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- PDB-7n99: SDE2 SAP domain apo structure -

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Basic information

Entry
Database: PDB / ID: 7n99
TitleSDE2 SAP domain apo structure
ComponentsIsoform 2 of Replication stress response regulator SDE2
KeywordsDNA BINDING PROTEIN / SAP Domain / SDE2 / Replication stress response regulator / ssDNA binding protein / apo
Function / homology
Function and homology information


endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA cis splicing, via spliceosome / snoRNA binding / mitotic G1 DNA damage checkpoint signaling / mRNA Splicing - Major Pathway / protein processing / cellular response to UV / DNA replication / damaged DNA binding / protein ubiquitination ...endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mRNA cis splicing, via spliceosome / snoRNA binding / mitotic G1 DNA damage checkpoint signaling / mRNA Splicing - Major Pathway / protein processing / cellular response to UV / DNA replication / damaged DNA binding / protein ubiquitination / nuclear speck / cell division / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sde2, N-terminal ubiquitin domain / Yeast Splicing regulator sde2, N-terminal ubiquitin domain / : / Replication stress response SDE2 C-terminal
Similarity search - Domain/homology
Splicing regulator SDE2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsPaung, Y. / Weinheimer, A.S. / Rageul, J. / Khan, A. / Ho, B. / Tong, M. / Alphonse, S. / Seeliger, M.A. / Kim, H.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
American Cancer Society United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Extended DNA-binding interfaces beyond the canonical SAP domain contribute to the function of replication stress regulator SDE2 at DNA replication forks.
Authors: Weinheimer, A.S. / Paung, Y. / Rageul, J. / Khan, A. / Lo, N. / Ho, B. / Tong, M. / Alphonse, S. / Seeliger, M.A. / Kim, H.
History
DepositionJun 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2May 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

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Assembly

Deposited unit
A: Isoform 2 of Replication stress response regulator SDE2


Theoretical massNumber of molelcules
Total (without water)8,2951
Polymers8,2951
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Isoform 2 of Replication stress response regulator SDE2


Mass: 8294.899 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDE2, C1orf55 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IQ49

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13DHNCACO
131isotropic13D HN(CO)CA
141isotropic13D HNCO
151isotropic13D HN(CA)CB
161isotropic13D HN(COCA)CB
171isotropic23D C(CO)NH
181isotropic13D 1H-15N TOCSY
191isotropic12D 1H-13C HSQC
1101isotropic22D 1H-15N HSQC
1111isotropic23D 1H-15N NOESY
1121isotropic23D 1H-13C NOESY

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Sample preparation

DetailsType: solution
Contents: 300 uM [U-100% 13C; U-100% 15N] SDE2-DNA Binding protein, 90% H2O/10% D2O
Details: Buffer condition: 0.05 M Na/K pH 6.5, 0.05 M NaCl, 1 mM DTT
Label: 15N_13C_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 300 uM / Component: SDE2-DNA Binding protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 mM / Label: NMR_condition / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD7001
Bruker AVANCE III HDBrukerAVANCE III HD8502

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Processing

NMR software
NameDeveloperClassification
NMRFAM-SPARKYWoongHe, Leedata analysis
PONDEROSAWoonghe, Leestructure calculation
TopSpinBruker Biospincollection
I-PINELee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markleychemical shift assignment
ARIAFabrice Allain, Fabien Mareuil, Herve Menager, Michael Nilges, Benjamin Bardiauxrefinement
NMRFAM-SPARKYWoonghee, Leepeak picking
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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