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- PDB-5v21: Crystal structure of human SETD2 SET-domain in complex with H3K36... -

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Basic information

Entry
Database: PDB / ID: 5v21
TitleCrystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM
Components
  • Histone H3K36M peptide
  • Histone-lysine N-methyltransferase SETD2
KeywordsTRANSFERASE / Methyltransferase
Function / homology
Function and homology information


mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / pericardium development ...mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / pericardium development / regulation of mRNA export from nucleus / stem cell development / histone H3K36 methyltransferase activity / nucleosome organization / protein-lysine N-methyltransferase activity / response to type I interferon / embryonic cranial skeleton morphogenesis / positive regulation of ossification / response to alkaloid / 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 / Chromatin modifying enzymes / positive regulation of autophagy / forebrain development / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / regulation of cytokinesis / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / neural tube closure / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / stem cell differentiation / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / transcription elongation by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / response to organic cyclic compound / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / gene expression / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / angiogenesis / defense response to virus / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / metal ion binding / 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. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / 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 H3.1 / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.415 Å
AuthorsZhang, Y. / Tong, L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10-OD012018 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM085145 United States
CitationJournal: Sci Rep / Year: 2017
Title: Molecular basis for the role of oncogenic histone mutations in modulating H3K36 methylation.
Authors: Zhang, Y. / Shan, C.M. / Wang, J. / Bao, K. / Tong, L. / Jia, S.
History
DepositionMar 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SETD2
B: Histone H3K36M peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6056
Polymers36,0102
Non-polymers5954
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-14 kcal/mol
Surface area13440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.493, 76.316, 77.179
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / SET domain-containing protein 2 / hSET2 / p231HBP


Mass: 34368.156 Da / Num. of mol.: 1 / Fragment: SET domain (UNP residues 1435-1711)
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 (E. coli)
References: UniProt: Q9BYW2, histone-lysine N-methyltransferase
#2: Protein/peptide Histone H3K36M peptide


Mass: 1641.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Zn
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M KSCN, 24% (v/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.42→30 Å / Num. obs: 13529 / % possible obs: 98.1 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.1
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1280

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4h12

4h12


Resolution: 2.415→29.528 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 671 5.13 %
Rwork0.204 --
obs0.2073 13077 95.08 %
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.355 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.3995 Å2-0 Å2-0 Å2
2---4.3866 Å2-0 Å2
3----12.0129 Å2
Refinement stepCycle: LAST / Resolution: 2.415→29.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2081 0 30 36 2147
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162169
X-RAY DIFFRACTIONf_angle_d1.4152911
X-RAY DIFFRACTIONf_dihedral_angle_d17.282819
X-RAY DIFFRACTIONf_chiral_restr0.105293
X-RAY DIFFRACTIONf_plane_restr0.007380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4154-2.60180.35361250.28342271X-RAY DIFFRACTION90
2.6018-2.86340.33191260.25982396X-RAY DIFFRACTION93
2.8634-3.27730.28061370.22892460X-RAY DIFFRACTION96
3.2773-4.12720.28571370.19212569X-RAY DIFFRACTION98
4.1272-29.52970.20721460.16432710X-RAY DIFFRACTION99

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