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- PDB-4ype: ASH1L SET domain H2193F mutant in complex with S-adenosyl methion... -

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Basic information

Entry
Database: PDB / ID: 4ype
TitleASH1L SET domain H2193F 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 / [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 MAPK cascade / negative regulation of acute inflammatory response / decidualization / single fertilization / 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 / 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 (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: 2.2 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 12, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)53,24010
Polymers52,0512
Non-polymers1,1898
Water1,928107
1
A: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6205
Polymers26,0261
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)26,6205
Polymers26,0261
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.838, 58.838, 232.152
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: 26025.543 Da / Num. of mol.: 2 / Fragment: SET domain (UNP residues 2074-2293) / Mutation: H2193F
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.: 107 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
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: Jun 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 21349 / % possible obs: 86.1 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.032 / Rrim(I) all: 0.08 / Χ2: 1.224 / Net I/av σ(I): 24.368 / Net I/σ(I): 9.6 / Num. measured all: 112070
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.245.70.3859450.9230.150.4160.69279.5
2.24-2.285.70.3649450.9310.1430.3930.69777
2.28-2.325.50.3219650.9410.1280.3480.70479.2
2.32-2.375.50.2979590.960.1170.3220.70178.8
2.37-2.425.40.2659540.9680.1060.2870.67979.8
2.42-2.485.40.2089660.9760.0850.2260.68879.2
2.48-2.545.30.1969610.9780.0790.2130.69779
2.54-2.615.10.1589640.9820.0650.1730.71280
2.61-2.6950.13510000.9870.0560.1480.73679.3
2.69-2.774.90.1229720.9880.0520.1340.76981.8
2.77-2.874.80.1110090.9910.0470.120.7982.9
2.87-2.994.60.08810500.9930.0390.0970.81484.6
2.99-3.124.50.08610810.9910.0410.0971.06587.5
3.12-3.294.40.0811190.9890.0390.091.34889.6
3.29-3.494.40.0711280.9930.0350.0791.62691.5
3.49-3.764.60.06311630.9940.0320.0711.87694.2
3.76-4.144.80.05612290.9950.0270.0621.92996.8
4.14-4.745.30.0512380.9970.0230.0551.78997.1
4.74-5.9760.05313030.9970.0230.0581.90899.6
5.97-507.40.05313980.9970.020.0562.33299.4

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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: 2.2→42.56 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.933 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.396 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 1094 5.1 %RANDOM
Rwork0.2165 ---
obs0.2188 20191 85.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.43 Å2 / Biso mean: 32.169 Å2 / Biso min: 5.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: final / Resolution: 2.2→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 60 107 3553
Biso mean--27.97 28.37 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223539
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9564768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6435422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.17224.021189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.315621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5331528
X-RAY DIFFRACTIONr_chiral_restr0.1320.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212743
X-RAY DIFFRACTIONr_mcbond_it1.2541.52093
X-RAY DIFFRACTIONr_mcangle_it2.30523364
X-RAY DIFFRACTIONr_scbond_it3.10131446
X-RAY DIFFRACTIONr_scangle_it4.7384.51401
LS refinement shellResolution: 2.198→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 79 -
Rwork0.238 1301 -
all-1380 -
obs--75.62 %

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