.0110.40548.532317.4347-7.312
110.6581-0.2241-0.35940.5242-0.29820.4828-0.28620.0129-0.11180.26130.10080.66380.2046-0.2772-0.00230.29620.0055-0.02590.2811-0.03440.4258-7.050814.5042-20.5813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 193 through 202 )
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 212 )
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 229 )
4X-RAY DIFFRACTION4chain 'A' and (resid 230 through 245 )
5X-RAY DIFFRACTION5chain 'A' and (resid 246 through 264 )
6X-RAY DIFFRACTION6chain 'A' and (resid 265 through 277 )
7X-RAY DIFFRACTION7chain 'A' and (resid 278 through 297 )
8X-RAY DIFFRACTION8chain 'A' and (resid 298 through 307 )
9X-RAY DIFFRACTION9chain 'A' and (resid 308 through 312 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 11 )
11X-RAY DIFFRACTION11chain 'B' and (resid 12 through 26 )

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