+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2274 | |||||||||
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Title | human crm1 extended conformation | |||||||||
Map data | extended conformation of human crm1 | |||||||||
Sample |
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Keywords | Xpo-1 / crm1 / human | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 20.0 Å | |||||||||
Authors | Doelker N / Blanchet CE / Haselbach D / Voss B / Kappel C / Monecke T / Svergun D / Stark H / Ficner R / Zacharias U ...Doelker N / Blanchet CE / Haselbach D / Voss B / Kappel C / Monecke T / Svergun D / Stark H / Ficner R / Zacharias U / Grubmueller H / Dickmanns A | |||||||||
Citation | Journal: Structure / Year: 2013 Title: Structural determinants and mechanism of mammalian CRM1 allostery. Authors: Nicole Dölker / Clement E Blanchet / Béla Voß / David Haselbach / Christian Kappel / Thomas Monecke / Dmitri I Svergun / Holger Stark / Ralf Ficner / Ulrich Zachariae / Helmut Grubmüller / Achim Dickmanns / Abstract: Proteins carrying nuclear export signals cooperatively assemble with the export factor CRM1 and the effector protein RanGTP. In lower eukaryotes, this cooperativity is coupled to CRM1 conformational ...Proteins carrying nuclear export signals cooperatively assemble with the export factor CRM1 and the effector protein RanGTP. In lower eukaryotes, this cooperativity is coupled to CRM1 conformational changes; however, it is unknown if mammalian CRM1 maintains its compact conformation or shows similar structural flexibility. Here, combinations of small-angle X-ray solution scattering and electron microscopy experiments with molecular dynamics simulations reveal pronounced conformational flexibility in mammalian CRM1 and demonstrate that RanGTP binding induces association of its N- and C-terminal regions to form a toroid structure. The CRM1 toroid is stabilized mainly by local interactions between the terminal regions, rather than by global strain. The CRM1 acidic loop is key in transmitting the effect of this RanGTP-induced global conformational change to the NES-binding cleft by shifting its population to the open state, which displays enhanced cargo affinity. Cooperative CRM1 export complex assembly thus constitutes a highly dynamic process, encompassing an intricate interplay of global and local structural changes. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2274.map.gz | 461.8 KB | EMDB map data format | |
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Header (meta data) | emd-2274-v30.xml emd-2274.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | EMD-2274.png | 97 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2274 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2274 | HTTPS FTP |
-Validation report
Summary document | emd_2274_validation.pdf.gz | 204.3 KB | Display | EMDB validaton report |
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Full document | emd_2274_full_validation.pdf.gz | 203.3 KB | Display | |
Data in XML | emd_2274_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2274 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2274 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2274.map.gz / Format: CCP4 / Size: 602.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | extended conformation of human crm1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : extended conformation of human crm1
Entire | Name: extended conformation of human crm1 |
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Components |
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-Supramolecule #1000: extended conformation of human crm1
Supramolecule | Name: extended conformation of human crm1 / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: monomer / Number unique components: 1 |
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Molecular weight | Theoretical: 110 KDa |
-Macromolecule #1: xpo-1
Macromolecule | Name: xpo-1 / type: protein_or_peptide / ID: 1 / Name.synonym: crm1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human |
Molecular weight | Theoretical: 110 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 Details: 50mM NaCl, 50 mM HEPES/NaOH pH 7.5, 2 mM MgOAc and 2 mM DTT |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated on 2% w/v uranyl acetate for 20 seconds. |
Grid | Details: 200 mesh cupper grid with thin and thick carbon support |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Date | Sep 28, 2012 |
Image recording | Number real images: 250 |
Electron beam | Acceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 122000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
CTF correction | Details: each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: imagic / Number images used: 19254 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |