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- PDB-2m85: PHD Domain from Human SHPRH -

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Basic information

Entry
Database: PDB / ID: 2m85
TitlePHD Domain from Human SHPRH
ComponentsE3 ubiquitin-protein ligase SHPRH
KeywordsHYDROLASE / LIGASE / shprh / SNF2 / histone linker / PHD finger / RING finger / helicase
Function / homology
Function and homology information


ATP-dependent chromatin remodeler activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RING-type E3 ubiquitin transferase / nucleosome assembly / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nucleosome / E3 ubiquitin ligases ubiquitinate target proteins ...ATP-dependent chromatin remodeler activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RING-type E3 ubiquitin transferase / nucleosome assembly / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / nucleosome / E3 ubiquitin ligases ubiquitinate target proteins / protein ubiquitination / hydrolase activity / DNA repair / DNA damage response / ubiquitin protein ligase binding / DNA binding / nucleoplasm / ATP binding / metal ion binding
Similarity search - Function
: / : / E3 ubiquitin-protein ligase SHPRH, second helical domain / E3 ubiquitin-protein ligase SHPRH, first helical domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 ...: / : / E3 ubiquitin-protein ligase SHPRH, second helical domain / E3 ubiquitin-protein ligase SHPRH, first helical domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / linker histone H1 and H5 family / Linker histone H1/H5, domain H15 / Linker histone H1/H5 globular (H15) domain profile. / Domain in histone families 1 and 5 / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger, PHD-type, conserved site / Ring finger / Zinc finger PHD-type signature. / Helicase conserved C-terminal domain / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase SHPRH
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsMachado, L.E.S.F. / Pustovalova, Y. / Pozhidaeva, A. / Almeida, F.C.L. / Bezsonova, I. / Korzhnev, D.M.
CitationJournal: J.Biomol.Nmr / Year: 2013
Title: PHD domain from human SHPRH.
Authors: Machado, L.E. / Pustovalova, Y. / Kile, A.C. / Pozhidaeva, A. / Cimprich, K.A. / Almeida, F.C. / Bezsonova, I. / Korzhnev, D.M.
History
DepositionMay 7, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase SHPRH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7213
Polymers8,5901
Non-polymers1312
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein E3 ubiquitin-protein ligase SHPRH / SNF2 / histone-linker / PHD and RING finger domain-containing helicase


Mass: 8589.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHPRH, KIAA2023 / Production host: Escherichia coli (E. coli)
References: UniProt: Q149N8, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ...References: UniProt: Q149N8, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D HNCO
1613D (H)CCH-TOCSY
1713D CBCA(CO)NH
1813D HBHA(CO)NH
1913D 1H-13C NOESY aliphatic
11013D 1H-13C NOESY aromatic
11113D CCH-TOCSY

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Sample preparation

DetailsContents: 50 mM [U-100% 13C; U-100% 15N] HEPES, 150 mM [U-100% 13C; U-100% 15N] sodium chloride, 0.05 mM [U-100% 13C; U-100% 15N] ZINC ION, 1 mM [U-100% 13C; U-100% 15N] DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMHEPES-1[U-100% 13C; U-100% 15N]1
150 mMsodium chloride-2[U-100% 13C; U-100% 15N]1
0.05 mMZINC ION-3[U-100% 13C; U-100% 15N]1
1 mMDTT-4[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 150 / pH: 7.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian AvanceVarianAvance5001
Varian AvanceVarianAvance8002

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8Keller and Wuthrichchemical shift assignment
CARA1.8Keller and Wuthrichpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS2.2Cornilescu, Delaglio and Baxstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
ABACUS-CNS2.5Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
Molmol2K.2Koradi, Billeter and Wuthrichdata analysis
ABACUS-CNS2.5Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: distance geometry / Software ordinal: 1
NMR constraintsNOE constraints total: 1343 / NOE intraresidue total count: 824 / NOE long range total count: 319 / NOE medium range total count: 200 / NOE sequential total count: 824
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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