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- PDB-1no8: SOLUTION STRUCTURE OF THE NUCLEAR FACTOR ALY RBD DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1no8
TitleSOLUTION STRUCTURE OF THE NUCLEAR FACTOR ALY RBD DOMAIN
ComponentsALY
KeywordsRNA BINDING PROTEIN / RBD / ALY / REF1-I / BEF / mRNA EXPORT FACTOR
Function / homology
Function and homology information


mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / C5-methylcytidine-containing RNA reader activity / mRNA Splicing - Major Pathway / RNA export from nucleus / mRNA transport ...mRNA 3'-end processing / RNA Polymerase II Transcription Termination / Transport of Mature mRNA derived from an Intron-Containing Transcript / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / C5-methylcytidine-containing RNA reader activity / mRNA Splicing - Major Pathway / RNA export from nucleus / mRNA transport / RNA splicing / spliceosomal complex / mRNA processing / single-stranded DNA binding / nuclear speck / RNA binding / nucleus / cytoplasm
Similarity search - Function
Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / RRM (RNA recognition motif) domain / 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 ...Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / RRM (RNA recognition motif) domain / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
THO complex subunit 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics molecular dynamics
AuthorsPerez-Alvarado, G.C. / Martinez-Yamout, M. / Allen, M.M. / Grosschedl, R. / Dyson, H.J. / Wright, P.E.
CitationJournal: Biochemistry / Year: 2003
Title: Structure of the Nuclear Factor ALY: Insights into Post-Transcriptional Regulatory and mRNA Nuclear Export Processes
Authors: Perez-Alvarado, G.C. / Martinez-Yamout, M. / Allen, M.M. / Grosschedl, R. / Dyson, H.J. / Wright, P.E.
History
DepositionJan 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Author determined the helix structure.
Remark 700SHEET Author determined the sheet records.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALY


Theoretical massNumber of molelcules
Total (without water)11,5091
Polymers11,5091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)32 / 92Structures with the lowest energy and lowest constraint energy
RepresentativeModel #1lowest energy

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Components

#1: Protein ALY


Mass: 11508.897 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ALY / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O08583

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1233D 13C-HMQC-NOESY
1323D 15n/13C-NOESY-HSQC
142HNCA, HNCO, HN(CA)CB
152CBCA(CO)NH, C(CO)NH-TOCSY, HC(CO)NH-TOCSY
161HNHA
173(H)CCH-COSY, CCH-COSY, (H)CCH-TOCSY
181HNHB
1912D TOCSY
11023D 13C-separated NOESY
NMR detailsText: The structure was determined using restraints derived from a combination of NOESY spectra and triple resonance spectra.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM ALY77-182-15N; 20mM Tris-HCl-d8, 100mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
20.5mM ALY77-182-15N, 13C; 20mM Tris-HCl-d8, 100mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
30.5mM ALY77-182-15N, 13C; 20mM Tris-HCl-d8, 100mM NaCl; 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100mM NaCl 6.5ambient 296 K
2100mM NaCl 6.5ambient 289 K
3100mM NaCl 5.9ambient 296 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002
Bruker AMXBrukerAMX5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukercollection
NMRPipe1.8, 2.1Delaglio, F., Grzesiek, S., Vuister, G.W., Guang, Z., Pfeifer, J. and Bax, A.processing
NMRDraw1.8, 2.1Delaglio, F., Grzesiek, S., Vuister, G.W., Guang, Z., Pfeifer, J. and Bax, A.processing
NMRView3Johnson, B.A. and Blevins, R.A.data analysis
DYANA1.5Gunter, P., Mumenthaler, C. and Wuthrich, K.structure solution
Amber6, 7Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham III, T.E., Wang, J., Ross, W.S.,Simmerling, C., Darden, T., Merz, K.M., Stanton, R.V., Cheng, A., Vincent, J.J., Crowley, M., Tsui, V., Gohlke, H., Radmer, R., et al. and Kollman, P.A.refinement
RefinementMethod: simulated annealing torsion angle dynamics molecular dynamics
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. RESIDUES 77-104 ARE HIGHLY DISORDERED AND DO NOT PRESENT A DEFINED STRUCTURE IN SOLUTION. RESIDUES 77-104 ARE NOT INCLUDED IN THIS ENTRY.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Structures with the lowest energy and lowest constraint energy
Conformers calculated total number: 92 / Conformers submitted total number: 32

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