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- PDB-3oa6: Human MSL3 Chromodomain bound to DNA and H4K20me1 peptide -

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Basic information

Entry
Database: PDB / ID: 3oa6
TitleHuman MSL3 Chromodomain bound to DNA and H4K20me1 peptide
Components
  • DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)-3')
  • DNA (5'-D(*GP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)-3')
  • H4 peptide monomethylated at lysine 20
  • Male-specific lethal 3 homolog
KeywordsDNA BINDING PROTEIN/DNA / Chromodomain / MSL3 / histone H4 tail / DNA backbone recognition / methyllysine recognition / H4K20me1 / aromatic cage / MSL complex / transcription upregulation / DNA BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN / DNA
Function / homology
Function and homology information


MSL complex / Rpd3S complex / histone H4K16 acetyltransferase activity / NuA4 histone acetyltransferase complex / methylated histone binding / HATs acetylate histones / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus
Similarity search - Function
MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain ...MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / SH3 type barrels. - #140 / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
IMIDAZOLE / DNA / DNA (> 10) / MSL complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsKim, D. / Huang, P. / Rastinejad, F. / Khorasanizadeh, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain.
Authors: Kim, D. / Blus, B.J. / Chandra, V. / Huang, P. / Rastinejad, F. / Khorasanizadeh, S.
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionAug 18, 2010ID: 3M9P
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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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: DNA (5'-D(*GP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)-3')
D: DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)-3')
E: DNA (5'-D(*GP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)-3')
F: DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)-3')
G: H4 peptide monomethylated at lysine 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5518
Polymers48,4827
Non-polymers691
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.976, 44.094, 67.500
Angle α, β, γ (deg.)81.350, 89.840, 90.040
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A10 - 91
2112B10 - 91

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Components

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain DNA (5'-D(*GP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)-3')


Mass: 4947.229 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)-3')


Mass: 4849.153 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein / Protein/peptide , 2 types, 3 molecules ABG

#1: Protein Male-specific lethal 3 homolog / Male-specific lethal-3 protein-like 1 / MSL3-like 1 / Male-specific lethal-3 homolog 1


Mass: 13101.143 Da / Num. of mol.: 2 / Fragment: Chromodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSL3, MSL3L1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q8N5Y2
#4: Protein/peptide H4 peptide monomethylated at lysine 20


Mass: 2687.177 Da / Num. of mol.: 1 / Fragment: Histone H4 / Source method: obtained synthetically

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Non-polymers , 2 types, 109 molecules

#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.04M Barium acetate, 0.05M sodium cacodylate, 18% 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Barium acetate11
2sodium cacodylate11
32-methyl-2,4-pentanediol11
4Barium acetate12
5sodium cacodylate12
62-methyl-2,4-pentanediol12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99999 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 17458 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Rmerge(I) obs: 0.049 / Χ2: 1.03
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.35-2.4420.4217421.20397.6
2.44-2.5420.29917851.04197.9
2.54-2.6620.22617231.00997.8
2.66-2.820.15817650.98898.3
2.8-2.9720.11117731.01298.3
2.97-3.220.08317591.0197.3
3.2-3.5220.07316981.00695
3.52-4.0320.04617611.01298
4.03-5.0820.03917421.01397.6
5.08-4020.02817101.00294.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→9.93 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 20.793 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2773 880 5.1 %RANDOM
Rwork0.2265 ---
obs0.229 16389 97.19 %-
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 max: 100.92 Å2 / Biso mean: 77.65 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.21 Å2-0.18 Å2
2--0.2 Å20.02 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.35→9.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1435 1300 5 108 2848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212928
X-RAY DIFFRACTIONr_bond_other_d0.0040.021660
X-RAY DIFFRACTIONr_angle_refined_deg1.942.5034215
X-RAY DIFFRACTIONr_angle_other_deg1.64134057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.535170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58522.17978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.19815266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8721519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022291
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02464
X-RAY DIFFRACTIONr_mcbond_it1.4732858
X-RAY DIFFRACTIONr_mcbond_other0.2452345
X-RAY DIFFRACTIONr_mcangle_it2.55731373
X-RAY DIFFRACTIONr_scbond_it1.27322070
X-RAY DIFFRACTIONr_scangle_it2.07332842
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
485TIGHT POSITIONAL0.030.05
721MEDIUM POSITIONAL0.070.5
485TIGHT THERMAL0.130.5
721MEDIUM THERMAL0.092
LS refinement shellResolution: 2.35→2.408 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 61 -
Rwork0.312 1091 -
all-1152 -
obs--92.31 %
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)
10.0017-0.0243-0.08010.37450.96376.5049-0.1190.0381-0.00780.01040.01740.0693-0.04040.1160.10170.21320.16910.11220.0381-0.09160.0917-7.367-1.6468.829
20.2965-0.3116-0.4360.33220.58754.0979-0.037-0.0659-0.1910.2067-0.00340.00450.5442-0.00570.04040.27220.0960.122-0.12160.05480.100810.903-11.561-1.568
321.2686-5.193312.78948.46613.680914.12170.2827-0.1217-1.97811.4839-1.25560.32034.8634.90850.97281.0193-0.1920.13110.6373-0.14820.5324-0.574-9.80321.061
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 91
2X-RAY DIFFRACTION1B10 - 91
3X-RAY DIFFRACTION2C1 - 16
4X-RAY DIFFRACTION2E1 - 16
5X-RAY DIFFRACTION2D1 - 16
6X-RAY DIFFRACTION2F1 - 16
7X-RAY DIFFRACTION3G18 - 22
8X-RAY DIFFRACTION3B102

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