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- EMDB-2111: Negative structure of closed conformation of crm1 -

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Basic information

Entry
Database: EMDB / ID: EMD-2111
TitleNegative structure of closed conformation of crm1
Map dataReconstruction of Chaetomium thermophilum crm1 in closed conformation
Sample
  • Sample: crm1 closed conformation
  • Protein or peptide: crm1
Keywordscrm1 / closed conformation
Biological speciesChaetomium thermophilum (fungus)
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
AuthorsMonecke T / Haselbach D / Neumann P / Thomson E / Hurt E / Stark H / 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
DepositionMay 31, 2012-
Header (metadata) releaseOct 3, 2012-
Map releaseJan 23, 2013-
UpdateJan 23, 2013-
Current statusJan 23, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2111.png

Downloads & links

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Map

FileDownload / File: emd_2111.map.gz / Format: CCP4 / Size: 602.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Chaetomium thermophilum crm1 in closed conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.7 Å/pix.
x 54 pix.
= 199.8 Å		3.7 Å/pix.
x 54 pix.
= 199.8 Å		3.7 Å/pix.
x 54 pix.
= 199.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.04 / Movie #1: 0.025
Minimum - Maximum-0.21286955 - 1.10374773
Average (Standard dev.)0.00379507 (±0.04504067)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions545454
Spacing545454
CellA=B=C: 199.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.73.73.7
M x/y/z545454
origin x/y/z0.0000.0000.000
length x/y/z199.800199.800199.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS545454
D min/max/mean-0.2131.1040.004

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Supplemental data

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Sample components

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Entire : crm1 closed conformation

EntireName: crm1 closed conformation
Components
  • Sample: crm1 closed conformation
  • Protein or peptide: crm1

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Supramolecule #1000: crm1 closed conformation

SupramoleculeName: crm1 closed conformation / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: crm1

MacromoleculeName: crm1 / type: protein_or_peptide / ID: 1 / Name.synonym: exportin1 Xpo1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Chaetomium thermophilum (fungus)
Molecular weightTheoretical: 120 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET24d

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 150 mM NaCl, 20 mM HEPES/NaOH pH 7.5, 2 mM MgCl2, 4 mM DTT
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 2% w/v uranyl formate for 60 seconds
GridDetails: 200 mesh copper grid with thin carbon support, freshly floated on protein solution
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 298 K
DateMar 21, 2012
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Number real images: 300
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 155000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

CTF correctionDetails: each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: imagic / Number images used: 13000

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