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- PDB-4ypu: ASH1L SET domain K2264L mutant in complex with S-adenosyl methion... -

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Basic information

Entry
Database: PDB / ID: 4ypu
TitleASH1L SET domain K2264L 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 / uterus morphogenesis / [histone H3]-lysine9 N-methyltransferase / histone H3K36 trimethyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K36 methyltransferase activity ...uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / uterus morphogenesis / [histone H3]-lysine9 N-methyltransferase / histone H3K36 trimethyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K36 methyltransferase activity / flagellated sperm motility / 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 / zinc ion binding / nucleoplasm / 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 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / 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: 2.6 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 13, 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
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)53,19010
Polymers52,0012
Non-polymers1,1898
Water64936
1
A: Histone-lysine N-methyltransferase ASH1L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5955
Polymers26,0001
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)26,5955
Polymers26,0001
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.108, 59.108, 226.043
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: 26000.494 Da / Num. of mol.: 2 / Fragment: SET domain (UNP residues 2074-2293) / Mutation: K2264L
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.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.89 %
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-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14871 / % possible obs: 99.4 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.03 / Rrim(I) all: 0.093 / Χ2: 2.07 / Net I/av σ(I): 42.244 / Net I/σ(I): 11.8 / Num. measured all: 135638
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6490.4837160.9350.160.511.00498.2
2.64-2.698.60.447620.9540.1470.4651.03797.4
2.69-2.749.20.4126750.9590.1360.4341.05199.6
2.74-2.88.80.3617280.9640.120.3811.10199.2
2.8-2.8690.3017040.9750.10.3181.17698.6
2.86-2.9390.2657380.9810.0890.2811.2899.9
2.93-38.80.2257310.9820.0760.2381.28699.7
3-3.089.10.2067340.9870.0690.2171.546100
3.08-3.179.20.1677190.9920.0560.1761.72299.9
3.17-3.289.10.1427510.9930.0480.1511.82698.9
3.28-3.399.30.1277270.9940.0430.1342.0299.9
3.39-3.539.30.1057300.9950.0360.1112.143100
3.53-3.699.40.0937420.9970.0310.0982.37699.3
3.69-3.889.50.0847350.9970.0280.0882.572100
3.88-4.139.40.0787470.9960.0260.0822.885100
4.13-4.459.30.0687590.9970.0230.0723.1499.9
4.45-4.899.20.0657630.9970.0230.0693.26299.3
4.89-5.69.70.0627600.9980.0210.0652.987100
5.6-7.059.90.0627830.9980.020.0652.697100
7.05-5080.0598670.9970.0220.0643.54899.1

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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: 2.6→75.35 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.875 / SU B: 14.035 / SU ML: 0.312 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.521 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3053 749 5.1 %RANDOM
Rwork0.2379 ---
obs0.2412 14072 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 max: 93.34 Å2 / Biso mean: 53.136 Å2 / Biso min: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 2.6→75.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 60 36 3373
Biso mean--52.23 48.56 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213406
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9574586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2435400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.18124.044183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29515596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0351527
X-RAY DIFFRACTIONr_chiral_restr0.0980.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212634
X-RAY DIFFRACTIONr_mcbond_it0.8961.52009
X-RAY DIFFRACTIONr_mcangle_it1.69323226
X-RAY DIFFRACTIONr_scbond_it2.04331397
X-RAY DIFFRACTIONr_scangle_it3.3674.51360
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 74 -
Rwork0.271 984 -
all-1058 -
obs--98.33 %

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