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- PDB-4wpm: Structure of the Chaetomium thermophilum Mex67:Mtr2 Complex -

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Basic information

Entry
Database: PDB / ID: 4wpm
TitleStructure of the Chaetomium thermophilum Mex67:Mtr2 Complex
ComponentsmRNA export protein
KeywordsTRANSPORT PROTEIN / mRNA nuclear export
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 / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Putative mRNA export protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 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 20, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 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

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Assembly

Deposited unit
A: mRNA export protein
B: mRNA export protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1795
Polymers26,8902
Non-polymers2883
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-28 kcal/mol
Surface area9780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.731, 29.796, 52.453
Angle α, β, γ (deg.)90.00, 96.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein mRNA export protein


Mass: 13445.239 Da / Num. of mol.: 2 / Fragment: RRM domain, UNP residues 93-200
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 (E. coli) / References: UniProt: G0SET4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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

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: DECTRIS 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: 2.4→40.7 Å / Num. obs: 7066 / % possible obs: 99.6 % / Redundancy: 4 % / Net I/σ(I): 5.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2.4→40.679 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 323 4.58 %
Rwork0.2286 --
obs0.2294 7056 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→40.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1321 0 15 53 1389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021351
X-RAY DIFFRACTIONf_angle_d0.6771820
X-RAY DIFFRACTIONf_dihedral_angle_d13.044512
X-RAY DIFFRACTIONf_chiral_restr0.029208
X-RAY DIFFRACTIONf_plane_restr0.002229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-3.02370.28471590.28053320X-RAY DIFFRACTION99
3.0237-40.68460.2291640.20343413X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.03330.0395-0.03120.0441-0.03640.02770.0286-0.146-0.09110.0486-0.0705-0.0056-0.1341-0.0206-0.00380.15810.00740.00170.13690.04220.179625.8673-2.037316.2746
20.00920.0120.01490.05380.01530.02410.0035-0.0201-0.0094-0.01410.0218-0.07680.01650.01870.01590.10960.0238-0.0270.0695-0.0480.112635.1802-5.35619.263
30.1699-0.0297-0.0760.00540.01180.03520.0974-0.08310.0114-0.183-0.1021-0.11480.01490.05850.04240.12330.02190.07770.11210.03060.08830.94644.16679.8652
40.3822-0.1676-0.22810.19070.15850.17070.08890.10760.0187-0.03920.024-0.09750.0064-0.09760.14910.1677-0.0121-0.04010.0454-0.01290.053324.80242.668710.0348
50.10490.1141-0.12290.2417-0.09540.15370.0932-0.00920.06440.09370.03550.0230.0033-0.00140.06820.08580.0382-0.00430.1892-0.01120.23787.356711.647825.9834
60.0018-0.00390.00310.009-0.0080.00620.01060.04730.0336-0.02-0.01710.0222-0.0113-0.00230.01320.05250.0784-0.07480.1574-0.01370.16365.508316.896918.252
70.0038-0.0044-0.00150.01030.00590.0033-0.0739-0.0322-0.01050.1241-0.030.04740.0597-0.0605-0.00010.4828-0.1318-0.1330.36960.04740.33834.092411.981612.1337
80.0229-0.00640.01960.0704-0.030.0413-0.0977-0.0871-0.0326-0.0594-0.09550.01870.009-0.024-0.04960.1179-0.01880.01380.1192-0.0240.117710.58888.927519.6393
90.0351-0.00570.09190.0894-0.12030.3704-0.0450.0056-0.05020.007-0.0341-0.0103-0.02320.0913-0.01060.115-0.07290.10520.04240.01540.246510.23330.3522.7885
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 98 through 118 )
2X-RAY DIFFRACTION2chain 'A' and (resid 119 through 137 )
3X-RAY DIFFRACTION3chain 'A' and (resid 138 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 182 )
5X-RAY DIFFRACTION5chain 'B' and (resid 97 through 118 )
6X-RAY DIFFRACTION6chain 'B' and (resid 119 through 129 )
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 171 )
9X-RAY DIFFRACTION9chain 'B' and (resid 172 through 181 )

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