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- PDB-4fgv: Crystal structure of free CRM1 (crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 4fgv
TitleCrystal structure of free CRM1 (crystal form 1)
ComponentsChromosome region maintenance 1 (CRM1) or Exportin 1 (Xpo1)
KeywordsTRANSPORT 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 / ribosomal large subunit export from nucleus / ribosomal small subunit export from nucleus / protein export from nucleus / nucleus / cytoplasm
Similarity search - Function
Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 ...Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Exportin-1 C-terminal domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.941 Å
AuthorsMonecke, T. / Neumann, P. / Dickmanns, A. / Ficner, R.
CitationJournal: 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
DepositionJun 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Chromosome region maintenance 1 (CRM1) or Exportin 1 (Xpo1)


Theoretical massNumber of molelcules
Total (without water)124,6421
Polymers124,6421
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.122, 139.073, 174.875
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chromosome region maintenance 1 (CRM1) or Exportin 1 (Xpo1)


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
Sequence detailsAUTHORS 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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.15 Å3/Da / Density % sol: 70.38 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2012 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.94-3.13.30.5451.41783654130.54584.5
3.1-3.293.60.38522194360430.38599
3.29-3.513.60.2083.72058856690.20899.1
3.51-3.83.60.1295.91938053210.12998.9
3.8-4.163.60.0868.71772448800.08698.8
4.16-4.653.60.06610.61606944320.06698.6
4.65-5.373.60.0738.61413739140.07398.2
5.37-6.573.60.0946.31192333290.09497.9
6.57-9.33.50.03714.2915925810.03797.2
9.3-48.0953.30.02621.3481014670.02695.1

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GJX

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
RfactorNum. reflection% reflection
Rfree0.2428 2149 5 %
Rwork0.2203 --
obs0.2214 43006 95.83 %
Solvent computationShrinkage 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 parametersBiso max: 336.98 Å2 / Biso mean: 93.0633 Å2 / Biso min: 12.93 Å2
Baniso -1Baniso -2Baniso -3
1--5.9326 Å2-0 Å20 Å2
2---6.908 Å20 Å2
3---12.8406 Å2
Refinement stepCycle: LAST / Resolution: 2.941→45.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8595 0 0 0 8595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048763
X-RAY DIFFRACTIONf_angle_d0.88411860
X-RAY DIFFRACTIONf_chiral_restr0.0571348
X-RAY DIFFRACTIONf_plane_restr0.0041530
X-RAY DIFFRACTIONf_dihedral_angle_d16.4313295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9411-3.00950.38041170.35792327244483
3.0095-3.08480.38641250.33572347247284
3.0848-3.16820.32621420.31052672281495
3.1682-3.26140.31121460.29192774292099
3.2614-3.36660.29281450.27592763290899
3.3666-3.48690.28371470.2482772291999
3.4869-3.62650.29371440.23512765290999
3.6265-3.79140.24711490.22062804295398
3.7914-3.99120.26331460.21862782292898
3.9912-4.24110.2331450.19052775292098
4.2411-4.56830.18451480.17482778292698
4.5683-5.02750.21470.16612796294398
5.0275-5.75380.23741480.2262801294998
5.7538-7.24460.27411480.25912824297297
7.2446-45.85860.17841520.17532877302995
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)
10.0148-0.01430.0040.02530.00360.00580.0150.15410.04230.13960.0280.0027-0.0265-0.0464-00.6565-0.1634-0.00510.24330.15810.547820.960622.4781-20.893
20.02870.02180.02620.0427-0.02540.0605-0.17420.06590.0697-0.04940.26490.00360.0890.047100.1849-0.1769-0.02980.27190.15810.23334.9646-19.7438-21.6949
30.0685-0.00890.04130.0617-0.12590.1802-0.12630.00360.0813-0.26080.20390.11870.0269-0.17810-0.18710.21380.070.0788-0.02690.07864.4025-23.121324.0309
4-0.02720.0059-0.02390.0115-0.02710.0206-0.13440.03720.0497-0.01970.0514-0.0196-0.0262-0.0668-00.54460.31630.06970.0276-0.0570.4177-8.84387.270716.0369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 22:286)A22 - 286
2X-RAY DIFFRACTION2chain 'A' and (resseq 287:568)A287 - 568
3X-RAY DIFFRACTION3chain 'A' and (resseq 569:973)A569 - 973
4X-RAY DIFFRACTION4chain 'A' and (resseq 974:1098)A974 - 1098

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