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- PDB-2mgx: NMR structure of SRA1p C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 2mgx
TitleNMR structure of SRA1p C-terminal domain
ComponentsSteroid receptor RNA activator 1
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


steroid receptor RNA activator RNA binding / SCAR complex / negative regulation of myoblast differentiation / intercellular bridge / cellular response to estrogen stimulus / regulation of mitotic cell cycle / nuclear receptor coactivator activity / microtubule cytoskeleton / regulation of apoptotic process / cell differentiation ...steroid receptor RNA activator RNA binding / SCAR complex / negative regulation of myoblast differentiation / intercellular bridge / cellular response to estrogen stimulus / regulation of mitotic cell cycle / nuclear receptor coactivator activity / microtubule cytoskeleton / regulation of apoptotic process / cell differentiation / transcription coactivator activity / ribonucleoprotein complex / apoptotic process / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Steroid receptor RNA activator 1 / RNA Binding Protein, Prp18; Chain A / Functional domain of the splicing factor Prp18 / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Steroid receptor RNA activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBilinovich, S.M. / Davis, C.M. / Morris, D.L. / Ray, L.A. / Prokop, J.W. / Buchan, G.J. / Leeper, T.C.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: The C-Terminal Domain of SRA1p Has a Fold More Similar to PRP18 than to an RRM and Does Not Directly Bind to the SRA1 RNA STR7 Region.
Authors: Bilinovich, S.M. / Davis, C.M. / Morris, D.L. / Ray, L.A. / Prokop, J.W. / Buchan, G.J. / Leeper, T.C.
History
DepositionNov 10, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Database references
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / 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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Steroid receptor RNA activator 1


Theoretical massNumber of molelcules
Total (without water)14,7701
Polymers14,7701
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)15 / 30structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Steroid receptor RNA activator 1 / Steroid receptor RNA activator protein / SRAP


Mass: 14769.751 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 107-236)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRA1, PP7684 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HD15

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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 HNCO
1313D HNCA
1413D HBHA(CO)NH
1523D (H)CCH-TOCSY
1613D HN(CA)CB
1723D 1H-13C NOESY aliphatic
1813D 1H-15N NOESY
1922D 1H-1H NOESY
11022D 1H-13C HSQC
11113D HN(COCA)CB
11222D 1H-15N HSQC
11312D 1H-13C HSQC
11413d HNCAintra
11513D HNCACBintra
11613D 1H-13C NOESY aromatic
11712D HBCBCGCDCDHE
11812D (HB)CB(CGCD)HD
11913D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate, 2 mM DTT, 50 mM sodium chloride, 0.6 mM [U-98% 13C; U-98% 15N] SRA1p C-terminal domain, 95% H2O/5% D2O95% H2O/5% D2O
250 mM sodium phosphate, 2 mM DTT, 50 mM sodium chloride, 0.6 mM [U-98% 13C; U-98% 15N] SRA1p C-terminal domain, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
2 mMDTT-21
50 mMsodium chloride-31
0.6 mMSRA1p C-terminal domain-4[U-98% 13C; U-98% 15N]1
50 mMsodium phosphate-52
2 mMDTT-62
50 mMsodium chloride-72
0.6 mMSRA1p C-terminal domain-8[U-98% 13C; U-98% 15N]2
Sample conditionsIonic strength: 100 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.3Linge, O'Donoghue and Nilgesrefinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure solution
CCPNCCPNchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2036 / NOE intraresidue total count: 985 / NOE long range total count: 213 / NOE medium range total count: 120 / NOE sequential total count: 385 / Protein phi angle constraints total count: 92 / Protein psi angle constraints total count: 92
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 30 / Conformers submitted total number: 15

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