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- PDB-2l08: Solution NMR Structure of Nonsense mRNA reducing factor 3A from H... -

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Basic information

Entry
Database: PDB / ID: 2l08
TitleSolution NMR Structure of Nonsense mRNA reducing factor 3A from H. Sapiens, Northeast Structural Genomics Consortium Target HR4714B
ComponentsRegulator of nonsense transcripts 3A
KeywordsTRANSPORT PROTEIN / NESG / Nonsense regulator / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / telomeric DNA binding / mRNA transport / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of translation / Regulation of expression of SLITs and ROBOs / spermatogenesis / in utero embryonic development ...negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / telomeric DNA binding / mRNA transport / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of translation / Regulation of expression of SLITs and ROBOs / spermatogenesis / in utero embryonic development / neuron projection / mRNA binding / intracellular membrane-bounded organelle / nucleolus / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nonsense-mediated mRNA decay protein 3 / Smg-4/UPF3 family / UPF3 domain / RRM (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
Regulator of nonsense transcripts 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMani, R. / Mao, L. / Ciccosanti, C. / Shastry, R. / Acton, T.B. / Xiao, R. / Swapna, G.V.T. / Everett, J.K. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of Nonsense mRNA reducing factor 3A from H. Sapiens, Northeast Structural Genomics Consortium Target HR4714B
Authors: Mani, R. / Mao, L. / Ciccosanti, C. / Shastry, R. / Acton, T.B. / Xiao, R. / Swapna, G.V.T. / Everett, J.K. / Montelione, G.T.
History
DepositionJun 30, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 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: Regulator of nonsense transcripts 3A


Theoretical massNumber of molelcules
Total (without water)11,5961
Polymers11,5961
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)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Regulator of nonsense transcripts 3A / Nonsense mRNA reducing factor 3A / Up-frameshift suppressor 3 homolog A / hUpf3


Mass: 11596.175 Da / Num. of mol.: 1 / Fragment: sequence database residues 70-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UPF3A, RENT3A, UPF3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ magic / References: UniProt: Q9H1J1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: HR4714B is a 97 residue protein consisiting of a 10 residue N-terminal tag. N-HSQC spectrum shows only 71 peaks out of the 87 peaks (excluding tag) that are expected. The line broeadening of ...Details: HR4714B is a 97 residue protein consisiting of a 10 residue N-terminal tag. N-HSQC spectrum shows only 71 peaks out of the 87 peaks (excluding tag) that are expected. The line broeadening of the peaks occur from residue D45 to S54. Also, M11, R16, S81 NH's are missing from N-HSQC spectrum. The reason for line broadening is not known.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1412D 1H-13C HSQC
1522D 1H-13C HSQC
1613D CBCA(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D HBHA(CO)NH
11113D C(CO)NH-TOCSY
11213D CCH-TOCSY
11323D HNHA
11413D simul NOESY
11513D arom NOESY
NMR detailsText: The Structure was obtained using triple resonance NMR spectroscopy for backbone and side chain assignments. Automated NOESY assignments were made using Autostructure and CYANA3.0. Dihedral ...Text: The Structure was obtained using triple resonance NMR spectroscopy for backbone and side chain assignments. Automated NOESY assignments were made using Autostructure and CYANA3.0. Dihedral angle constraints were obtained using TALOS. The structure calculation was done excluding the 10-residue N-terminal tag. Completeness of assignment excluding the tag: Backbone - 80%, Sidechain - 80%. Peaks for 13 residues in NHSQC spectra are missing due to line broadening.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.82 mM [U-100% 13C; U-100% 15N] HR4714B, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-10% 13C; U-99% 15N] HR4714B, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.82 mMHR4714B-1[U-100% 13C; U-100% 15N]1
0.9 mMHR4714B-2[U-10% 13C; U-99% 15N]2
Sample conditionsIonic strength: 100mM NaCl, 10mM Tris-HCl / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Final structure quality (excluding 10 residue tag) determined using PSVS-v1.4: Ordered residues are defines as: 10-19,22-34,36-45,54-72,76-94. (a) RMSD (ordered residues) all backbone aroms: ...Details: Final structure quality (excluding 10 residue tag) determined using PSVS-v1.4: Ordered residues are defines as: 10-19,22-34,36-45,54-72,76-94. (a) RMSD (ordered residues) all backbone aroms: 0.6A. and heavy atoms 1.0A. (b) Ramachandran statistics for ordered residues: Most favored region: 85.1% Additionally favored region: 14.8% Generaously allowed region: 0.1% Disallowed region: 0.1%. (c) Procheck scores for ordered residues (RAW/Z): Phi/psi -0.73/-2.56, all -0.65/-3.84, (d) Molprobity clashscores (RAW/Z)22.41/-2.32 (e) RPF scores for the goodness fit to NOESY data: Recall: 89, Precision: 94, F-measure: 92, final dp-score - (f) RMS deviation for bond angles - 6.15, RMS deviation for bond lengths 0.01A.
NMR constraintsNOE constraints total: 1729 / NOE intraresidue total count: 281 / NOE long range total count: 333 / NOE medium range total count: 536 / NOE sequential total count: 471 / Protein phi angle constraints total count: 108 / Protein psi angle constraints total count: 108
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.25 Å / Maximum torsion angle constraint violation: 8.5 ° / Maximum upper distance constraint violation: 1.7 Å
NMR ensemble rmsDistance rms dev: 0.01 Å

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