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- PDB-8vlf: Crystal structure of Ash1L PHD finger in complex with histone H3K4me3 -

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Basic information

Entry
Database: PDB / ID: 8vlf
TitleCrystal structure of Ash1L PHD finger in complex with histone H3K4me3
Components
  • Histone H3.3C
  • Histone-lysine N-methyltransferase ASH1L
KeywordsTRANSFERASE / Ash1L / H3K4me2 / zinc finger / transcriptional regulation
Function / homology
Function and homology information


uterine gland development / tarsal gland development / histone H3K9 monomethyltransferase activity / [histone H3]-lysine36 N-trimethyltransferase / uterus morphogenesis / histone H3K36 trimethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / 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 H3K36 trimethyltransferase activity / [histone H3]-lysine9 N-methyltransferase / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K36 methyltransferase activity / flagellated sperm motility / histone H3K4 methyltransferase activity / histone H3 methyltransferase activity / nucleosomal DNA binding / negative regulation of acute inflammatory response / decidualization / single fertilization / bicellular tight junction / negative regulation of MAPK cascade / post-embryonic development / skeletal system development / euchromatin / PKMTs methylate histone lysines / structural constituent of chromatin / MAPK cascade / nucleosome / chromosome / positive regulation of cell growth / methylation / transcription by RNA polymerase II / inflammatory response / protein heterodimerization activity / 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H3.3C / Histone-lysine N-methyltransferase ASH1L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsVann, K.R. / 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
P: Histone H3.3C
T: Histone H3.3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9048
Polymers15,6424
Non-polymers2624
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-41 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.800, 49.800, 46.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Histone-lysine N-methyltransferase ASH1L


Mass: 6470.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASH1L / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NR48
#2: Protein/peptide Histone H3.3C / Histone H3.5


Mass: 1350.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synpeptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6NXT2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.83 Å3/Da / Density % sol: 32.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 1.6 M sodium citrate pH 6.5 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.34→20.07 Å / Num. obs: 49203 / % possible obs: 99.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 15.78 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.5
Reflection shellResolution: 1.34→1.39 Å / Rmerge(I) obs: 0.41 / Num. unique obs: 2524

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7U7P

7u7p
PDB Unreleased entry


Resolution: 1.34→20.07 Å / SU ML: 0.1296 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.4216
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1884 2654 5.39 %
Rwork0.1549 46549 -
obs0.1568 49203 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.61 Å2
Refinement stepCycle: LAST / Resolution: 1.34→20.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 4 123 1141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571028
X-RAY DIFFRACTIONf_angle_d0.95611384
X-RAY DIFFRACTIONf_chiral_restr0.0898150
X-RAY DIFFRACTIONf_plane_restr0.0096178
X-RAY DIFFRACTIONf_dihedral_angle_d5.0478146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.360.27861020.23522311X-RAY DIFFRACTION92.74
1.36-1.390.23651420.21532421X-RAY DIFFRACTION95.53
1.39-1.420.26481340.18572446X-RAY DIFFRACTION97.84
1.42-1.450.18631370.17342451X-RAY DIFFRACTION97.92
1.45-1.480.21371830.17292386X-RAY DIFFRACTION98.2
1.48-1.520.21751480.15822398X-RAY DIFFRACTION97.59
1.52-1.560.19011240.15992494X-RAY DIFFRACTION98.57
1.56-1.610.1821520.14822398X-RAY DIFFRACTION98.23
1.61-1.660.20121220.14662545X-RAY DIFFRACTION98.85
1.66-1.720.15741600.14012410X-RAY DIFFRACTION98.43
1.72-1.790.17971080.13642483X-RAY DIFFRACTION98.59
1.79-1.870.18141630.1672420X-RAY DIFFRACTION99.04
1.87-1.970.17011870.17672438X-RAY DIFFRACTION99.43
1.97-2.090.18391580.17322442X-RAY DIFFRACTION99.12
2.09-2.250.1737930.15912547X-RAY DIFFRACTION99.32
2.25-2.480.2341760.1772572X-RAY DIFFRACTION99.74
2.48-2.830.24441650.18222448X-RAY DIFFRACTION99.77
2.83-3.570.16451260.152499X-RAY DIFFRACTION99.39
3.57-20.070.17281740.11752440X-RAY DIFFRACTION99.58

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