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- PDB-2y0m: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN DOSAGE COMPENSATION FACT... -

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Basic information

Entry
Database: PDB / ID: 2y0m
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN DOSAGE COMPENSATION FACTORS MSL1 AND MOF
Components
  • MALE-SPECIFIC LETHAL 1 HOMOLOG
  • PROBABLE HISTONE ACETYLTRANSFERASE MYST1
KeywordsTRANSCRIPTION / CHROMATIN / X CHROMOSOME / MSL COMPLEX
Function / homology
Function and homology information


positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / HATs acetylate histones / protein propionyltransferase activity / histone H4 acetyltransferase activity / regulation of mRNA processing / dosage compensation by inactivation of X chromosome / myeloid cell differentiation / post-embryonic hemopoiesis ...positive regulation of skeletal muscle satellite cell differentiation / regulation of mitochondrial transcription / MSL complex / HATs acetylate histones / protein propionyltransferase activity / histone H4 acetyltransferase activity / regulation of mRNA processing / dosage compensation by inactivation of X chromosome / myeloid cell differentiation / post-embryonic hemopoiesis / 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 / positive regulation of transcription initiation by RNA polymerase II / histone H4K16 acetyltransferase activity / 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 / 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 - #2000 / 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 - #2000 / 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
ACETYL COENZYME *A / Male-specific lethal 1 homolog / Histone acetyltransferase KAT8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKadlec, J. / Hallacli, E. / Lipp, M. / Holz, H. / Sanchez Weatherby, J. / Cusack, S. / Akhtar, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural Basis for Mof and Msl3 Recruitment Into the Dosage Compensation Complex by Msl1.
Authors: Kadlec, J. / Hallacli, E. / Lipp, M. / Holz, H. / Sanchez-Weatherby, J. / Cusack, S. / Akhtar, A.
History
DepositionDec 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE HISTONE ACETYLTRANSFERASE MYST1
B: MALE-SPECIFIC LETHAL 1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4774
Polymers42,6022
Non-polymers8752
Water18010
1
A: PROBABLE HISTONE ACETYLTRANSFERASE MYST1
B: MALE-SPECIFIC LETHAL 1 HOMOLOG
hetero molecules

A: PROBABLE HISTONE ACETYLTRANSFERASE MYST1
B: MALE-SPECIFIC LETHAL 1 HOMOLOG
hetero molecules

A: PROBABLE HISTONE ACETYLTRANSFERASE MYST1
B: MALE-SPECIFIC LETHAL 1 HOMOLOG
hetero molecules

A: PROBABLE HISTONE ACETYLTRANSFERASE MYST1
B: MALE-SPECIFIC LETHAL 1 HOMOLOG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,90916
Polymers170,4098
Non-polymers3,5008
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation8_556-y,-x,-z+11
crystal symmetry operation15_556y,x,-z+11
Buried area18850 Å2
ΔGint-60.5 kcal/mol
Surface area64010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.940, 180.940, 80.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein PROBABLE HISTONE ACETYLTRANSFERASE MYST1 / MYST-1 / MOZ / YBF2/SAS3 / SAS2 AND TIP60 PROTEIN 1 / HMOF


Mass: 33752.094 Da / Num. of mol.: 1 / Fragment: HAT DOMAIN, RESIDUES 174-458
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHA COLI (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9H7Z6
#2: Protein MALE-SPECIFIC LETHAL 1 HOMOLOG / MSL-1 / HAMPIN / MALE-SPECIFIC LETHAL 1-LIKE 1 / MSL1-LIKE 1 / MALE-SPECIFIC LETHAL-1 HOMOLOG 1 / MSL1


Mass: 8850.101 Da / Num. of mol.: 1 / Fragment: PEHE DOMAIN, RESIDUES 470-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHA COLI (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q6PDM1
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.88 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 5 / Details: 0.1 M SODIUM ACETATE (PH 5), 1.0 M SODIUM FORMATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.7→48 Å / Num. obs: 18543 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.05
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.16 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0085refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GIV

2giv


Resolution: 2.7→42.65 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.913 / SU B: 25.034 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25587 946 5.1 %RANDOM
Rwork0.22316 ---
obs0.22477 17596 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.031 Å2
Baniso -1Baniso -2Baniso -3
1-18.55 Å20 Å20 Å2
2--18.55 Å20 Å2
3----37.09 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 52 10 2704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222766
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9451.9923742
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9215313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.32223.516128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00215498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0521517
X-RAY DIFFRACTIONr_chiral_restr0.0640.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212057
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.699→2.768 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 64 -
Rwork0.304 1229 -
obs--96.78 %
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)
11.7501-0.66720.40913.5069-1.17073.23440.0139-0.03070.03710.2604-0.1386-0.0054-0.23480.08510.12470.1293-0.0818-0.00920.1371-0.03650.0249-22.905-20.162419.7029
213.8995-3.215715.80692.8318-3.813722.3872-0.0052-0.53080.55470.1575-0.1033-0.2125-0.611-0.05750.10850.4877-0.29880.04670.2248-0.03070.377-10.5628-0.703421.078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A177 - 449
2X-RAY DIFFRACTION2B495 - 536

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