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- EMDB-5564: Compact conformation of human crm1 -

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Basic information

Entry
Database: EMDB / ID: EMD-5564
TitleCompact conformation of human crm1
Map dataCompact human crm1
Sample
  • Sample: Compact conformation of human crm1
  • Protein or peptide: xpo-1
Keywordscompact conformation / crm1 / xpo1
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsDoelker N / Blanchet CE / Haselbach D / Voss B / Kappel C / Monecke T / Svergun D / Stark H / Ficner R / Zacharie U ...Doelker N / Blanchet CE / Haselbach D / Voss B / Kappel C / Monecke T / Svergun D / Stark H / Ficner R / Zacharie U / Grubmueller H / Dickmanns A
CitationJournal: 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
DepositionJan 7, 2013-
Header (metadata) releaseJun 5, 2013-
Map releaseOct 16, 2013-
UpdateOct 16, 2013-
Current statusOct 16, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5564_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5564.map.gz / Format: CCP4 / Size: 602.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCompact human crm1
Voxel sizeX=Y=Z: 3.7 Å
Density
Contour LevelBy AUTHOR: 0.28 / Movie #1: 0.18
Minimum - Maximum-0.5959112 - 2.60678411
Average (Standard dev.)-0.00034445 (±0.13915393)
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-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS545454
D min/max/mean-0.5962.607-0.000

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Supplemental data

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Sample components

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Entire : Compact conformation of human crm1

EntireName: Compact conformation of human crm1
Components
  • Sample: Compact conformation of human crm1
  • Protein or peptide: xpo-1

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Supramolecule #1000: Compact conformation of human crm1

SupramoleculeName: Compact conformation of human crm1 / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 110 KDa

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Macromolecule #1: xpo-1

MacromoleculeName: xpo-1 / type: protein_or_peptide / ID: 1 / Name.synonym: crm1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightTheoretical: 110 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration0.2 mg/mL
BufferpH: 7.5
Details: 50 mM NaCl, 50 mM HEPES/NaOH, pH 7.5, 2 mM MgOAc, 2 mM DTT
StainingType: NEGATIVE
Details: Grids with adsorbed protein were floated on 2% w/v uranyl acetate for 20 seconds.
GridDetails: 200 mesh copper grid with thin carbon support
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
DateSep 28, 2012
Image recordingNumber real images: 250

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Image processing

CTF correctionDetails: each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: imagic / Number images used: 22854

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Atomic model buiding 1

Initial modelPDB ID:

3gb8

SoftwareName: Chimera
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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