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- PDB-6ine: Crystal Structure of human ASH1L-MRG15 complex -

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Basic information

Entry
Database: PDB / ID: 6ine
TitleCrystal Structure of human ASH1L-MRG15 complex
Components
  • Histone-lysine N-methyltransferase ASH1L
  • Mortality factor 4-like protein 1
KeywordsTRANSFERASE/PROTEIN BINDING / Complex / H3K36 methyltransferase / TRANSFERASE / TRANSFERASE-PROTEIN BINDING 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 / 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 / regulation of double-strand break repair / histone H3K4 methyltransferase activity / histone H3 methyltransferase activity / NuA4 histone acetyltransferase complex / Sin3-type complex / negative regulation of acute inflammatory response / decidualization / bicellular tight junction / single fertilization / negative regulation of MAPK cascade / positive regulation of double-strand break repair via homologous recombination / 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 / regulation of apoptotic process / methylation / 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
MRG domain / ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain ...MRG domain / ASH1-like, PHD finger / ASH1-like, Bromodomain / PhD finger domain / MRG / MRG domain / MRG, C-terminal domain superfamily / MRG / MRG domain profile. / RNA binding activity-knot of a chromodomain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / RNA binding activity-knot of a chromodomain / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / Enzyme I; Chain A, domain 2 / 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. / Chromo-like domain superfamily / 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. / 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 / Histone-lysine N-methyltransferase ASH1L / Mortality factor 4-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHou, P. / Huang, C. / Liu, C.P. / Yu, T. / Yin, Y. / Zhu, B. / Xu, R.M.
Funding support China, 7items
OrganizationGrant numberCountry
National Natural Science Foundation of China31521002 China
National Natural Science Foundation of China31530037 China
Ministry of Science and Technology (China)2015CB856200 China
Ministry of Science and Technology (China)2017YFA0506600 China
Chinese Academy of SciencesXDB08010100 China
Chinese Academy of SciencesXDB08010103 China
Chinese Academy of Sciences2018127 China
CitationJournal: Structure / Year: 2019
Title: Structural Insights into Stimulation of Ash1L's H3K36 Methyltransferase Activity through Mrg15 Binding.
Authors: Hou, P. / Huang, C. / Liu, C.P. / Yang, N. / Yu, T. / Yin, Y. / Zhu, B. / Xu, R.M.
History
DepositionOct 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 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 1.2Nov 22, 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: Mortality factor 4-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3547
Polymers51,6672
Non-polymers6875
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-20 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.120, 73.120, 202.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 31208.645 Da / Num. of mol.: 1
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 protein 1 / MORF-related gene 15 protein / Protein MSL3-1 / Transcription factor-like protein MRG15


Mass: 20458.438 Da / Num. of mol.: 1
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: Q9UBU8

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Non-polymers , 4 types, 72 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE OF THE CHAIN A WAS BASED ON ISOFORM 2 OF DATABASE Q9NR48 (ASH1L_HUMAN)

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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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 20 % PEG 6000, 0.2 M Trimethylamine-N-oxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 17625 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.093 / Χ2: 0.764 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.696.40.58517090.8450.2470.6360.79599.8
2.69-2.860.44417320.8910.1940.4860.8199.8
2.8-2.936.30.32217410.9420.1370.350.79499.9
2.93-3.086.60.24817370.9680.1030.2690.81299.9
3.08-3.286.60.17117330.9810.0710.1850.78599.9
3.28-3.536.40.11317570.9910.0480.1230.79999.8
3.53-3.8860.0717700.9950.030.0770.834100
3.88-4.456.60.04917780.9970.020.0530.77699.6
4.45-5.660.03918100.9950.0170.0430.68399.3
5.6-505.80.03119370.9910.0140.0350.54797.8

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Processing

Software
NameVersionClassification
SCALEPACKHKL-2000data scaling
PHENIX1.14_3247refinement
PDB_EXTRACT3.24data extraction
HKL-2000HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YNM, 2AQL

4ynm

2aql


Resolution: 2.6→50 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.73
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1768 10.03 %Random selection
Rwork0.1931 ---
obs0.1975 17625 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.39 Å2 / Biso mean: 47.0485 Å2 / Biso min: 17.71 Å2
Refinement stepCycle: final / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 36 67 3437
Biso mean--47.66 36.66 -
Num. residues----406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6002-2.6450.3343900.285976985954
2.645-2.69310.2988940.264283993357
2.6931-2.74490.26731010.2711904100562
2.7449-2.80090.26381100.2717962107266
2.8009-2.86180.3151180.25231061117973
2.8618-2.92830.30181260.24121184131081
2.9283-3.00150.34491440.23571273141790
3.0015-3.08260.28431570.24991432158997
3.0826-3.17330.29311650.23161442160799
3.1733-3.27560.27781610.220314141575100
3.2756-3.39260.27051580.228514591617100
3.3926-3.52840.25991530.20514581611100
3.5284-3.68880.26031560.190614661622100
3.6888-3.88310.20981630.182314431606100
3.8831-4.1260.19291650.169714521617100
4.126-4.44410.23691660.152114321598100
4.4441-4.89030.17791600.14521457161799
4.8903-5.59570.18731630.15731415157899
5.5957-7.04150.1961630.1861427159098
7.0415-36.20510.221520.17141407155996
Refinement TLS params.Method: refined / Origin x: -42.3307 Å / Origin y: -9.3884 Å / Origin z: -10.8905 Å
111213212223313233
T0.2047 Å20.0035 Å2-0.0419 Å2-0.1699 Å20.0485 Å2--0.1507 Å2
L0.7921 °20.7633 °20.3464 °2-1.0745 °20.7021 °2--0.4824 °2
S0.0034 Å °0.034 Å °-0.0584 Å °0.0224 Å °0.0341 Å °-0.0118 Å °0.0234 Å °0.0725 Å °-0.0007 Å °
Refinement TLS groupSelection details: all

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