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- PDB-4wp5: Chaetomium thermophilum Mex67 NTF2-like domain complexed with Mtr2 -

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Basic information

Entry
Database: PDB / ID: 4wp5
TitleChaetomium thermophilum Mex67 NTF2-like domain complexed with Mtr2
Components
  • Mtr2
  • mRNA export protein
KeywordsTRANSPORT PROTEIN / nuclear export factor
Function / homology
Function and homology information


mRNA transport / nucleus
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 RNA export factor, NTF2 domain / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. ...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 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 / Leucine-rich repeat profile. / Nuclear Transport Factor 2; Chain: A, / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Putative mRNA export protein / NTF2 domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsAibara, S. / Valkov, E. / Stewart, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structural characterization of the principal mRNA-export factor Mex67-Mtr2 from Chaetomium thermophilum.
Authors: Aibara, S. / Valkov, E. / Lamers, M.H. / Dimitrova, L. / Hurt, E. / Stewart, M.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mRNA export protein
B: Mtr2


Theoretical massNumber of molelcules
Total (without water)44,7352
Polymers44,7352
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-19 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.215, 103.215, 89.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-168-

ARG

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Components

#1: Protein mRNA export protein


Mass: 23811.693 Da / Num. of mol.: 1 / Fragment: UNP residues 365-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0059630 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SET4
#2: Protein Mtr2


Mass: 20923.633 Da / Num. of mol.: 1 / Fragment: UNP residues 11-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0065500 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SG92
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: see publication for details

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.9→44.7 Å / Num. obs: 12265 / Redundancy: 4.3 % / Net I/σ(I): 11.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2.9→44.646 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 593 4.85 %
Rwork0.2207 --
obs0.2222 12232 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→44.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 0 20 2964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033032
X-RAY DIFFRACTIONf_angle_d0.7014127
X-RAY DIFFRACTIONf_dihedral_angle_d14.4641107
X-RAY DIFFRACTIONf_chiral_restr0.028446
X-RAY DIFFRACTIONf_plane_restr0.003541
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.19190.40891490.34332885X-RAY DIFFRACTION99
3.1919-3.65350.27651660.2622888X-RAY DIFFRACTION99
3.6535-4.60230.23251370.19972909X-RAY DIFFRACTION98
4.6023-44.65130.22121410.19262957X-RAY DIFFRACTION96

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