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- PDB-9g4a: Structure of human SETD2 T1663M mutant in complex with SAM and H3... -

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Basic information

Entry
Database: PDB / ID: 9g4a
TitleStructure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide
Components
  • Histone H3
  • Histone-lysine N-methyltransferase SETD2
KeywordsTRANSFERASE / Histone-Lysine N-Methyltransferase
Function / homology
Function and homology information


peptidyl-lysine trimethylation / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / regulation of mRNA export from nucleus / histone H3K36 trimethyltransferase activity / histone H3K36 methyltransferase activity / response to alkaloid / nucleosome organization / response to type I interferon / protein-lysine N-methyltransferase activity ...peptidyl-lysine trimethylation / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / regulation of mRNA export from nucleus / histone H3K36 trimethyltransferase activity / histone H3K36 methyltransferase activity / response to alkaloid / nucleosome organization / response to type I interferon / protein-lysine N-methyltransferase activity / positive regulation of ossification / regulation of protein localization to chromatin / response to metal ion / histone H3 methyltransferase activity / regulation of double-strand break repair via homologous recombination / endodermal cell differentiation / positive regulation of interferon-alpha production / alpha-tubulin binding / mismatch repair / positive regulation of autophagy / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of cytokinesis / stem cell differentiation / transcription elongation by RNA polymerase II / PKMTs methylate histone lysines / structural constituent of chromatin / nucleosome / regulation of gene expression / chromosome / defense response to virus / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains ...Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / TFIIS/LEDGF domain superfamily / Post-SET domain / Post-SET domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / 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
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Histone H3 / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 Å
AuthorsMechaly, A.E. / Michail, C. / Haouz, A. / Rodrigues-Lima, F.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
CitationJournal: To Be Published
Title: Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide
Authors: Mechaly, A.E. / Michail, C. / Haouz, A. / Rodrigues-Lima, F.
History
DepositionJul 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD2
B: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3826
Polymers35,7872
Non-polymers5954
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-24 kcal/mol
Surface area13860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.835, 76.633, 77.055
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histone-lysine N-methyltransferase SETD2 / HIF-1 / Huntingtin yeast partner B / Huntingtin-interacting protein 1 / HIP-1 / Huntingtin- ...HIF-1 / Huntingtin yeast partner B / Huntingtin-interacting protein 1 / HIP-1 / Huntingtin-interacting protein B / Lysine N-methyltransferase 3A / Protein-lysine N-methyltransferase SETD2 / SET domain-containing protein 2 / hSET2 / p231HBP


Mass: 34128.906 Da / Num. of mol.: 1 / Mutation: T1663M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9BYW2, [histone H3]-lysine36 N-trimethyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein/peptide Histone H3


Mass: 1657.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A0A1X8XL64
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 32% w/v PEG 4K, 100mM Tris, 800mM LiCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 1.653→54.336 Å / Num. obs: 18723 / % possible obs: 93.7 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.028 / Rrim(I) all: 0.102 / Net I/σ(I): 12.7
Reflection shellResolution: 1.653→1.875 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.218 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 936 / CC1/2: 0.835 / Rpim(I) all: 0.343 / Rrim(I) all: 1.266 / % possible all: 78.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
XDSJun 30, 202data reduction
autoPROC1.0.5data scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.653→22.5 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.215 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.239 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 939 -RANDOM
Rwork0.1973 ---
obs0.1994 18701 44.1 %-
Displacement parametersBiso mean: 39.62 Å2
Baniso -1Baniso -2Baniso -3
1-12.6911 Å20 Å20 Å2
2---2.9636 Å20 Å2
3----9.7275 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.653→22.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 30 226 2357
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092172HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.012914HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d792SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes378HARMONIC5
X-RAY DIFFRACTIONt_it2172HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion265SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1902SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion19.89
LS refinement shellResolution: 1.653→1.79 Å
RfactorNum. reflection% reflection
Rfree0.3492 18 -
Rwork0.2576 --
obs--4.61 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8553-0.85921.67521.3991-0.48064.0080.0275-0.03120.0485-0.03120.01960.09870.04850.0987-0.04710.05980.02490.0377-0.22940.003-0.2946-12.1911-5.24142.3541
29.4903-2.83736.07861.8923-1.81389.15620.0211-0.72150.287-0.7215-0.09340.86490.2870.86490.07230.20190.08570.0461-0.2564-0.0146-0.4325-8.4204-11.5142-8.0914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1446 - 1703
2X-RAY DIFFRACTION1{ A|* }A1801 - 1803
3X-RAY DIFFRACTION2{ B|* }B29 - 43

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