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- PDB-2y0n: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN DOSAGE COMPENSATION FACT... -

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Basic information

Entry
Database: PDB / ID: 2y0n
TitleCRYSTAL STRUCTURE OF THE COMPLEX BETWEEN DOSAGE COMPENSATION FACTORS MSL1 AND MSL3
Components
  • MALE-SPECIFIC LETHAL 1 HOMOLOG
  • MALE-SPECIFIC LETHAL 3 HOMOLOG
KeywordsTRANSCRIPTION / CHROMATIN / X CHROMOSOME / MSL COMPLEX
Function / homology
Function and homology information


MSL complex / HATs acetylate histones / Rpd3S complex / histone H4K16 acetyltransferase activity / NuA4 histone acetyltransferase complex / methylated histone binding / HATs acetylate histones / nuclear speck / chromatin remodeling / chromatin binding ...MSL complex / HATs acetylate histones / Rpd3S complex / histone H4K16 acetyltransferase activity / NuA4 histone acetyltransferase complex / methylated histone binding / HATs acetylate histones / nuclear speck / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Protein male-specific lethal-1 / Protein male-specific lethal-1, dimerisation domain / Dimerisation domain of Male-specific-Lethal 1 / MRG domain / PEHE domain / PEHE domain / PEHE / MRG / MRG domain / MRG, C-terminal domain superfamily ...Protein male-specific lethal-1 / Protein male-specific lethal-1, dimerisation domain / Dimerisation domain of Male-specific-Lethal 1 / MRG domain / PEHE domain / PEHE domain / PEHE / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / Enzyme I; Chain A, domain 2 / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Male-specific lethal 1 homolog / MSL complex subunit 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 4, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MALE-SPECIFIC LETHAL 3 HOMOLOG
B: MALE-SPECIFIC LETHAL 3 HOMOLOG
C: MALE-SPECIFIC LETHAL 3 HOMOLOG
D: MALE-SPECIFIC LETHAL 3 HOMOLOG
E: MALE-SPECIFIC LETHAL 1 HOMOLOG
F: MALE-SPECIFIC LETHAL 1 HOMOLOG
G: MALE-SPECIFIC LETHAL 1 HOMOLOG
H: MALE-SPECIFIC LETHAL 1 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)124,1918
Polymers124,1918
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19080 Å2
ΔGint-148.3 kcal/mol
Surface area41010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.230, 127.270, 79.680
Angle α, β, γ (deg.)90.00, 118.46, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
13G
23H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A171 - 210
2111B171 - 210
3111C171 - 210
4111D171 - 210
1211A251 - 464
2211B251 - 464
3211C251 - 464
4211D251 - 464
1311A212 - 215
2311B212 - 215
3311C212 - 215
4311D212 - 215
1411A466 - 488
2411B466 - 488
3411C466 - 488
4411D466 - 488
1511A490 - 503
2511B490 - 503
3511C490 - 503
4511D490 - 503
1121E569 - 594
2121F569 - 594
1131G569 - 590
2131H569 - 590
1231G553 - 558
2231H553 - 558

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1, -0.00019, -0.00018), (-0.00019, -1, -6.0E-5), (-0.00018, 6.0E-5, -1)0.08857, -1.53947, 70.05445
2given(-0.98588, 0.00487, 0.16741), (-0.00643, 0.99774, -0.06688), (-0.16736, -0.06701, -0.98362)-0.1248, 7.97456, 70.28783
3given(-0.98537, 0.00463, 0.17034), (0.00645, -0.9979, 0.06442), (0.17028, 0.06457, 0.98328)-0.26853, -9.47295, -0.25216
4given(1, 0.00172, -0.00158), (0.00172, -1, 0.00161), (-0.00158, -0.00161, -1)0.06299, -1.59342, 70.06078
5given(1, -0.00047, 0.00152), (-0.00047, -1, -0.00158), (0.00152, 0.00158, -1)0.00417, -1.50081, 70.04503

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Components

#1: Protein
MALE-SPECIFIC LETHAL 3 HOMOLOG / MALE-SPECIFIC LETHAL-3 HOMOLOG 1 / MALE-SPECIFIC LETHAL-3 PROTEIN-LIKE 1 / MSL3-LIKE 1 / MSL3


