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- PDB-8vlh: Crystal structure of Ash1L PHD-BAH domains -

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Basic information

Entry
Database: PDB / ID: 8vlh
TitleCrystal structure of Ash1L PHD-BAH domains
ComponentsHistone-lysine N-methyltransferase ASH1L
KeywordsTRANSFERASE / Ash1L / methyltransferase / zinc finger / PHD / BAH
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 / Bromo adjacent homology domain ...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 / 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. / 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
Similarity search - Domain/homology
STRONTIUM ION / Histone-lysine N-methyltransferase ASH1L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsVann, K.R. / Tencer, A.H. / Kutateladze, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat Commun / Year: 2025
Title: Structure-function relationship of ASH1L and histone H3K36 and H3K4 methylation.
Authors: Vann, K.R. / Sharma, R. / Hsu, C.C. / Devoucoux, M. / Tencer, A.H. / Zeng, L. / Lin, K. / Zhu, L. / Li, Q. / Lachance, C. / Ospina, R.R. / Tong, Q. / Cheung, K.L. / Yang, S. / Biswas, S. / ...Authors: Vann, K.R. / Sharma, R. / Hsu, C.C. / Devoucoux, M. / Tencer, A.H. / Zeng, L. / Lin, K. / Zhu, L. / Li, Q. / Lachance, C. / Ospina, R.R. / Tong, Q. / Cheung, K.L. / Yang, S. / Biswas, S. / Xuan, H. / Gatchalian, J. / Alamillo, L. / Wang, J. / Jang, S.M. / Klein, B.J. / Lu, Y. / Ernst, P. / Strahl, B.D. / Rothbart, S.B. / Walsh, M.J. / Cleary, M.L. / Cote, J. / Shi, X. / Zhou, M.M. / Kutateladze, T.G.
History
DepositionJan 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)62,2697
Polymers61,9202
Non-polymers3495
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.110, 60.575, 53.588
Angle α, β, γ (deg.)90.000, 97.920, 90.000
Int Tables number5
Space group name H-MC121

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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: 30959.809 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 H3]-lysine36 N-trimethyltransferase, [histone H3]-lysine9 N-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane pH 10, 0.25 M strontium chloride, 0.01 M ammonium sulfate, and 25% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.4→48.2 Å / Num. obs: 20953 / % possible obs: 97 % / Redundancy: 2.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.077 / Net I/σ(I): 12.2
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1987 / CC1/2: 0.841 / Rrim(I) all: 0.429

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L58 and 1W4S

4l58

1w4s


Resolution: 2.403→48.2 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.884 / SU B: 11.689 / SU ML: 0.267 / Cross valid method: FREE R-VALUE / ESU R: 0.44 / ESU R Free: 0.325 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2845 1062 5.069 %
Rwork0.2298 19889 -
all0.233 --
obs-20951 96.852 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.147 Å2
Baniso -1Baniso -2Baniso -3
1-2.487 Å20 Å20.021 Å2
2---0.082 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 2.403→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4101 0 5 145 4251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124236
X-RAY DIFFRACTIONr_angle_refined_deg0.7361.6495733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.73720.152263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3215728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9061543
X-RAY DIFFRACTIONr_chiral_restr0.0640.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023304
X-RAY DIFFRACTIONr_nbd_refined0.1760.21630
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2190
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.403-2.4660.323720.2971266X-RAY DIFFRACTION84.1509
2.466-2.5330.251780.2981435X-RAY DIFFRACTION96.9872
2.533-2.6070.383640.2891390X-RAY DIFFRACTION97.6494
2.607-2.6870.351720.281366X-RAY DIFFRACTION97.8231
2.687-2.7750.32930.2631291X-RAY DIFFRACTION97.6711
2.775-2.8720.356710.2591305X-RAY DIFFRACTION99.8549
2.872-2.980.352680.2671242X-RAY DIFFRACTION99.9237
2.98-3.1020.305640.2481197X-RAY DIFFRACTION99.7627
3.102-3.240.334610.2591168X-RAY DIFFRACTION99.8375
3.24-3.3980.338580.2531118X-RAY DIFFRACTION99.1568
3.398-3.5810.303480.2441053X-RAY DIFFRACTION98.7444
3.581-3.7980.314520.227948X-RAY DIFFRACTION94.9668
3.798-4.0590.276420.2914X-RAY DIFFRACTION96.6633
4.059-4.3840.23410.188859X-RAY DIFFRACTION96.7742
4.384-4.8010.232400.176776X-RAY DIFFRACTION95.6624
4.801-5.3660.187390.18728X-RAY DIFFRACTION97.0886
5.366-6.1920.176340.207633X-RAY DIFFRACTION97.5146
6.192-7.5730.307290.208545X-RAY DIFFRACTION96.796
7.573-10.6690.292230.185412X-RAY DIFFRACTION95.815
10.669-48.20.245130.253243X-RAY DIFFRACTION93.0909

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