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- PDB-6oie: The double PHD finger (DPF) of MORF in complex with histone H3K14cr -

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Basic information

Entry
Database: PDB / ID: 6oie
TitleThe double PHD finger (DPF) of MORF in complex with histone H3K14cr
Components
  • Histone H3.1t peptide
  • Histone acetyltransferase KAT6B
KeywordsTRANSFERASE / DPF / acetylation / crotonylation
Function / homology
Function and homology information


spermatogonial cell division / histone H3 acetyltransferase activity / DNA replication-dependent chromatin assembly / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity ...spermatogonial cell division / histone H3 acetyltransferase activity / DNA replication-dependent chromatin assembly / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K4 acetyltransferase activity / protein-lysine-acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone acetyltransferase activity / regulation of cell differentiation / heterochromatin / histone acetyltransferase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / Condensation of Prophase Chromosomes / condensed nuclear chromosome / transcription coregulator activity / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / chromatin organization / Processing of DNA double-strand break ends / transcription coactivator activity / chromosome, telomeric region / protein heterodimerization activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein-containing complex binding / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus
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 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / 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 H3.1t / Histone acetyltransferase KAT6B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.075 Å
AuthorsKlein, B.J. / Kutateladze, T.G.
CitationJournal: Nat Commun / Year: 2019
Title: Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation.
Authors: Klein, B.J. / Jang, S.M. / Lachance, C. / Mi, W. / Lyu, J. / Sakuraba, S. / Krajewski, K. / Wang, W.W. / Sidoli, S. / Liu, J. / Zhang, Y. / Wang, X. / Warfield, B.M. / Kueh, A.J. / Voss, A.K. ...Authors: Klein, B.J. / Jang, S.M. / Lachance, C. / Mi, W. / Lyu, J. / Sakuraba, S. / Krajewski, K. / Wang, W.W. / Sidoli, S. / Liu, J. / Zhang, Y. / Wang, X. / Warfield, B.M. / Kueh, A.J. / Voss, A.K. / Thomas, T. / Garcia, B.A. / Liu, W.R. / Strahl, B.D. / Kono, H. / Li, W. / Shi, X. / Cote, J. / Kutateladze, T.G.
History
DepositionApr 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _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 KAT6B
B: Histone acetyltransferase KAT6B
C: Histone H3.1t peptide
D: Histone H3.1t peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,84312
Polymers30,3204
Non-polymers5238
Water3,963220
1
A: Histone acetyltransferase KAT6B
D: Histone H3.1t peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4216
Polymers15,1602
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-3 kcal/mol
Surface area7610 Å2
MethodPISA
2
B: Histone acetyltransferase KAT6B
C: Histone H3.1t peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4216
Polymers15,1602
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-13 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.583, 69.535, 70.187
Angle α, β, γ (deg.)90.00, 97.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone acetyltransferase KAT6B / Histone acetyltransferase MOZ2 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 4 / MYST-4 / Monocytic ...Histone acetyltransferase MOZ2 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 4 / MYST-4 / Monocytic leukemia zinc finger protein-related factor


Mass: 13015.296 Da / Num. of mol.: 2 / Fragment: residues 211-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT6B, KIAA0383, MORF, MOZ2, MYST4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WYB5, histone acetyltransferase
#2: Protein/peptide Histone H3.1t peptide / H3t / H3/g


Mass: 2144.481 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16695
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.1-1.3 M sodium citrate tribasic and 0.1 M sodium hepes
PH range: 8.4-8.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.075→37 Å / Num. obs: 18819 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 20.3
Reflection shellResolution: 2.08→2.12 Å / Rmerge(I) obs: 0.264 / Num. unique obs: 1810

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U2J

5u2j


Resolution: 2.075→24.6 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.63
RfactorNum. reflection% reflection
Rfree0.2191 1861 10.01 %
Rwork0.1659 --
obs0.1713 18589 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.075→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 8 220 2174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072002
X-RAY DIFFRACTIONf_angle_d0.942686
X-RAY DIFFRACTIONf_dihedral_angle_d9.6791486
X-RAY DIFFRACTIONf_chiral_restr0.051284
X-RAY DIFFRACTIONf_plane_restr0.005356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0754-2.13150.23631360.18621226X-RAY DIFFRACTION93
2.1315-2.19420.26111420.17341280X-RAY DIFFRACTION99
2.1942-2.2650.25431390.18171259X-RAY DIFFRACTION98
2.265-2.34590.25681400.18241255X-RAY DIFFRACTION97
2.3459-2.43970.27241410.18321267X-RAY DIFFRACTION99
2.4397-2.55070.25941460.17981316X-RAY DIFFRACTION99
2.5507-2.6850.21831450.17491281X-RAY DIFFRACTION99
2.685-2.8530.25041420.18321280X-RAY DIFFRACTION99
2.853-3.07290.23931460.17791316X-RAY DIFFRACTION99
3.0729-3.38140.23541430.18391286X-RAY DIFFRACTION99
3.3814-3.8690.20221470.14541313X-RAY DIFFRACTION100
3.869-4.86840.17411440.13651308X-RAY DIFFRACTION100
4.8684-24.60130.17721500.15921341X-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)
11.50311.66281.47854.05461.94092.22030.0067-0.0909-0.02450.02810.0363-0.09460.0096-0.0107-0.04920.15830.01190.03020.16260.01750.1228107.1028-6.843630.3172
21.4698-0.9984-0.5854.37271.55072.1540.02860.1135-0.0624-0.09190.02820.0984-0.0172-0.1313-0.09410.1235-0.0293-0.01340.18520.02440.135695.2885-12.94874.6613
32.835-3.5124-0.77116.88363.23695.50980.10750.6875-0.7049-0.3848-0.23490.93920.1859-0.30370.13170.1958-0.031-0.04620.3025-0.05540.275188.5356-16.4041-2.6652
40.16470.7017-0.11094.7113-0.51220.07340.0668-0.3070.42950.0295-0.46631.49630.0209-0.11410.36510.240.06580.02410.2998-0.17020.41699.7535-3.3436.3884
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 211 through 320)
2X-RAY DIFFRACTION2(chain 'B' and resid 211 through 320)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 16)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 16)

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