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- PDB-2n9e: Structure of SUMO-2 bound to phosphorylated RAP80 SIM -

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Basic information

Entry
Database: PDB / ID: 2n9e
TitleStructure of SUMO-2 bound to phosphorylated RAP80 SIM
Components
  • BRCA1-A complex subunit RAP80
  • Small ubiquitin-related modifier 2
KeywordsPROTEIN BINDING / SUMO-2-phosphoRAP80 / SUMO-2-phosphoSIM
Function / homology
Function and homology information


BRCA1-A complex / ubiquitin-modified histone reader activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / mitotic G2/M transition checkpoint / SUMOylation of RNA binding proteins / DNA repair-dependent chromatin remodeling ...BRCA1-A complex / ubiquitin-modified histone reader activity / SUMO is proteolytically processed / SUMO is conjugated to E1 (UBA2:SAE1) / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Vitamin D (calciferol) metabolism / SUMOylation of SUMOylation proteins / mitotic G2/M transition checkpoint / SUMOylation of RNA binding proteins / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / ubiquitin-like protein ligase binding / mitotic G2 DNA damage checkpoint signaling / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / protein sumoylation / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / positive regulation of DNA repair / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Nonhomologous End-Joining (NHEJ) / SUMOylation of intracellular receptors / G2/M DNA damage checkpoint / Metalloprotease DUBs / PML body / Formation of Incision Complex in GG-NER / protein tag activity / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / histone binding / nuclear body / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
BRCA1-A complex subunit RAP80 / RAP80, N-terminal / RAP80 N-terminal ubiquitin interaction motif / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin-interacting motif. / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. ...BRCA1-A complex subunit RAP80 / RAP80, N-terminal / RAP80 N-terminal ubiquitin interaction motif / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin-interacting motif. / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 2 / BRCA1-A complex subunit RAP80
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics, torsion angle dynamics
AuthorsAnamika, A. / Spyracopoulos, L.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Molecular Basis for Phosphorylation-dependent SUMO Recognition by the DNA Repair Protein RAP80.
Authors: Anamika / Spyracopoulos, L.
History
DepositionNov 15, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BRCA1-A complex subunit RAP80
B: Small ubiquitin-related modifier 2


Theoretical massNumber of molelcules
Total (without water)12,4672
Polymers12,4672
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-6 kcal/mol
Surface area8810 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide BRCA1-A complex subunit RAP80 / Receptor-associated protein 80 / Retinoid X receptor-interacting protein 110 / Ubiquitin ...Receptor-associated protein 80 / Retinoid X receptor-interacting protein 110 / Ubiquitin interaction motif-containing protein 1


Mass: 1580.415 Da / Num. of mol.: 1 / Fragment: SUMO interacting motif (UNP residues 37-49) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96RL1
#2: Protein Small ubiquitin-related modifier 2 / SUMO-2 / HSMT3 / SMT3 homolog 2 / SUMO-3 / Sentrin-2 / Ubiquitin-like protein SMT3B / Smt3B


Mass: 10886.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUMO2, SMT3B, SMT3H2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61956

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HNCO
1413D HCACO
1513D HN(CA)CB
1612D 1H-13C HSQC aromatic
1712D 1H-1H TOCSY
1812D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.2 mM peptide, 0.4 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMpeptide-11
0.4 mMprotein-2[U-100% 13C; U-100% 15N]1
Sample conditionsIonic strength: 25 / pH: 7.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
SPARKY3.113Goddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
AMBER14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanstructure solution
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
AMBER14Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: molecular dynamics, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 45 / NOE intraresidue total count: 3 / NOE long range total count: 0 / NOE medium range total count: 6 / NOE sequential total count: 21 / Protein chi angle constraints total count: 30 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 68 / Protein psi angle constraints total count: 68
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 2 Å

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