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- PDB-2jp7: NMR structure of the Mex67 UBA domain -

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Basic information

Entry
Database: PDB / ID: 2jp7
TitleNMR structure of the Mex67 UBA domain
ComponentsmRNA export factor MEX67
KeywordsTRANSLATION / Mex67 / UBA
Function / homology
Function and homology information


nuclear RNA export factor complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / U4 snRNA binding / poly(A)+ mRNA export from nucleus / porin activity / ribosomal large subunit export from nucleus / U5 snRNA binding / ribosomal small subunit export from nucleus / U2 snRNA binding / U6 snRNA binding ...nuclear RNA export factor complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / U4 snRNA binding / poly(A)+ mRNA export from nucleus / porin activity / ribosomal large subunit export from nucleus / U5 snRNA binding / ribosomal small subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / nuclear pore / U1 snRNA binding / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
Mex67, RNA recognition motif / RNA recognition motif / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Ubiquitin-associated (UBA) domain ...Mex67, RNA recognition motif / RNA recognition motif / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Ubiquitin-associated (UBA) domain / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. / Helicase, Ruva Protein; domain 3 / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
mRNA export factor MEX67
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsHobeika, M. / Brockmann, C. / Iglesias, N. / Gwizdek, C. / Neuhaus, D. / Stutz, F. / Stewart, M. / Divita, G. / Dargemont, C.
CitationJournal: Mol.Cell.Biol. / Year: 2007
Title: Coordination of Hpr1 and ubiquitin binding by the UBA domain of the mRNA export factor Mex67
Authors: Hobeika, M. / Brockmann, C. / Iglesias, N. / Gwizdek, C. / Neuhaus, D. / Stutz, F. / Stewart, M. / Divita, G. / Dargemont, C.
History
DepositionApr 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA export factor MEX67


Theoretical massNumber of molelcules
Total (without water)6,6791
Polymers6,6791
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)20 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein mRNA export factor MEX67


Mass: 6678.602 Da / Num. of mol.: 1 / Fragment: TAP-C domain, residues 543-599
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MEX67 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99257

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 25 mM NaPi, 50 mM NaCl, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
25 mMNaPi1
50 mMNaCl1
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.13Schwieters, Kuszewski, Tjandra and Clorestructure solution
XwinNMR3.5Bruker Biospincollection
XwinNMR3.5Bruker Biospinprocessing
CcpNmr Analysis1.0.13Vranken, Boucher, Stevens, Fogh, Pajon, Llinas, Ulrich, Markley, Ionides, Lauechemical shift assignment
X-PLOR NIH2.13Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: water refinement in explicit water
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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