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- PDB-5b77: Crystal structrue of MOZ double PHD finger in complex with histon... -

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Basic information

Entry
Database: PDB / ID: 5b77
TitleCrystal structrue of MOZ double PHD finger in complex with histone H3 propionylation at K14
Components
  • Histone H3
  • Histone acetyltransferase KAT6A
KeywordsTRANSFERASE / MOZ double PHD finger
Function / homology
Function and homology information


histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H4K16 acetyltransferase activity / myeloid cell differentiation / regulation of developmental process / MOZ/MORF histone acetyltransferase complex / regulation of hemopoiesis / protein acetylation ...histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H4K16 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 / nucleosome assembly / structural constituent of chromatin / nucleosome / cellular senescence / HATs acetylate histones / DNA-binding transcription factor binding / transcription coactivator activity / nuclear speck / protein heterodimerization activity / negative regulation of DNA-templated transcription / positive regulation of gene expression / nucleolus / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / 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 / Linker histone H1/H5 globular (H15) domain profile. ...: / 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 / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / 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: 1.551 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

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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)18,0748
Polymers17,6202
Non-polymers4546
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-33 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.708, 48.028, 75.168
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: 2689.146 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 291 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: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.55→33.8 Å / Num. obs: 25683 / % possible obs: 99.9 % / Redundancy: 5.9 % / Net I/σ(I): 32.2
Reflection shellResolution: 1.55→1.58 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: 1.551→33.8 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.07
RfactorNum. reflection% reflection
Rfree0.204 1309 5.1 %
Rwork0.174 --
obs0.1755 25683 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.551→33.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 14 187 1289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111121
X-RAY DIFFRACTIONf_angle_d1.2571504
X-RAY DIFFRACTIONf_dihedral_angle_d16.457712
X-RAY DIFFRACTIONf_chiral_restr0.069159
X-RAY DIFFRACTIONf_plane_restr0.008196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5505-1.61260.26911600.25372641X-RAY DIFFRACTION100
1.6126-1.6860.2561410.20622651X-RAY DIFFRACTION100
1.686-1.77490.2321270.17942709X-RAY DIFFRACTION100
1.7749-1.8860.17951430.17532653X-RAY DIFFRACTION100
1.886-2.03170.20731400.1742695X-RAY DIFFRACTION100
2.0317-2.23610.20151660.17162673X-RAY DIFFRACTION100
2.2361-2.55950.17631370.17462728X-RAY DIFFRACTION100
2.5595-3.22430.21571460.1812757X-RAY DIFFRACTION100
3.2243-33.85530.19681490.162867X-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)
11.7314-0.2133-0.3332.1611-0.96242.6197-0.09260.1076-0.11880.13040.07180.07610.1975-0.14970.01480.1527-0.0412-0.01090.1583-0.00760.180819.11812.80728.6639
21.27310.5561-0.64553.3595-1.43422.5875-0.11380.03340.42540.0705-0.0371-0.3133-0.34140.09070.16030.2449-0.0152-0.03080.22580.02210.379527.822111.73254.7841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 197 through 312)
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 25)

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