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- PDB-6vdb: SETD2 in complex with a H3-variant super-substrate peptide -

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Basic information

Entry
Database: PDB / ID: 6vdb
TitleSETD2 in complex with a H3-variant super-substrate peptide
Components
  • ALA-PRO-ARG-PHE-GLY-GLY-VAL-MET-ARG-PRO-ASN-ARG
  • Histone-lysine N-methyltransferase SETD2
KeywordsTRANSFERASE / Structural Genomics / Structural Genomics Consortium / SGC
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 / stem cell development / nucleosome organization / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / response to type I interferon / positive regulation of ossification / embryonic cranial skeleton morphogenesis / 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 / alpha-tubulin binding / positive regulation of interferon-alpha production / mismatch repair / positive regulation of autophagy / forebrain development / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of cytokinesis / neural tube closure / transcription elongation by RNA polymerase II / stem cell differentiation / response to organic cyclic compound / PKMTs methylate histone lysines / chromosome / regulation of gene expression / angiogenesis / defense response to virus / regulation of DNA-templated transcription / nucleoplasm / nucleus / metal ion binding / cytoplasm
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
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / THIOCYANATE ION / Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsBeldar, S. / Tempel, W. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Jeltsch, A. / Min, J. / Structural Genomics Consortium / Structural Genomics Consortium (SGC)
CitationJournal: Commun Biol / Year: 2020
Title: Sequence specificity analysis of the SETD2 protein lysine methyltransferase and discovery of a SETD2 super-substrate.
Authors: Schuhmacher, M.K. / Beldar, S. / Khella, M.S. / Brohm, A. / Ludwig, J. / Tempel, W. / Weirich, S. / Min, J. / Jeltsch, A.
History
DepositionDec 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 11, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Oct 11, 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
H: ALA-PRO-ARG-PHE-GLY-GLY-VAL-MET-ARG-PRO-ASN-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,72727
Polymers35,7802
Non-polymers1,94725
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, PDB entry 5JLB
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-17 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.37, 76.52, 77.61
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AH

#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: 34098.812 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 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus RIL (Stratagen)
References: UniProt: Q9BYW2, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein/peptide ALA-PRO-ARG-PHE-GLY-GLY-VAL-MET-ARG-PRO-ASN-ARG


Mass: 1680.978 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 49 molecules

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


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C14H20N6O5S
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Zn
#6: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M KSCN, 0.1 M Tris-HCl pH 8.5, and 26% PEG 3350

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Data collection

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-IDSerial crystal experiment
1100used in intermediate refinement steps1N
2100used in latest refinement steps1N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.97918
ROTATING ANODERIGAKU FR-E21.5418
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELNov 14, 2019
RIGAKU SATURN A2002CCDOct 21, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
21.54181
ReflectionResolution: 2.3→47.65 Å / Num. obs: 16627 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.142 / Rrim(I) all: 0.153 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allNet I/σ(I) obs
8.9-47.6599.75.80.0483410.9980.05333
2.3-2.381007.11.21616120.6641.3121.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 5jlb

5jlb


Resolution: 2.3→47.65 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.854 / SU R Cruickshank DPI: 0.236 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.239 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.21
Details: Latest refinement rounds were against the earlier collected "in-house" copper anode data, out of concern about radiation-induced crystal damage. Cys1471 appears to be covalently modified. ...Details: Latest refinement rounds were against the earlier collected "in-house" copper anode data, out of concern about radiation-induced crystal damage. Cys1471 appears to be covalently modified. Density support is weak and/or ambiguous for significant model features, for example SETD2 Gln1676, ligand peptide R31, R37. Two conformations of the R37 side chain were modeled to denote uncertainty in the actual conformation, rather than observation of those specific conformations, as we failed to fit a favored rotamer to the weak density.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 735 -RANDOM
Rwork0.212 ---
obs0.214 16545 100 %-
Displacement parametersBiso mean: 46.45 Å2
Baniso -1Baniso -2Baniso -3
1--19.9216 Å20 Å20 Å2
2--10.3802 Å20 Å2
3---9.5413 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 52 24 1988
LS refinement shellResolution: 2.3→2.32 Å
RfactorNum. reflection% reflection
Rfree0.1987 14 -
Rwork0.2289 --
obs0.2282 460 99.55 %

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