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- PDB-6ago: Crystal structure of MRG15-ASH1L Histone methyltransferase complex -

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Basic information

Entry
Database: PDB / ID: 6ago
TitleCrystal structure of MRG15-ASH1L Histone methyltransferase complex
Components
  • Histone-lysine N-methyltransferase ASH1L
  • Mortality factor 4 like 1
KeywordsTRANSFERASE/GENE REGULATION / nucleosome / methylation / activation / regulation / GENE REGULATION / TRANSFERASE-GENE REGULATION complex
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 ...: / 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 / regulation of double-strand break repair / histone H3K4 methyltransferase activity / histone H3 methyltransferase activity / negative regulation of MAPK cascade / Sin3-type complex / NuA4 histone acetyltransferase complex / negative regulation of acute inflammatory response / decidualization / positive regulation of double-strand break repair via homologous recombination / single fertilization / bicellular tight junction / post-embryonic development / skeletal system development / double-strand break repair via homologous recombination / PKMTs methylate histone lysines / MAPK cascade / nucleosome / chromatin organization / chromosome / HATs acetylate histones / methylation / regulation of apoptotic process / transcription by RNA polymerase II / regulation of cell cycle / nuclear speck / inflammatory response / chromatin binding / regulation of DNA-templated transcription / positive 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
Mortality factor 4-like protein 1 / MRG domain / ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. ...Mortality factor 4-like protein 1 / MRG domain / ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / 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 / Enzyme I; Chain A, domain 2 / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology (BAH) domain / BAH domain profile. / Post-SET domain / Post-SET domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / 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. / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Mortality factor 4 like 1 / Histone-lysine N-methyltransferase ASH1L / Mortality factor 4-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.103 Å
AuthorsLee, Y. / Song, J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2016R1A2B3006293 Korea, Republic Of
National Research Foundation (Korea)NRF-2016K1A1A2912057 Korea, Republic Of
CitationJournal: Structure / Year: 2019
Title: Structural Basis of MRG15-Mediated Activation of the ASH1L Histone Methyltransferase by Releasing an Autoinhibitory Loop.
Authors: Lee, Y. / Yoon, E. / Cho, S. / Schmahling, S. / Muller, J. / Song, J.J.
History
DepositionAug 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
C: Mortality factor 4 like 1
D: Mortality factor 4 like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,00511
Polymers100,2144
Non-polymers7917
Water00
1
A: Histone-lysine N-methyltransferase ASH1L
C: Mortality factor 4 like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7026
Polymers50,1072
Non-polymers5954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-12 kcal/mol
Surface area21340 Å2
MethodPISA
2
B: Histone-lysine N-methyltransferase ASH1L
D: Mortality factor 4 like 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3035
Polymers50,1072
Non-polymers1963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-51 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.757, 115.757, 209.282
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112

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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: 30005.180 Da / Num. of mol.: 2
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: Protein Mortality factor 4 like 1 / MRG15


Mass: 20102.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MORF4L1, MRG15, FWP006, HSPC008, HSPC061, PP368 / Production host: Escherichia coli (E. coli) / References: UniProt: A5D8W6, UniProt: Q9UBU8*PLUS
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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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: 3.91 Å3/Da / Density % sol: 68.56 %
Crystal growTemperature: 295 K / Method: evaporation / Details: Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 29386 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 103.89 Å2 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.03 / Rrim(I) all: 0.071 / Χ2: 0.798 / Net I/σ(I): 8 / Num. measured all: 147885
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.154.60.73614610.8140.3730.830.45299.9
3.15-3.214.80.66114720.8730.3260.740.4899.9
3.21-3.274.90.44214410.9330.2170.4940.564100
3.27-3.344.90.36614500.9530.1780.4090.491100
3.34-3.415.40.30314800.9650.140.3350.50599.9
3.41-3.495.30.25814290.9660.1190.2860.515100
3.49-3.585.30.20314630.9890.0930.2240.548100
3.58-3.685.30.17214680.9890.0790.190.581100
3.68-3.785.30.15114440.9880.070.1670.582100
3.78-3.915.20.11514610.9940.0520.1270.677100
3.91-4.045.20.08714550.9970.0390.0960.73999.9
4.04-4.215.10.07514710.9970.0340.0830.761100
4.21-4.44.90.06914580.9970.0320.0770.86799.9
4.4-4.634.50.05714820.9970.0280.0630.965100
4.63-4.924.80.05614480.9970.0270.0631.087100
4.92-5.35.20.05114970.9970.0240.0571.047100
5.3-5.835.30.04914670.9980.0220.0541.048100
5.83-6.675.20.04814830.9980.0210.0531.20999.9
6.67-8.44.80.03715020.9980.0190.0421.22699.9
8.4-504.80.03315540.9980.0160.0371.64599.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.103→33.917 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2723 2015 6.89 %
Rwork0.22 27229 -
obs0.2235 29244 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 238.23 Å2 / Biso mean: 122.5747 Å2 / Biso min: 69.73 Å2
Refinement stepCycle: final / Resolution: 3.103→33.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6506 0 33 0 6539
Biso mean--149.88 --
Num. residues----791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1031-3.18060.43351430.36711924206799
3.1806-3.26650.38781430.31521909205299
3.2665-3.36260.38431450.26941925207099
3.3626-3.4710.34811410.272419232064100
3.471-3.59490.34291460.26881929207599
3.5949-3.73870.31331430.248419472090100
3.7387-3.90860.29661430.228719202063100
3.9086-4.11440.28861410.219219502091100
4.1144-4.37160.22111440.214919272071100
4.3716-4.70840.24861430.188119502093100
4.7084-5.18070.23241420.195519542096100
5.1807-5.92690.27091460.22119602106100
5.9269-7.45420.27941460.238419832129100
7.4542-33.91870.23441490.185920282177100
Refinement TLS params.Method: refined / Origin x: 77.9672 Å / Origin y: 76.125 Å / Origin z: 208.9734 Å
111213212223313233
T0.9084 Å20.2806 Å20.1214 Å2-0.8246 Å20.0771 Å2--0.8306 Å2
L1.2418 °20.2275 °2-0.9376 °2-0.755 °2-0.1554 °2--5.1385 °2
S0.0652 Å °0.1444 Å °0.1457 Å °0.1614 Å °0.0554 Å °0.0294 Å °0.4202 Å °0.2297 Å °-0.1057 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2035 - 4
2X-RAY DIFFRACTION1allB2036 - 4
3X-RAY DIFFRACTION1allC155 - 321
4X-RAY DIFFRACTION1allD155 - 320

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