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- PDB-2mxt: NMR structure of the acidic domain of SYNCRIP (hnRNPQ) -

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Basic information

Entry
Database: PDB / ID: 2mxt
TitleNMR structure of the acidic domain of SYNCRIP (hnRNPQ)
ComponentsHeterogeneous nuclear ribonucleoprotein Q
KeywordsSPLICING / Structural Genomics / PSI-Biology / Acidic domain / SYNCRIP / Splicing factor / Joint Center for Structural Genomics / JCSG / Partnership for T-Cell Biology / TCELL
Function / homology
Function and homology information


mRNA editing complex / CRD-mediated mRNA stability complex / mRNA modification / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / : / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / histone pre-mRNA 3'end processing complex / positive regulation of cytoplasmic translation ...mRNA editing complex / CRD-mediated mRNA stability complex / mRNA modification / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / : / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / histone pre-mRNA 3'end processing complex / positive regulation of cytoplasmic translation / GAIT complex / RNA processing / catalytic step 2 spliceosome / RNA splicing / mRNA 5'-UTR binding / mRNA splicing, via spliceosome / osteoblast differentiation / cellular response to type II interferon / negative regulation of translation / ribonucleoprotein complex / endoplasmic reticulum / RNA binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Heterogeneous nuclear ribonucleoprotein Q, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein Q, RNA recognition motif 2 / Heterogeneous nuclear ribonucleoprotein Q acidic domain / Heterogeneous nuclear ribonucleoprotein Q acidic domain / HnRNP R/Q splicing factor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein Q
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsSerrano, P. / Wuthrich, K. / Beuck, C. / Joint Center for Structural Genomics (JCSG) / Partnership for T-Cell Biology (TCELL)
CitationJournal: To be Published
Title: NMR structure of the acidic domain of SYNCRIP
Authors: Serrano, P. / Beuck, C. / Wuthrich, K.
History
DepositionJan 14, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Other
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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:
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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein Q


Theoretical massNumber of molelcules
Total (without water)9,4951
Polymers9,4951
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)19 / 40target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein Q / hnRNP Q / Glycine- and tyrosine-rich RNA-binding protein / GRY-RBP / NS1-associated protein 1 / ...hnRNP Q / Glycine- and tyrosine-rich RNA-binding protein / GRY-RBP / NS1-associated protein 1 / Synaptotagmin-binding / cytoplasmic RNA-interacting protein


Mass: 9494.643 Da / Num. of mol.: 1 / Fragment: acidic domain (UNP residues 24-107)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNCRIP, HNRPQ, NSAP1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O60506

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111APSY 4D-HACANH
121APSY 5D-(HA)CA(CO)NH
131APSY 5D-CBCA(CO)NH
1412D 1H-15N HSQC
1513D 1H-15N NOESY
1613D 1H-13C NOESY aliphatic
1713D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 1.2 mM [U-99% 13C; U-98% 15N] protein, 20 mM sodium phosphate, 50 mM sodium chloride, 5 mM sodium azide, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMprotein-1[U-99% 13C; U-98% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
5 mMsodium azide-41
Sample conditionsIonic strength: 0.0798 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR softwareName: OPALp / Classification: refinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1516 / NOE intraresidue total count: 401 / NOE long range total count: 274 / NOE medium range total count: 471 / NOE sequential total count: 370
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 40 / Conformers submitted total number: 19

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