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- PDB-4wwu: Structure of Mex67:Mtr2 -

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Basic information

Entry
Database: PDB / ID: 4wwu
TitleStructure of Mex67:Mtr2
Components
  • mRNA export factor MEX67
  • mRNA transport regulator MTR2
KeywordsTRANSPORT PROTEIN / mRNA nuclear export factor
Function / homology
Function and homology information


nuclear RNA export factor complex / nuclear pore central transport channel / 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 ...nuclear RNA export factor complex / nuclear pore central transport channel / 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
Nuclear pore RNA shuttling protein Mtr2 / Nuclear pore RNA shuttling protein Mtr2 / Mex67, RNA recognition motif / RNA recognition motif / Nuclear transport factor 2/Mtr2 / 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 pore RNA shuttling protein Mtr2 / Nuclear pore RNA shuttling protein Mtr2 / Mex67, RNA recognition motif / RNA recognition motif / Nuclear transport factor 2/Mtr2 / 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
mRNA transport regulator MTR2 / mRNA export factor MEX67
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.301 Å
AuthorsAibara, S. / Valkov, E. / Stewart, M.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Domain organization within the nuclear export factor Mex67:Mtr2 generates an extended mRNA binding surface.
Authors: Aibara, S. / Valkov, E. / Lamers, M. / Stewart, M.
History
DepositionNov 12, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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 export factor MEX67
C: mRNA transport regulator MTR2
D: mRNA export factor MEX67
E: mRNA export factor MEX67
F: mRNA transport regulator MTR2
G: mRNA export factor MEX67
H: mRNA export factor MEX67
I: mRNA transport regulator MTR2
J: mRNA export factor MEX67
K: mRNA export factor MEX67
L: mRNA transport regulator MTR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)526,42324
Polymers525,63812
Non-polymers78512
Water00
1
A: mRNA export factor MEX67
B: mRNA export factor MEX67
C: mRNA transport regulator MTR2
J: mRNA export factor MEX67
K: mRNA export factor MEX67
L: mRNA transport regulator MTR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,27713
Polymers262,8196
Non-polymers4587
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: mRNA export factor MEX67
E: mRNA export factor MEX67
F: mRNA transport regulator MTR2
G: mRNA export factor MEX67
H: mRNA export factor MEX67
I: mRNA transport regulator MTR2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,14611
Polymers262,8196
Non-polymers3275
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.610, 76.720, 199.120
Angle α, β, γ (deg.)90.00, 94.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
mRNA export factor MEX67


Mass: 55303.551 Da / Num. of mol.: 8 / Fragment: RRM domain, UNP residues 1-487
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MEX67, YPL169C, P2520 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99257
#2: Protein
mRNA transport regulator MTR2


Mass: 20802.506 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: MTR2, YKL186C / Production host: Escherichia coli (E. coli) / References: UniProt: P34232
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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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 publication for details. Precipitant was 10 % PEG 8000, 0.01 M zinc acetate, 0.1 M Tris-HCl pH 8.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.3→49.7 Å / Num. obs: 44836 / % possible obs: 97.4 % / Redundancy: 3.7 % / Net I/σ(I): 5.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 3.301→49.653 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2843 1990 4.97 %
Rwork0.2283 --
obs0.2311 40011 86.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.301→49.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18785 0 12 0 18797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419162
X-RAY DIFFRACTIONf_angle_d0.81325948
X-RAY DIFFRACTIONf_dihedral_angle_d13.0567113
X-RAY DIFFRACTIONf_chiral_restr0.0332941
X-RAY DIFFRACTIONf_plane_restr0.0043340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3007-3.38320.4103560.3085941X-RAY DIFFRACTION30
3.3832-3.47460.3564970.31341715X-RAY DIFFRACTION55
3.4746-3.57690.35471470.30022271X-RAY DIFFRACTION75
3.5769-3.69230.34051560.28192828X-RAY DIFFRACTION91
3.6923-3.82420.30261820.27063048X-RAY DIFFRACTION98
3.8242-3.97720.32311330.25833050X-RAY DIFFRACTION98
3.9772-4.15820.32111430.25153053X-RAY DIFFRACTION98
4.1582-4.37730.28141470.22383064X-RAY DIFFRACTION97
4.3773-4.65130.24911470.19572797X-RAY DIFFRACTION90
4.6513-5.01020.22461500.18822994X-RAY DIFFRACTION96
5.0102-5.51380.2711400.20273141X-RAY DIFFRACTION99
5.5138-6.31020.30321720.2173083X-RAY DIFFRACTION99
6.3102-7.9450.23991700.20963062X-RAY DIFFRACTION97
7.945-49.65880.21721500.17542974X-RAY DIFFRACTION91

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