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- EMDB-1099: Architecture of CRM1/Exportin1 suggests how cooperativity is achi... -

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Basic information

Entry
Database: EMDB / ID: EMD-1099
TitleArchitecture of CRM1/Exportin1 suggests how cooperativity is achieved during formation of a nuclear export complex.
Map data3D image reconstruction of human CRM1
Sample
  • Sample: human CRM1
  • Protein or peptide: CRM1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 Å
AuthorsPetosa C
CitationJournal: Mol Cell / Year: 2004
Title: Architecture of CRM1/Exportin1 suggests how cooperativity is achieved during formation of a nuclear export complex.
Authors: Carlo Petosa / Guy Schoehn / Peter Askjaer / Ulrike Bauer / Martine Moulin / Ulrich Steuerwald / Montserrat Soler-López / Florence Baudin / Iain W Mattaj / Christoph W Müller /
Abstract: CRM1/Exportin1 mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES) by forming a cooperative ternary complex with the NES-bearing substrate and the small GTPase ...CRM1/Exportin1 mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES) by forming a cooperative ternary complex with the NES-bearing substrate and the small GTPase Ran. We present a structural model of human CRM1 based on a combination of X-ray crystallography, homology modeling, and electron microscopy. The architecture of CRM1 resembles that of the import receptor transportin1, with 19 HEAT repeats and a large loop implicated in Ran binding. Residues critical for NES recognition are identified adjacent to the cysteine residue targeted by leptomycin B (LMB), a specific CRM1 inhibitor. We present evidence that a conformational change of the Ran binding loop accounts for the cooperativity of Ran- and substrate binding and for the selective enhancement of CRM1-mediated export by the cofactor RanBP3. Our findings indicate that a single architectural and mechanistic framework can explain the divergent effects of RanGTP on substrate binding by many import and export receptors.
History
DepositionOct 7, 2004-
Header (metadata) releaseOct 8, 2004-
Map releaseDec 7, 2004-
UpdateApr 16, 2014-
Current statusApr 16, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9.836062
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 9.836062
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1099.gif

Downloads & links

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Map

FileDownload / File: emd_1099.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D image reconstruction of human CRM1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
3.5 Å/pix.
x 64 pix.
= 224. Å		3.5 Å/pix.
x 64 pix.
= 224. Å		3.5 Å/pix.
x 64 pix.
= 224. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.5 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 3.32 / Movie #1: 9.836062
Minimum - Maximum-9.97268 - 24.726800000000001
Average (Standard dev.)0.168238 (±2.10376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 224 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z224.000224.000224.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S213
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-9.97324.7270.168

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Supplemental data

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Sample components

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Entire : human CRM1

EntireName: human CRM1
Components
  • Sample: human CRM1
  • Protein or peptide: CRM1

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Supramolecule #1000: human CRM1

SupramoleculeName: human CRM1 / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 123.385 KDa

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Macromolecule #1: CRM1

MacromoleculeName: CRM1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human
Molecular weightExperimental: 123.385 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pQE-60

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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

Concentration0.1 mg/mL
BufferpH: 7.5 / Details: 50 mM NaCl, 20 mM HEPES
StainingType: NEGATIVE
Details: Grids with adsorbed protein floated on 1% (w/v) sodium silicotungstate pH 7
GridDetails: 400 mesh copper/
VitrificationCryogen name: NONE

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Electron microscopy

MicroscopeJEOL 1200EXII
TemperatureAverage: 293 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 200,000 times magnification
DetailsLow dose. Microscope JEOL 1200 EX II.
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 6 / Average electron dose: 10 e/Å2 / Od range: 1 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsCalibrated magnification: 39950 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder: side entry room temperature holder / Specimen holder model: OTHER

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: back projection of 196 class average using Spider / Number images used: 5000
Final angle assignmentDetails: SPIDER : Theta : 180 degrees, phi 90 degrees
Final two d classificationNumber classes: 196

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Atomic model buiding 1

Initial modelPDB ID:

1w9c

SoftwareName: Situs, Colores
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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