+Open data
-Basic information
Entry | Database: PDB / ID: 4fgv | ||||||
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Title | Crystal structure of free CRM1 (crystal form 1) | ||||||
Components | Chromosome region maintenance 1 (CRM1) or Exportin 1 (Xpo1) | ||||||
Keywords | TRANSPORT PROTEIN / HEAT repeat protein / Importin-beta superfamily / Nuclear export of numerous protein and RNP cargoes | ||||||
Function / homology | Function and homology information nuclear export signal receptor activity / tRNA processing / protein export from nucleus / nucleus Similarity search - Function | ||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.941 Å | ||||||
Authors | Monecke, T. / Neumann, P. / Dickmanns, A. / Ficner, R. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2013 Title: Structural basis for cooperativity of CRM1 export complex formation. Authors: Thomas Monecke / David Haselbach / Béla Voß / Andreas Russek / Piotr Neumann / Emma Thomson / Ed Hurt / Ulrich Zachariae / Holger Stark / Helmut Grubmüller / Achim Dickmanns / Ralf Ficner / Abstract: In eukaryotes, the nucleocytoplasmic transport of macromolecules is mainly mediated by soluble nuclear transport receptors of the karyopherin-β superfamily termed importins and exportins. The highly ...In eukaryotes, the nucleocytoplasmic transport of macromolecules is mainly mediated by soluble nuclear transport receptors of the karyopherin-β superfamily termed importins and exportins. The highly versatile exportin chromosome region maintenance 1 (CRM1) is essential for nuclear depletion of numerous structurally and functionally unrelated protein and ribonucleoprotein cargoes. CRM1 has been shown to adopt a toroidal structure in several functional transport complexes and was thought to maintain this conformation throughout the entire nucleocytoplasmic transport cycle. We solved crystal structures of free CRM1 from the thermophilic eukaryote Chaetomium thermophilum. Surprisingly, unbound CRM1 exhibits an overall extended and pitched superhelical conformation. The two regulatory regions, namely the acidic loop and the C-terminal α-helix, are dramatically repositioned in free CRM1 in comparison with the ternary CRM1-Ran-Snurportin1 export complex. Single-particle EM analysis demonstrates that, in a noncrystalline environment, free CRM1 exists in equilibrium between extended, superhelical and compact, ring-like conformations. Molecular dynamics simulations show that the C-terminal helix plays an important role in regulating the transition from an extended to a compact conformation and reveal how the binding site for nuclear export signals of cargoes is modulated by different CRM1 conformations. Combining these results, we propose a model for the cooperativity of CRM1 export complex assembly involving the long-range allosteric communication between the distant binding sites of GTP-bound Ran and cargo. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fgv.cif.gz | 430.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fgv.ent.gz | 354.5 KB | Display | PDB format |
PDBx/mmJSON format | 4fgv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/4fgv ftp://data.pdbj.org/pub/pdb/validation_reports/fg/4fgv | HTTPS FTP |
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-Related structure data
Related structure data | 2110C 2111C 4hzkC 3gjxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 124642.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal GST tag Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0RZB7*PLUS |
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Sequence details | AUTHORS STATE THAT THE UNP REFERENCE G0RZB7 IS INCORRECT WITH THE REMOVAL OF TWO REGIONS. THE ...AUTHORS STATE THAT THE UNP REFERENCE G0RZB7 IS INCORRECT WITH THE REMOVAL OF TWO REGIONS. THE CURRENT SEQUENCE IN THIS MODEL IS CORRECT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 22% Polyacrylic acid 5100, 20 mM MgCl2, 0.1 M CHES/NaOH pH 9.0, 4% (v/v) 2,5 hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2012 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.941→46.358 Å / Num. all: 43049 / Num. obs: 43049 / % possible obs: 96.4 % / Redundancy: 3.6 % / Rsym value: 0.087 / Net I/σ(I): 9.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3GJX Resolution: 2.941→45.853 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8164 / SU ML: 0.43 / σ(F): 0 / Phase error: 25.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.069 Å2 / ksol: 0.313 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 336.98 Å2 / Biso mean: 93.0633 Å2 / Biso min: 12.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.941→45.853 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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