Mass: 24776.662 Da / Num. of mol.: 4 / Fragment: MRG DOMAIN, RESIDUES 167-289 AND 442-518
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: Q8N5Y2
#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: 6271.082 Da / Num. of mol.: 4 / Fragment: PEHE DOMAIN, RESIDUES 545-597
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
Sequence detailsRESIDUES 290-441 IN UNP Q8N5Y2 WERE SUBSTITUTED WITH AN INSERTION SEQUENCE YDIPPTTEF. YDIPPTT WERE ...RESIDUES 290-441 IN UNP Q8N5Y2 WERE SUBSTITUTED WITH AN INSERTION SEQUENCE YDIPPTTEF. YDIPPTT WERE ASSIGNED RESIDUE NUMBERS 290-296; EF WAS ASSIGNED RESIDUE NUMBERS 440 AND 441.

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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: 2.72 Å3/Da / Density % sol: 54.8 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M ADA (PH 6.5), 0.1M LI2SO4, 0.9M MGSO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3→46 Å / Num. obs: 25057 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 100 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 16.37
Reflection shellResolution: 3→3.12 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.04 / % possible all: 94.9

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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 2F5J

2f5j


Resolution: 3→46.13 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.916 / SU B: 51.587 / SU ML: 0.398 / Cross valid method: THROUGHOUT / ESU R: 0.889 / ESU R Free: 0.413 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25295 1260 5 %RANDOM
Rwork0.23229 ---
obs0.23337 23794 93.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.475 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å2-0.24 Å2
2---0.13 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 3→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 0 0 6492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226669
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.999042
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0215771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.56223.872297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.769151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8791528
X-RAY DIFFRACTIONr_chiral_restr0.0780.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0224976
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: 3.002→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 71 -
Rwork0.384 1693 -
obs--89.59 %
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)
19.95081.08772.10998.91562.28916.96480.5673-0.0156-0.811-0.46640.07520.21570.7734-0.0439-0.64250.2526-0.0329-0.20930.0853-0.06210.2864-5.5077-21.149913.8155
29.4236-0.8696-1.70419.74082.46416.74640.55990.01850.68920.49490.04720.2982-0.8006-0.0565-0.60710.23170.02510.20990.1029-0.05940.2848-5.416319.608656.2284
39.8682-1.3209-0.57537.2985-2.511710.95080.58940.5731.1159-0.62890.0027-0.0863-1.99930.7991-0.5920.6538-0.23230.2430.28380.02310.28997.342312.457511.138
49.85521.15650.44566.6783-2.34911.54550.6288-0.5306-0.96990.6163-0.0197-0.08312.01830.8551-0.60920.63320.2437-0.23750.28390.0250.29687.425-13.968158.9181
53.76521.21272.05823.31562.84956.12170.6102-0.5963-0.60440.708-0.2411-0.40320.74710.4581-0.3690.2926-0.038-0.08630.44770.04460.26045.6629-9.643832.8313
63.1098-1.1301-3.26241.14461.219112.69080.4902-0.36620.12460.296-0.46660.2022-1.2899-0.2049-0.02360.5526-0.34570.1130.551-0.24880.1337-0.65633.685830.2523
73.7203-0.8827-2.73792.49912.65267.09670.54990.60890.5755-0.6409-0.1892-0.2495-0.71610.2924-0.36060.30240.08890.05530.42280.0430.25154.47347.826637.8492
81.95731.76482.70021.97882.532913.59750.32970.2118-0.1049-0.0501-0.28620.12991.3032-0.2323-0.04350.59150.4052-0.20520.5514-0.28390.2228-0.6329-5.227839.7978
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A171 - 508
2X-RAY DIFFRACTION2B171 - 508
3X-RAY DIFFRACTION3C171 - 508
4X-RAY DIFFRACTION4D171 - 508
5X-RAY DIFFRACTION5E551 - 594
6X-RAY DIFFRACTION6G551 - 594
7X-RAY DIFFRACTION7F551 - 594
8X-RAY DIFFRACTION8H551 - 594

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