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- PDB-2a7o: Solution Structure of the hSet2/HYPB SRI domain -

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Basic information

Entry
Database: PDB / ID: 2a7o
TitleSolution Structure of the hSet2/HYPB SRI domain
ComponentsHuntingtin interacting protein B
KeywordsTRANSCRIPTION / SRI domain / SRI / hSRI / Set2 / hSet2 / phosphoCTD associating protein / Set2 Rpb1-interacting domain / PCID / PCAP
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 / 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 / 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 / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Set2, Rpb1 interacting domain / 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 ...Set2, Rpb1 interacting domain / 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 / Rna Polymerase Sigma Factor; Chain: A / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histone-lysine N-methyltransferase SETD2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsLi, M. / Phatnani, H.P. / Guan, Z. / Sage, H. / Greenleaf, A. / Zhou, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Solution structure of the Set2 Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1
Authors: Li, M. / Phatnani, H.P. / Guan, Z. / Sage, H. / Greenleaf, A. / Zhou, P.
History
DepositionJul 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Huntingtin interacting protein B


Theoretical massNumber of molelcules
Total (without water)13,1471
Polymers13,1471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 25structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Huntingtin interacting protein B


Mass: 13147.174 Da / Num. of mol.: 1
Fragment: Set2 Rpb1-interacting (SRI) domain, HSET2/HYBP SRI domain, residues 1954-2061
Source method: isolated from a genetically manipulated source
Details: isoform 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: hSet2/HYPB / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STAR / References: UniProt: Q9BYW2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1243D 13C-separated NOESY
1352D NOESY
1452D TOCSY
152HNCA
162HN(CO)CA
172HN(CA)CB
182HN(COCA)CB
192HNCO
1102HNCA-J
11124D HC(CCO)NH-TOCSY
112315N-HSQC
1136high-resolution 13C-HSQC
1142RDC experiment in phage

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N (random labeling) HYPB, 90% H2O, 10% D2O90% H2O/10% D2O
2U-95% 13C, U-98% 15N labeled HYPB, 90% H2O, 10% D2O90% H2O/10% D2O
3Residue selective labeling with 15N-lysine HYPB, 90% H2O, 10% D2O90% H2O/10% D2O
4U-95% 13C, U-98% 15N HYPB, 100% D2O100% D2O
5Unlabeled HYPB,100% D2O100% D2O
610% 13C (fractional labeling) HYPB,100% D2O100% D2O
Sample conditionsIonic strength: 100 mM KCl / pH: 7.0 / Pressure: ambient / Temperature: 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionClassification
NMRPipeprocessing
XEASY1.2data analysis
DYANA1.5structure solution
CYANA2structure solution
XPLOR-NIH2.9.7refinement
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: Structures were initially calculated using DYANA. CYANA 2.0 was used for automated data analysis to obtain additional NOE constraints. The structures were then refined against residual ...Details: Structures were initially calculated using DYANA. CYANA 2.0 was used for automated data analysis to obtain additional NOE constraints. The structures were then refined against residual dipolar couplings using XPLOR-NIH and a water-refinement protocol.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 25 / Conformers submitted total number: 20

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