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- PDB-7xx9: Solution structure of RRM2 of Human SART3 -

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Basic information

Entry
Database: PDB / ID: 7xx9
TitleSolution structure of RRM2 of Human SART3
ComponentsSquamous cell carcinoma antigen recognized by T-cells 3
KeywordsRNA BINDING PROTEIN / RNA binding protein RNA recognition motif RNA processing
Function / homology
Function and homology information


U6atac snRNA binding / ASAP complex / U4 snRNA binding / hematopoietic stem cell proliferation / transcription elongation-coupled chromatin remodeling / ubiquitin-specific protease binding / homeostasis of number of cells / spliceosomal tri-snRNP complex assembly / Cajal body / U6 snRNA binding ...U6atac snRNA binding / ASAP complex / U4 snRNA binding / hematopoietic stem cell proliferation / transcription elongation-coupled chromatin remodeling / ubiquitin-specific protease binding / homeostasis of number of cells / spliceosomal tri-snRNP complex assembly / Cajal body / U6 snRNA binding / spliceosomal snRNP assembly / cell morphogenesis / mRNA splicing, via spliceosome / nucleosome assembly / histone binding / regulation of gene expression / nuclear speck / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / LSM-interacting domain / Lsm interaction motif / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...SART3, RNA recognition motif 1 / SART3, RNA recognition motif 2 / LSM-interacting associated unstructured / LSM-interacting domain / Lsm interaction motif / HAT (Half-A-TPR) repeat / HAT (Half-A-TPR) repeats / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Tetratricopeptide-like helical domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Squamous cell carcinoma antigen recognized by T-cells 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKim, I. / Bang, K.M. / Park, C. / Kim, N.K. / Suh, J.Y.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1A4A1018890 Korea, Republic Of
CitationJournal: To Be Published
Title: Solution structure of RRM1 of Human SART3
Authors: Kim, I. / Bang, K.M. / Park, C. / Kim, N.K. / Suh, J.Y.
History
DepositionMay 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: 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: Squamous cell carcinoma antigen recognized by T-cells 3


Theoretical massNumber of molelcules
Total (without water)9,3521
Polymers9,3521
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Squamous cell carcinoma antigen recognized by T-cells 3 / SART-3 / Tat-interacting protein of 110 kDa / Tip110 / p110 nuclear RNA-binding protein


Mass: 9351.867 Da / Num. of mol.: 1 / Fragment: RRM2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SART3, KIAA0156, TIP110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15020

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
1101isotropic12D 1H-13C HSQC aliphatic
121isotropic13D CBCA(CO)NH
131isotropic13D HN(CA)CB
141isotropic13D HNCO
151isotropic13D HBHA(CO)NH
161isotropic13D (H)CCH-TOCSY
171isotropic13D 1H-15N NOESY
181isotropic13D 1H-13C NOESY aliphatic
191isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.8 mM [U-100% 13C; U-100% 15N] Human SART3 RRM2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O
Label: 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMHuman SART3 RRM2[U-100% 13C; U-100% 15N]1
20 mMsodium phosphatenatural abundance1
1 mMDTTnatural abundance1
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker ascend / Manufacturer: Bruker / Model: ascend / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYNMRFAM-SPARKYchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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