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- PDB-3s32: Crystal structure of Ash2L N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 3s32
TitleCrystal structure of Ash2L N-terminal domain
ComponentsSet1/Ash2 histone methyltransferase complex subunit ASH2
KeywordsTRANSCRIPTION / histone / chromatin / trithorax / Helix-wing-helix / C4-zinc finger / trithorax group protein / Myeloid Lymphoma leukemia protein / nucleus
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / hemopoiesis / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / hemopoiesis / transcription initiation-coupled chromatin remodeling / Deactivation of the beta-catenin transactivating complex / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / euchromatin / PKMTs methylate histone lysines / beta-catenin binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / response to estrogen / transcription cis-regulatory region binding / DNA damage response / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA primase DNAg catalytic core, N-terminal domain - #20 / DNA primase DNAg catalytic core, N-terminal domain / : / ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / Histone methyltransferase complex subunit ASH2 / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain ...DNA primase DNAg catalytic core, N-terminal domain - #20 / DNA primase DNAg catalytic core, N-terminal domain / : / ASH2, PHD zinc finger / Set1/Ash2 histone methyltransferase complex subunit ASH2-like, WH / Histone methyltransferase complex subunit ASH2 / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Set1/Ash2 histone methyltransferase complex subunit ASH2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsSarvan, S. / Avdic, V. / Tremblay, V. / Chaturvedi, C.-P. / Zhang, P. / Lanouette, S. / Blais, A. / Brunzelle, J.S. / Brand, M. / Couture, J.-F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Crystal structure of the trithorax group protein ASH2L reveals a forkhead-like DNA binding domain.
Authors: Sarvan, S. / Avdic, V. / Tremblay, V. / Chaturvedi, C.P. / Zhang, P. / Lanouette, S. / Blais, A. / Brunzelle, J.S. / Brand, M. / Couture, J.F.
History
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Set1/Ash2 histone methyltransferase complex subunit ASH2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1052
Polymers22,0391
Non-polymers651
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.893, 49.893, 167.542
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Set1/Ash2 histone methyltransferase complex subunit ASH2 / ASH2-like protein


Mass: 22039.441 Da / Num. of mol.: 1 / Fragment: N-terminal domain residues 95-280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH2L, ASH2L1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9UBL3
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M MgAcetate and 17-20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 1, 2009
RadiationMonochromator: diamond laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. all: 9475 / Num. obs: 9437 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 18.9 % / Net I/σ(I): 55.3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.45-2.491100
2.49-2.541100
2.54-2.591100
2.59-2.641100
2.64-2.71100
2.7-2.761100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→24.95 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.9 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26342 448 4.8 %RANDOM
Rwork0.22549 ---
all0.307 9437 --
obs0.22734 8970 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.021 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.45→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 1 7 1294
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221359
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9411845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85624.69766
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.97815230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.302156
X-RAY DIFFRACTIONr_chiral_restr0.1230.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211051
X-RAY DIFFRACTIONr_mcbond_it1.0681.5826
X-RAY DIFFRACTIONr_mcangle_it1.93721339
X-RAY DIFFRACTIONr_scbond_it3.0493533
X-RAY DIFFRACTIONr_scangle_it4.4854.5504
LS refinement shellResolution: 2.45→2.515 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 38 -
Rwork0.331 630 -
obs--99.85 %
Refinement TLS params.Method: refined / Origin x: 44.37 Å / Origin y: 19.627 Å / Origin z: 10.841 Å
111213212223313233
T0.3386 Å2-0.1407 Å20.0739 Å2-0.173 Å2-0.0054 Å2--0.193 Å2
L2.4382 °20.6253 °21.4905 °2-1.2596 °2-0.2981 °2--3.0774 °2
S0.0451 Å °-0.3055 Å °-0.0852 Å °-0.0537 Å °-0.1354 Å °-0.058 Å °0.0996 Å °0.0071 Å °0.0904 Å °

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