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- PDB-4xm4: Structure of Chaetomium Mex67:Mtr2 subunits -

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Basic information

Entry
Database: PDB / ID: 4xm4
TitleStructure of Chaetomium Mex67:Mtr2 subunits
ComponentsMex67
KeywordsTRANSPORT PROTEIN / nuclear transport / mRNA export
Function / homology
Function and homology information


poly(A)+ mRNA export from nucleus / RNA binding / 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 transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear Transport Factor 2; Chain: A, - #50 ...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. / Nuclear Transport Factor 2; Chain: A, - #50 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / 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
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsAibara, S. / Valkov, M. / Stewart, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105178939 United Kingdom
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
DepositionJan 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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: Mex67
B: Mex67
C: Mex67
D: Mex67


Theoretical massNumber of molelcules
Total (without water)172,5104
Polymers172,5104
Non-polymers00
Water00
1
A: Mex67


Theoretical massNumber of molelcules
Total (without water)43,1281
Polymers43,1281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mex67


Theoretical massNumber of molelcules
Total (without water)43,1281
Polymers43,1281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mex67


Theoretical massNumber of molelcules
Total (without water)43,1281
Polymers43,1281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mex67


Theoretical massNumber of molelcules
Total (without water)43,1281
Polymers43,1281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.754, 96.087, 194.764
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
Mex67


Mass: 43127.504 Da / Num. of mol.: 4 / Fragment: UNP residues 180-564
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0059630 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SET4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: See manuscript for details

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→48.043 Å / Num. obs: 17888 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.2
Reflection shellResolution: 2.95→3.055 Å / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→48.043 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 924 5.17 %
Rwork0.2271 --
obs0.2292 17874 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→48.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5274 0 0 0 5274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035402
X-RAY DIFFRACTIONf_angle_d0.717348
X-RAY DIFFRACTIONf_dihedral_angle_d13.8761999
X-RAY DIFFRACTIONf_chiral_restr0.031823
X-RAY DIFFRACTIONf_plane_restr0.003955
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.10550.32071370.30172389X-RAY DIFFRACTION100
3.1055-3.30.34241420.27052371X-RAY DIFFRACTION100
3.3-3.55480.31431230.26042408X-RAY DIFFRACTION100
3.5548-3.91230.25621290.23442420X-RAY DIFFRACTION99
3.9123-4.47810.26771220.20862422X-RAY DIFFRACTION99
4.4781-5.64050.24571400.20152429X-RAY DIFFRACTION98
5.6405-48.04980.22851310.21562511X-RAY DIFFRACTION96

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