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- PDB-1of5: Crystal structure of Mex67-Mtr2 -

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Basic information

Entry
Database: PDB / ID: 1of5
TitleCrystal structure of Mex67-Mtr2
Components
  • MRNA EXPORT FACTOR MEX67
  • MRNA TRANSPORT REGULATOR MTR2
KeywordsNUCLEAR TRANSPORT / TRANSPORT / MRNA TRANSPORT / NUCLEAR PROTEIN / LEUCINE- RICH REPEAT
Function / homology
Function and homology information


nuclear RNA export factor complex / nuclear pore central transport channel / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA export from nucleus / U4 snRNA binding / tRNA processing / poly(A)+ mRNA export from nucleus / porin activity / ribosomal large subunit export from nucleus ...nuclear RNA export factor complex / nuclear pore central transport channel / tRNA re-export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA export from nucleus / U4 snRNA binding / tRNA processing / poly(A)+ mRNA export from nucleus / porin activity / ribosomal large subunit export from nucleus / U5 snRNA binding / U2 snRNA binding / U6 snRNA binding / nuclear pore / mRNA export from nucleus / U1 snRNA binding / ribosomal small subunit export from nucleus / tRNA binding / mRNA binding / RNA binding / nucleus / cytoplasm
Similarity search - Function
Nuclear pore RNA shuttling protein Mtr2 / Nuclear pore RNA shuttling protein Mtr2 / Mex67, RNA recognition motif / RNA recognition motif / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / NXF1/2/3/5 leucine-rich repeat domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor ...Nuclear pore RNA shuttling protein Mtr2 / Nuclear pore RNA shuttling protein Mtr2 / Mex67, RNA recognition motif / RNA recognition motif / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / NXF1/2/3/5 leucine-rich repeat domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear transport factor 2 domain / Nuclear Transport Factor 2; Chain: A, - #50 / UBA-like superfamily / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / mRNA transport regulator MTR2 / mRNA export factor MEX67
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsFribourg, S. / Conti, E.
CitationJournal: EMBO Rep. / Year: 2003
Title: Structural similarity in the absence of sequence homology of the messenger RNA export factors Mtr2 and p15.
Authors: Fribourg, S. / Conti, E.
History
DepositionApr 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2003Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jun 13, 2018Group: Data collection / Database references / Category: citation / diffrn_radiation
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_radiation.pdbx_diffrn_protocol
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MRNA EXPORT FACTOR MEX67
B: MRNA TRANSPORT REGULATOR MTR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9203
Polymers45,7192
Non-polymers2011
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-23.7 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.820, 83.712, 85.523
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MRNA EXPORT FACTOR MEX67 / MEX67 / YPL169C / P2520


Mass: 24916.484 Da / Num. of mol.: 1 / Fragment: NTF2-LIKE DOMAIN, RESIDUES 268-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q99257
#2: Protein MRNA TRANSPORT REGULATOR MTR2 / MTR2 / YKL186C


Mass: 20802.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P34232
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMEX67 INVOLVED IN THE EXPORT OF MRNA FROM THE NUCLEUS TO THE CYTOPLASM. MTR2 AFFECTS MRNA TRANSPORT ...MEX67 INVOLVED IN THE EXPORT OF MRNA FROM THE NUCLEUS TO THE CYTOPLASM. MTR2 AFFECTS MRNA TRANSPORT FROM THE NUCLEUS TO THE CYTOPLASM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.64 %
Crystal growpH: 7.5
Details: 100MM HEPES PH7.5, PEG 3000 20%, 0.2M CALCIUM ACETATE, pH 7.50
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG30001reservoir
2200 mMcalcium acetate1reservoir
3100 mMHEPES1reservoirpH7.5
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 9718 / % possible obs: 95.6 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2 / % possible all: 78.5
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 78.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 -5 %RANDOM
Rwork0.242 ---
obs0.242 9718 100 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.211 Å20 Å20 Å2
2---5.818 Å20 Å2
3----9.393 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 1 3 2253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008974
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.51263
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:WATER.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:ION.PARAM
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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