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- PDB-4ynp: ASH1L SET domain S2259M mutant in complex with S-adenosyl methion... -

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Basic information

Entry
Database: PDB / ID: 4ynp
TitleASH1L SET domain S2259M mutant in complex with S-adenosyl methionine (SAM)
ComponentsHistone-lysine N-methyltransferase ASH1L
KeywordsTRANSFERASE / histone methylation / SET domain
Function / homology
Function and homology information


uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / uterus morphogenesis / [histone H3]-lysine9 N-methyltransferase / flagellated sperm motility / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity ...uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / uterus morphogenesis / [histone H3]-lysine9 N-methyltransferase / flagellated sperm motility / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / histone H3 methyltransferase activity / negative regulation of MAPK cascade / single fertilization / decidualization / negative regulation of acute inflammatory response / bicellular tight junction / post-embryonic development / skeletal system development / PKMTs methylate histone lysines / MAPK cascade / chromosome / methylation / transcription by RNA polymerase II / inflammatory response / chromatin binding / regulation of DNA-templated transcription / Golgi apparatus / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Beta-clip-like ...ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Beta-clip-like / SET domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / BAH domain profile. / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Beta Complex / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Mainly Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase ASH1L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRogawski, D.S. / Ndoj, J. / Cho, H.-J. / Maillard, I. / Grembecka, J. / Cierpicki, T.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1R01CA160467 United States
Leukemia & Lymphoma Society6111-14 United States
Leukemia & Lymphoma Society1215-14 United States
American Cancer SocietyRSG-13-130-01-CDD United States
Michigan Economic Development Corporation085P1000817 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008597 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM007863 United States
CitationJournal: Biochemistry / Year: 2015
Title: Two Loops Undergoing Concerted Dynamics Regulate the Activity of the ASH1L Histone Methyltransferase.
Authors: Rogawski, D.S. / Ndoj, J. / Cho, H.J. / Maillard, I. / Grembecka, J. / Cierpicki, T.
History
DepositionMar 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Oct 4, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase ASH1L
B: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,31110
Polymers52,1212
Non-polymers1,1898
Water0
1
A: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6555
Polymers26,0611
Non-polymers5954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6555
Polymers26,0611
Non-polymers5954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.262, 59.262, 233.924
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Histone-lysine N-methyltransferase ASH1L / ASH1-like protein / huASH1 / Absent small and homeotic disks protein 1 homolog / Lysine N-methyltransferase 2H


Mass: 26060.633 Da / Num. of mol.: 2 / Fragment: SET domain (UNP residues 2074-2293) / Mutation: S2259M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH1L, KIAA1420, KMT2H / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NR48, histone-lysine N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S

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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: 2.39 Å3/Da / Density % sol: 48.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, 20 mM Tris / PH range: 7.3-7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 10910 / % possible obs: 96.1 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.032 / Rrim(I) all: 0.094 / Χ2: 1.417 / Net I/av σ(I): 25.222 / Net I/σ(I): 8.2 / Num. measured all: 83961
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.957.40.3935340.930.1350.4170.72996
2.95-37.90.3275170.9510.1120.3460.74794.7
3-3.0680.2935050.9510.1020.3110.7891.8
3.06-3.127.30.2495520.9630.0870.2650.82196.8
3.12-3.197.90.225020.9720.0770.2340.95393.3
3.19-3.277.70.1915230.9760.0670.2030.9794.6
3.27-3.357.70.1735100.9830.0620.1841.11393.9
3.35-3.447.70.1495140.9870.0530.1591.20691.5
3.44-3.547.50.1415230.9870.050.151.32396.1
3.54-3.657.60.1185290.9940.0420.1261.493.3
3.65-3.787.50.1115290.990.040.1181.84295.3
3.78-3.947.30.0995350.9930.0360.1061.68593
3.94-4.117.50.0955250.9930.0340.1021.98194.6
4.11-4.337.20.0895490.9930.0330.0952.21298
4.33-4.67.10.0895670.9920.0340.0962.53699
4.6-4.967.20.0825740.9920.0320.0892.41599.5
4.96-5.467.50.0785730.9930.0290.0842.01399.8
5.46-6.247.90.0655800.9970.0240.071.308100
6.24-7.868.90.0566050.9980.0190.0591.171100
7.86-508.80.0416640.9990.0140.0431.29199.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YNM

4ynm


Resolution: 2.9→47 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.812 / SU B: 22.19 / SU ML: 0.432 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.544 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3194 513 4.7 %RANDOM
Rwork0.2619 ---
obs0.2645 10352 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.47 Å2 / Biso mean: 54.671 Å2 / Biso min: 31.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.9→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 60 0 3364
Biso mean--54.13 --
Num. residues----406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213435
X-RAY DIFFRACTIONr_angle_refined_deg0.9731.9564625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5995403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68324.076184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62315609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3541527
X-RAY DIFFRACTIONr_chiral_restr0.0660.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212649
X-RAY DIFFRACTIONr_mcbond_it0.3521.52023
X-RAY DIFFRACTIONr_mcangle_it0.64923254
X-RAY DIFFRACTIONr_scbond_it0.53531412
X-RAY DIFFRACTIONr_scangle_it0.9424.51371
LS refinement shellResolution: 2.899→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 47 -
Rwork0.297 741 -
all-788 -
obs--94.71 %

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