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- PDB-4ynm: ASH1L wild-type SET domain in complex with S-adenosyl methionine (SAM) -

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Basic information

Entry
Database: PDB / ID: 4ynm
TitleASH1L wild-type SET domain 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 / [histone H3]-lysine9 N-methyltransferase / uterus morphogenesis / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / flagellated sperm motility ...uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / uterus morphogenesis / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / flagellated sperm motility / histone H3K36 methyltransferase activity / histone H3K4 methyltransferase activity / histone H3 methyltransferase activity / negative regulation of acute inflammatory response / decidualization / bicellular tight junction / single fertilization / negative regulation of MAPK cascade / 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 / nucleus / metal ion binding
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 domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / 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: 2.19 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
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
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
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)53,22210
Polymers52,0332
Non-polymers1,1898
Water1,874104
1
A: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6115
Polymers26,0171
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6115
Polymers26,0171
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.141, 59.141, 230.983
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A2069 - 2256
2113B2069 - 2256
1123A2266 - 2280
2123B2266 - 2280

NCS ensembles :
ID
1
2

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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: 26016.516 Da / Num. of mol.: 2 / Fragment: SET domain (UNP residues 2074-2293)
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


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
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: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 25099 / % possible obs: 99.9 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.033 / Rrim(I) all: 0.101 / Χ2: 1.645 / Net I/av σ(I): 33.696 / Net I/σ(I): 7.8 / Num. measured all: 228388
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.19-2.249.10.5912130.8650.2040.6260.757100
2.24-2.289.10.48812440.9140.1690.5170.796100
2.28-2.329.20.45111920.9120.1550.4770.828100
2.32-2.3790.40812650.9350.1430.4330.842100
2.37-2.429.10.36911840.9390.1290.3910.939100
2.42-2.4890.31212790.940.110.3321.028100
2.48-2.549.10.27711980.9630.0970.2941.034100
2.54-2.618.90.24112440.9710.0860.2571.127100
2.61-2.6990.20612420.9760.0720.2191.23100
2.69-2.7790.18812160.9810.0660.1991.282100
2.77-2.878.90.16212450.9860.0570.1721.38199.9
2.87-2.9990.14212560.9880.050.1511.57100
2.99-3.128.90.12712630.9910.0450.1351.747100
3.12-3.2990.10912450.9910.0390.1161.982100
3.29-3.4990.09712650.9930.0350.1032.309100
3.49-3.769.20.0912460.9950.0310.0952.73699.9
3.76-4.149.10.08412730.9960.0290.0893.162100
4.14-4.749.10.07912890.9960.0270.0843.469100
4.74-5.979.90.06713270.9970.0220.072.44100
5.97-509.40.05214130.9980.0180.0551.82299.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OPE

3ope


Resolution: 2.19→46.82 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.875 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2775 1271 5.1 %RANDOM
Rwork0.2421 ---
obs0.2438 23762 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 95.31 Å2 / Biso mean: 42.453 Å2 / Biso min: 20.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 2.19→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 60 104 3497
Biso mean--35.48 39.26 -
Num. residues----411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213464
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.9554664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9985408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59624.086186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65315608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2391527
X-RAY DIFFRACTIONr_chiral_restr0.1220.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212681
X-RAY DIFFRACTIONr_mcbond_it1.0991.52045
X-RAY DIFFRACTIONr_mcangle_it2.07123285
X-RAY DIFFRACTIONr_scbond_it2.99331419
X-RAY DIFFRACTIONr_scangle_it4.6784.51379
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
1684TIGHT POSITIONAL0.110.05
1716LOOSE POSITIONAL0.275
1684TIGHT THERMAL0.350.5
1716LOOSE THERMAL0.410
256TIGHT POSITIONAL0.10.05
252LOOSE POSITIONAL0.115
256TIGHT THERMAL0.310.5
252LOOSE THERMAL0.2610
LS refinement shellResolution: 2.192→2.249 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 92 -
Rwork0.276 1664 -
all-1756 -
obs--98.43 %

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