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- PDB-2khh: Structural requirements for the UBA domain of the mRNA export fac... -

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Basic information

Entry
Database: PDB / ID: 2khh
TitleStructural requirements for the UBA domain of the mRNA export factor Mex67 to bind its specific targets, the transcription elongation Tho complex component Hpr1 and nucleoporin FxFG repeats
Components
  • FxFG
  • mRNA export factor MEX67
KeywordsTRANSPORT PROTEIN / Mex67 / UBA / FxFG / mRNA Export / Cytoplasm / Leucine-rich repeat / mRNA transport / Nucleus / Transport
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
Model detailslowest energy, model 1
AuthorsHobeika, M. / Brockmann, C. / Gruessing, F. / Neuhaus, D. / Divita, G. / Stewart, M. / Dargemont, C.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural requirements for the ubiquitin-associated domain of the mRNA export factor Mex67 to bind its specific targets, the transcription elongation THO complex component Hpr1 and nucleoporin FXFG repeats
Authors: Hobeika, M. / Brockmann, C. / Gruessing, F. / Neuhaus, D. / Divita, G. / Stewart, M. / Dargemont, C.
History
DepositionApr 6, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA export factor MEX67
B: FxFG


Theoretical massNumber of molelcules
Total (without water)7,7552
Polymers7,7552
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 #1lowest energy

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Components

#1: Protein mRNA export factor MEX67


Mass: 6822.732 Da / Num. of mol.: 1 / Fragment: TAP-C domain, UNP residues 542-599
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
#2: Protein/peptide FxFG


Mass: 931.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HBHA(CO)NH
1613D (H)CCH-TOCSY
1713D (H)CCH-COSY
1813D 1H-13C NOESY
1913D 1H-15N NOESY
11022D 1H-1H TOCSY
11122D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Mex67-1, 5 mM FxFG-2, 25 mM sodium phosphate-3, 50 mM sodium chloride-4, 90% H2O/10% D2O90% H2O/10% D2O
25 mM FxFG-5, 25 mM sodium phosphate-6, 50 mM sodium chloride-7, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMMex67-1[U-100% 13C; U-100% 15N]1
5 mMFxFG-21
25 mMsodium phosphate-31
50 mMsodium chloride-41
5 mMFxFG-52
25 mMsodium phosphate-62
50 mMsodium chloride-72
Sample conditionspH: 7.4 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.6Bruker Biospincollection
XwinNMR3.6Bruker Biospinprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
CCPNMR1.0.18CCPNchemical shift assignment
TALOSCornilescu, Delaglio and Baxstructure solution
TALOSCornilescu, Delaglio and Baxrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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