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- PDB-4dnc: Crystal structure of human MOF in complex with MSL1 -

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Basic information

Entry
Database: PDB / ID: 4dnc
TitleCrystal structure of human MOF in complex with MSL1
Components
  • Histone acetyltransferase KAT8
  • Male-specific lethal 1 homolog
KeywordsTRANSCRIPTION / histone acetyltransferase / MOF / MSL / NSL
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / protein propionyltransferase activity / histone H4 acetyltransferase activity / regulation of mRNA processing / dosage compensation by inactivation of X chromosome / post-embryonic hemopoiesis / myeloid cell differentiation / NSL complex ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / protein propionyltransferase activity / histone H4 acetyltransferase activity / regulation of mRNA processing / dosage compensation by inactivation of X chromosome / post-embryonic hemopoiesis / myeloid cell differentiation / NSL complex / negative regulation of epithelial to mesenchymal transition / protein-lysine-acetyltransferase activity / negative regulation of type I interferon production / oogenesis / Formation of WDR5-containing histone-modifying complexes / NuA4 histone acetyltransferase complex / MLL1 complex / histone acetyltransferase complex / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H4K16 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K27 acetyltransferase activity / positive regulation of transcription initiation by RNA polymerase II / histone acetyltransferase / neurogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / kinetochore / nuclear matrix / HATs acetylate histones / chromosome / protein-macromolecule adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of autophagy / nuclear speck / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / enzyme binding / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3170 / Protein male-specific lethal-1 / Protein male-specific lethal-1, dimerisation domain / Dimerisation domain of Male-specific-Lethal 1 / PEHE domain / PEHE domain profile. / PEHE domain / PEHE / N-acetyl transferase-like / : ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3170 / Protein male-specific lethal-1 / Protein male-specific lethal-1, dimerisation domain / Dimerisation domain of Male-specific-Lethal 1 / PEHE domain / PEHE domain profile. / PEHE domain / PEHE / N-acetyl transferase-like / : / MYST, zinc finger domain / MYST family zinc finger domain / Histone acetyltransferase domain, MYST-type / MOZ/SAS family / MYST-type histone acetyltransferase (HAT) domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Acyl-CoA N-acyltransferase / Aminopeptidase / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Male-specific lethal 1 homolog / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHuang, J. / Lei, M.
CitationJournal: Cell Res. / Year: 2012
Title: Structural insight into the regulation of MOF in the male-specific lethal complex and the non-specific lethal complex.
Authors: Huang, J. / Wan, B. / Wu, L. / Yang, Y. / Dou, Y. / Lei, M.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone acetyltransferase KAT8
B: Histone acetyltransferase KAT8
D: Male-specific lethal 1 homolog
E: Male-specific lethal 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6266
Polymers79,4964
Non-polymers1312
Water2,720151
1
A: Histone acetyltransferase KAT8
D: Male-specific lethal 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8133
Polymers39,7482
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-12 kcal/mol
Surface area16320 Å2
MethodPISA
2
B: Histone acetyltransferase KAT8
E: Male-specific lethal 1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8133
Polymers39,7482
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-13 kcal/mol
Surface area16480 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-36 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.801, 111.518, 66.751
Angle α, β, γ (deg.)90.00, 111.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone acetyltransferase KAT8 / Lysine acetyltransferase 8 / MOZ / YBF2/SAS3 / SAS2 and TIP60 protein 1 / MYST-1 / hMOF


Mass: 33983.344 Da / Num. of mol.: 2 / Fragment: HAT domain (UNP residues 170-458)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KAT8, MOF, MYST1, PP7073 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H7Z6, histone acetyltransferase
#2: Protein/peptide Male-specific lethal 1 homolog / MSL-1 / Male-specific lethal 1-like 1 / MSL1-like 1 / Male-specific lethal-1 homolog 1


Mass: 5764.471 Da / Num. of mol.: 2 / Fragment: MOF-binding motif (UNP residues 473-520)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSL1, MSL1L1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q68DK7
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.6 M Li2SO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98159 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98159 Å / Relative weight: 1
ReflectionResolution: 2.05→100 Å / Num. obs: 54362

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→40.994 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 26.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2463 5527 10.18 %
Rwork0.2084 --
obs0.2123 54319 97.9 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.572 Å2 / ksol: 0.388 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.9333 Å20 Å2-4.0074 Å2
2--6.2053 Å20 Å2
3----0.272 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5219 0 2 151 5372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075360
X-RAY DIFFRACTIONf_angle_d1.0647244
X-RAY DIFFRACTIONf_dihedral_angle_d16.0362020
X-RAY DIFFRACTIONf_chiral_restr0.069761
X-RAY DIFFRACTIONf_plane_restr0.005909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07330.32991750.25771333X-RAY DIFFRACTION81
2.0733-2.09770.32251650.2421457X-RAY DIFFRACTION87
2.0977-2.12330.28131680.23241516X-RAY DIFFRACTION92
2.1233-2.15020.26571790.23571610X-RAY DIFFRACTION97
2.1502-2.17850.27661660.23571615X-RAY DIFFRACTION98
2.1785-2.20830.31181970.22961579X-RAY DIFFRACTION98
2.2083-2.23980.29931910.22471699X-RAY DIFFRACTION99
2.2398-2.27330.26821810.21851628X-RAY DIFFRACTION99
2.2733-2.30880.26171890.22131625X-RAY DIFFRACTION99
2.3088-2.34660.29931790.22821620X-RAY DIFFRACTION99
2.3466-2.38710.28841810.23411679X-RAY DIFFRACTION99
2.3871-2.43050.29841770.2331629X-RAY DIFFRACTION99
2.4305-2.47720.29351820.23251686X-RAY DIFFRACTION99
2.4772-2.52780.28071790.23661613X-RAY DIFFRACTION99
2.5278-2.58280.29171890.24621662X-RAY DIFFRACTION99
2.5828-2.64280.28441790.24421633X-RAY DIFFRACTION99
2.6428-2.70890.30721640.24031666X-RAY DIFFRACTION99
2.7089-2.78210.29461960.25181623X-RAY DIFFRACTION99
2.7821-2.8640.3231840.24741646X-RAY DIFFRACTION99
2.864-2.95640.28332090.25181626X-RAY DIFFRACTION100
2.9564-3.0620.2861950.24051658X-RAY DIFFRACTION99
3.062-3.18460.2821750.23251653X-RAY DIFFRACTION100
3.1846-3.32950.25541660.21441671X-RAY DIFFRACTION100
3.3295-3.50490.23641860.20331679X-RAY DIFFRACTION100
3.5049-3.72440.21381910.18571668X-RAY DIFFRACTION100
3.7244-4.01170.20052120.17421617X-RAY DIFFRACTION100
4.0117-4.4150.2092040.16121662X-RAY DIFFRACTION100
4.415-5.05280.17551890.1591678X-RAY DIFFRACTION100
5.0528-6.36220.21282020.20211664X-RAY DIFFRACTION100
6.3622-41.00220.21151770.19341697X-RAY DIFFRACTION98

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