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- PDB-5jlb: Crystal structure of SETD2 bound to histone H3.3 K36I peptide -

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Basic information

Entry
Database: PDB / ID: 5jlb
TitleCrystal structure of SETD2 bound to histone H3.3 K36I peptide
Components
  • Histone H3.3
  • Histone-lysine N-methyltransferase SETD2
KeywordsTRANSFERASE / SET domain
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 / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / stem cell development / histone H3K36 methyltransferase activity / muscle cell differentiation / nucleosome organization / embryonic cranial skeleton morphogenesis / pericentric heterochromatin formation / inner kinetochore / protein-lysine N-methyltransferase activity / response to type I interferon / positive regulation of ossification / response to alkaloid / regulation of protein localization to chromatin / response to metal ion / histone H3 methyltransferase activity / oocyte maturation / regulation of double-strand break repair via homologous recombination / nucleus organization / endodermal cell differentiation / positive regulation of interferon-alpha production / spermatid development / subtelomeric heterochromatin formation / single fertilization / alpha-tubulin binding / RNA polymerase II core promoter sequence-specific DNA binding / mismatch repair / Replacement of protamines by nucleosomes in the male pronucleus / positive regulation of autophagy / forebrain development / nucleosomal DNA binding / Inhibition of DNA recombination at telomere / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / 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) / 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) / 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 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / response to organic cyclic compound / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / osteoblast differentiation / male gonad development / structural constituent of chromatin / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromosome / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / regulation of gene expression / defense response to virus / angiogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / chromosome, telomeric region / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / regulation of DNA-templated transcription / protein-containing complex / extracellular exosome
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 / TFIIS/LEDGF domain superfamily ...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 / TFIIS/LEDGF domain superfamily / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / 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-ADENOSYL-L-HOMOCYSTEINE / THIOCYANATE ION / Histone H3.3 / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLi, H. / Yang, S.
CitationJournal: Genes Dev. / Year: 2016
Title: Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase
Authors: Yang, S. / Zheng, X. / Lu, C. / Li, G.M. / Allis, C.D. / Li, H.
History
DepositionApr 26, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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 SETD2
B: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,52411
Polymers33,5852
Non-polymers9399
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-26 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.593, 76.844, 77.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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: 32042.568 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 1434-1711
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SETD2 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9BYW2, histone-lysine N-methyltransferase
#2: Protein/peptide Histone H3.3


Mass: 1542.784 Da / Num. of mol.: 1 / Fragment: H3 peptide, UNP residues 30-43 / Mutation: K36I / Source method: obtained synthetically / Details: chemically synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243

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Non-polymers , 5 types, 339 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.68 Å3/Da / Density % sol: 54.07 % / Mosaicity: 0.313 ° / Mosaicity esd: 0.005 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 28, 2015 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 58483 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 17.87 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.024 / Rrim(I) all: 0.082 / Χ2: 2.335 / Net I/av σ(I): 55.42 / Net I/σ(I): 13.7 / Num. measured all: 541322
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.5-1.537.20.7541100
1.53-1.557.20.591100
1.55-1.587.20.4871100
1.58-1.627.20.4021100
1.62-1.657.20.351100
1.65-1.697.20.2751100
1.69-1.737.30.2311100
1.73-1.787.30.1851100
1.78-1.837.30.1541100
1.83-1.897.20.1261100
1.89-1.967.30.1121100
1.96-2.047.30.0951100
2.04-2.137.20.0861100
2.13-2.249.70.1231100
2.24-2.3814.20.1451100
2.38-2.5613.90.1171100
2.56-2.8213.70.0931100
2.82-3.2313.70.0781100
3.23-4.07130.0631100
4.07-5012.10.051199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4H12

4h12


Resolution: 1.5→34.516 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.8
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 2842 4.87 %random selection
Rwork0.1642 ---
obs0.1655 58391 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.92 Å2 / Biso mean: 29.4487 Å2 / Biso min: 12.34 Å2
Refinement stepCycle: final / Resolution: 1.5→34.516 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 50 330 2482
Biso mean--28.09 39.35 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052187
X-RAY DIFFRACTIONf_angle_d0.9142924
X-RAY DIFFRACTIONf_chiral_restr0.085295
X-RAY DIFFRACTIONf_plane_restr0.004382
X-RAY DIFFRACTIONf_dihedral_angle_d24.301843
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4994-1.52530.2661530.23432636278996
1.5253-1.5530.25091270.204927692896100
1.553-1.58290.19681410.198927422883100
1.5829-1.61520.19611430.182927302873100
1.6152-1.65030.1761520.17627372889100
1.6503-1.68870.19381630.165927452908100
1.6887-1.7310.19221460.164727492895100
1.731-1.77780.18761410.166627412882100
1.7778-1.83010.20091610.161127422903100
1.8301-1.88910.18851550.15927542909100
1.8891-1.95660.17591370.160527692906100
1.9566-2.0350.18121230.157527812904100
2.035-2.12760.17861570.159727532910100
2.1276-2.23970.19041390.162327752914100
2.2397-2.380.19171250.169927882913100
2.38-2.56370.20711190.176328432962100
2.5637-2.82160.20411300.173928122942100
2.8216-3.22970.16481110.166128602971100
3.2297-4.0680.1671620.14828453007100
4.068-34.52480.21381570.158829783135100
Refinement TLS params.

Method: refined / 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)
10.68550.2805-0.43310.517-0.39231.753-0.0157-0.2625-0.10540.2130.0135-0.15320.26190.52-0.00390.24020.0627-0.04950.32940.01260.2272-5.2886-0.46174.8632
20.5108-0.24150.36510.21070.19511.1495-0.0226-0.5209-0.16130.103-0.0887-0.1719-0.2471-0.1213-0.08410.23650.05030.06610.43880.07120.3828-33.24485.239123.7909
30.60970.19340.21010.9726-0.21280.9057-0.0184-0.1119-0.03460.0740.00390.05450.0881-0.19280.00050.18130.03010.00290.2010.01430.1729-28.60194.787216.9402
40.299-0.14480.20490.04810.06540.5586-0.09340.1208-0.1517-0.04870.06120.06990.4876-0.19260.00650.2375-0.02160.03230.16060.0090.2119-18.5968-6.5149-2.9909
50.85870.5542-0.36980.9155-0.70350.90340.0101-0.14380.06290.17980.0084-0.0343-0.18020.0939-0.00010.1669-0.0205-0.00540.14-0.02480.1796-9.851214.1609-2.3152
60.6714-0.0708-0.66710.5673-0.57311.5106-0.03870.0217-0.07490.01350.0450.01610.0181-0.0873-00.14910.0092-0.01430.1372-0.00740.1639-21.04383.7980.391
70.975-0.0056-0.14810.57020.3830.799-0.05760.28970.1514-0.28770.04770.0149-0.1891-0.1851-0.00080.21060.0104-0.01360.20080.01090.187-17.945511.2549-15.0039
80.1451-0.10440.20540.39930.12350.42910.12780.2805-0.1444-0.2459-0.1110.0323-0.3329-0.26420.01240.21120.0193-0.0110.2091-0.01810.1858-20.701312.11-8.3557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1447 through 1485 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 1486 through 1511 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 1512 through 1551 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1552 through 1574 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1575 through 1616 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1617 through 1662 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1663 through 1703 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 29 through 42 )B29 - 42

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