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- PDB-2mkg: Solution structure of the tandem UIMs of RAP80 -

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Basic information

Entry
Database: PDB / ID: 2mkg
TitleSolution structure of the tandem UIMs of RAP80
ComponentsBRCA1-A complex subunit RAP80
KeywordsSIGNALING PROTEIN / UIM / Ubiquitin-interacting motif / DNA damage response
Function / homology
Function and homology information


BRCA1-A complex / ubiquitin-modified histone reader activity / mitotic G2/M transition checkpoint / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / mitotic G2 DNA damage checkpoint signaling / regulation of DNA repair / positive regulation of DNA repair / Nonhomologous End-Joining (NHEJ) ...BRCA1-A complex / ubiquitin-modified histone reader activity / mitotic G2/M transition checkpoint / DNA repair-dependent chromatin remodeling / K63-linked polyubiquitin modification-dependent protein binding / response to ionizing radiation / mitotic G2 DNA damage checkpoint signaling / regulation of DNA repair / positive regulation of DNA repair / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Metalloprotease DUBs / double-strand break repair / 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 / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1800 / BRCA1-A complex subunit RAP80 / RAP80, N-terminal / RAP80 N-terminal ubiquitin interaction motif / Ubiquitin-interacting motif. / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1800 / BRCA1-A complex subunit RAP80 / RAP80, N-terminal / RAP80 N-terminal ubiquitin interaction motif / Ubiquitin-interacting motif. / Rad18, zinc finger UBZ4-type / Zinc finger UBZ4-type profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
BRCA1-A complex subunit RAP80
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailsclosest to the average, model6
AuthorsAnamika / Markin, C.J. / Rout, M.K. / Spyracopoulos, L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Molecular Basis for Impaired DNA Damage Response Function Associated with the RAP80 Delta E81 Defect.
Authors: Anamika / Markin, C.J. / Rout, M.K. / Spyracopoulos, L.
History
DepositionFeb 6, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BRCA1-A complex subunit RAP80


Theoretical massNumber of molelcules
Total (without water)7,0191
Polymers7,0191
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 / 20all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein 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: 7018.696 Da / Num. of mol.: 1 / Fragment: UIM 1-2 (UNP residues 74-131)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UIMC1, RAP80, RXRIP110 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RL1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D 1H-15N NOESY
1323D CBCA(CO)NH
1423D HN(CA)CB
1513D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.33 mM [U-100% 13C; U-100% 15N] RAP80-tUIM, 90% H2O/10% D2O90% H2O/10% D2O
21.2 mM [U-100% 13C; U-100% 15N] RAP80-tUIM, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.33 mMRAP80-tUIM-1[U-100% 13C; U-100% 15N]1
1.2 mMRAP80-tUIM-2[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 150 / pH: 7.3 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
VnmrJVariancollection
SparkyGoddardchemical shift assignment
CARAKeller and Wuthrichchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMR constraintsNOE constraints total: 65 / NOE intraresidue total count: 24 / NOE medium range total count: 1 / NOE sequential total count: 40 / Protein chi angle constraints total count: 15 / Protein phi angle constraints total count: 57 / Protein psi angle constraints total count: 57
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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