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- PDB-4hzk: Crystal structure of free CRM1 (crystal form 2) -

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Basic information

Entry
Database: PDB / ID: 4hzk
TitleCrystal structure of free CRM1 (crystal form 2)
ComponentsCRM1 Nuclear transport receptor
KeywordsTRANSPORT PROTEIN / HEAT repeat protein / Nuclear export receptor
Function / homology
Function and homology information


nuclear export signal receptor activity / tRNA processing / protein export from nucleus / nucleus
Similarity search - Function
Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1/5 ...Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / 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 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 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
DepositionNov 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Data collection / Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRM1 Nuclear transport receptor
B: CRM1 Nuclear transport receptor


Theoretical massNumber of molelcules
Total (without water)249,2842
Polymers249,2842
Non-polymers00
Water0
1
A: CRM1 Nuclear transport receptor


Theoretical massNumber of molelcules
Total (without water)124,6421
Polymers124,6421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CRM1 Nuclear transport receptor


Theoretical massNumber of molelcules
Total (without water)124,6421
Polymers124,6421
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.820, 89.820, 316.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein CRM1 Nuclear transport receptor


Mass: 124642.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0002400 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0RZB7
Sequence detailsTHE AUTHORS STATE THAT THESE RESIDUES ARE WRONGLY ASSIGNED INTRONS IN THE CHAETOMIUM THERMOPHILUM ...THE AUTHORS STATE THAT THESE RESIDUES ARE WRONGLY ASSIGNED INTRONS IN THE CHAETOMIUM THERMOPHILUM VAR. THERMOPHILUM DSM1495 CRM1 SEQUENCE. MULTIPLE SEQUENCE ALIGNMENTS WITH SEQUENCES FROM MORE THAN 10 SPECIES SHOWED, THAT THESE TWO INTRONS, THAT HAVE BEEN ASSIGNED, EXACTLY CORRESPOND TO A PROTEIN SEQUENCE, WHICH IS PRESENT AND CONSERVED IN ALL OTHER CRM1 SPECIES. IN ADDITION, ISOLATION OF THE CRM1 GENE OUT OF A CHAETOMIUM THERMOPHILUM CDNA LIBRARY WITH APPROPRIATE PRIMERS AMPLIFIED THE GENE INCLUDING THE WRONGLY ASSIGNED INTRONS.

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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: 2.95 Å3/Da / Density % sol: 58.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 22% Polyacrylic acid 5,100, 20 mM MgCl2, 100 mM CHES 9.0, 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: 1.2395 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
RadiationMonochromator: Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2395 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.46
ReflectionResolution: 3.1→50 Å / Num. all: 51788 / Num. obs: 50204 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 98.94 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 17.23
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.1-3.20.5622.18148224576198.5
3.2-3.30.4152.89130344095198.5
3.3-3.50.2554.98222216837198.2
3.5-40.11910.23685211601197.8
4-4.250.06517.28122923881196.8
4.25-4.50.05120.7895543051195.3
4.5-4.750.04523.873582418195.7
4.75-140.02535.394303413258195.8
14-170.01664.42781226191.1
17-500.01573.38992261183.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO / Packing: 0
Highest resolutionLowest resolution
Rotation3.1 Å49.07 Å
Translation3.1 Å49.07 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GJX

3gjx


Resolution: 3.1→49.07 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1.98 / Phase error: 24.93 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 2048 4.08 %RANDOM
Rwork0.2161 ---
obs0.2192 50204 97.09 %-
all-51788 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 229.69 Å2 / Biso mean: 112.1053 Å2 / Biso min: 69.22 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16642 0 0 0 16642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416973
X-RAY DIFFRACTIONf_angle_d0.86722972
X-RAY DIFFRACTIONf_chiral_restr0.0572611
X-RAY DIFFRACTIONf_plane_restr0.0042957
X-RAY DIFFRACTIONf_dihedral_angle_d13.0516385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1005-3.1780.34251500.32613426357695
3.178-3.26390.34831430.31153492363594
3.2639-3.35990.30261520.29453505365795
3.3599-3.46840.31511500.28253505365594
3.4684-3.59230.26411520.27353514366694
3.5923-3.7360.29141410.26243465360694
3.736-3.90590.23041390.25373464360394
3.9059-4.11170.25371290.24623425355493
4.1117-4.36910.2581410.22883383352493
4.3691-4.70610.23731380.21663429356791
4.7061-5.1790.24381270.2023387351493
5.179-5.92670.26191490.21973447359693
5.9267-7.46080.22571370.21553434357193
7.4608-43.2050.18091490.15343304345390

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