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- PDB-6j9j: crystal structure of SESTD2 in complex with H3.3S31phK36M peptide -

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Basic information

Entry
Database: PDB / ID: 6j9j
Titlecrystal structure of SESTD2 in complex with H3.3S31phK36M peptide
Components
  • H3.3S31phK36M(29-42)
  • 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 / regulation of mRNA export from nucleus ...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 / regulation of mRNA export from nucleus / pericardium development / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / stem cell development / nucleosome organization / histone H3K36 methyltransferase activity / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / 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 / oocyte maturation / regulation of double-strand break repair via homologous recombination / nucleus organization / endodermal cell differentiation / alpha-tubulin binding / spermatid development / single fertilization / subtelomeric heterochromatin formation / positive regulation of interferon-alpha production / nucleosomal DNA 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 / 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 / DNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / regulation of cytokinesis / PRC2 methylates histones and DNA / Defective pyroptosis / neural tube closure / transcription elongation by RNA polymerase II / stem cell differentiation / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / 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 / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / male gonad development / nucleosome / nucleosome assembly / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / regulation of gene expression / Oxidative Stress Induced Senescence / angiogenesis / defense response to virus / Estrogen-dependent gene expression / cell population proliferation / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / metal ion binding
Similarity search - Function
Histone-lysine N-methyltransferase SETD2, animal / Set2 Rpb1 interacting domain / Set2 Rpb1 interacting domain superfamily / SRI (Set2 Rpb1 interacting) domain / SETD2/Set2, SET 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 / Set2 Rpb1 interacting domain superfamily / SRI (Set2 Rpb1 interacting) domain / SETD2/Set2, SET 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 / SET domain superfamily / WW domain / SET domain / 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 / Resolution: 1.78 Å
AuthorsYang, S. / Li, H.T.
CitationJournal: Nature / Year: 2020
Title: Histone H3.3 phosphorylation amplifies stimulation-induced transcription.
Authors: Armache, A. / Yang, S. / Martinez de Paz, A. / Robbins, L.E. / Durmaz, C. / Cheong, J.Q. / Ravishankar, A. / Daman, A.W. / Ahimovic, D.J. / Klevorn, T. / Yue, Y. / Arslan, T. / Lin, S. / ...Authors: Armache, A. / Yang, S. / Martinez de Paz, A. / Robbins, L.E. / Durmaz, C. / Cheong, J.Q. / Ravishankar, A. / Daman, A.W. / Ahimovic, D.J. / Klevorn, T. / Yue, Y. / Arslan, T. / Lin, S. / Panchenko, T. / Hrit, J. / Wang, M. / Thudium, S. / Garcia, B.A. / Korb, E. / Armache, K.J. / Rothbart, S.B. / Hake, S.B. / Allis, C.D. / Li, H. / Josefowicz, S.Z.
History
DepositionJan 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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: H3.3S31phK36M(29-42)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,15010
Polymers31,3372
Non-polymers8138
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-33 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.112, 77.014, 77.412
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 / Protein-lysine N-methyltransferase SETD2 / SET domain-containing protein 2 / hSET2 / p231HBP


Mass: 29695.824 Da / Num. of mol.: 1
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, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein/peptide H3.3S31phK36M(29-42)


Mass: 1640.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243*PLUS

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Non-polymers , 4 types, 268 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


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


Mass: 58.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CNS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M potassium thiocyanate, 0.1M Bis-Tris propane,20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 35792 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Χ2: 0.964 / Net I/σ(I): 6.8 / Num. measured all: 233252
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.815.90.36517200.9250.160.3990.6197
1.81-1.846.70.33717710.9490.140.3650.66100
1.84-1.886.80.29217560.9630.120.3160.704100
1.88-1.926.70.25617510.9640.1060.2780.712100
1.92-1.966.70.22717850.9760.0950.2470.738100
1.96-26.50.20117440.9780.0850.2190.80299.9
2-2.056.20.17417910.980.0760.1910.789100
2.05-2.116.40.15717670.980.0670.1710.84299.9
2.11-2.176.80.13417450.9880.0550.1450.882100
2.17-2.246.80.12218010.990.050.1320.87100
2.24-2.326.70.11217640.9920.0470.1220.924100
2.32-2.426.50.10317910.990.0440.1120.91599.8
2.42-2.536.10.09317750.9910.040.1010.94599.9
2.53-2.666.70.08618080.9930.0360.0930.987100
2.66-2.836.80.07917850.9950.0330.0861.055100
2.83-3.046.70.07317910.9950.030.0791.146100
3.04-3.356.20.06418120.9950.0280.071.24999.9
3.35-3.836.80.06118240.9960.0250.0661.4299.9
3.83-4.836.30.05618550.9970.0240.0611.46599.9
4.83-506.20.05919560.9950.0250.0641.48999.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementResolution: 1.78→48.01 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2056 1768 4.9 %RANDOM
Rwork0.1891 ---
obs0.19 33966 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.69 Å2 / Biso mean: 31.201 Å2 / Biso min: 15.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.67 Å20 Å20 Å2
2---0.4 Å20 Å2
3----1.27 Å2
Refinement stepCycle: final / Resolution: 1.78→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2092 0 41 260 2393
Biso mean--28.58 37.42 -
Num. residues----261
LS refinement shellResolution: 1.779→1.825 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 108 -
Rwork0.207 2450 -
all-2558 -
obs--97.82 %

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