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- PDB-1w9c: Proteolytic fragment of CRM1 spanning six C-terminal HEAT repeats -

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Basic information

Entry
Database: PDB / ID: 1w9c
TitleProteolytic fragment of CRM1 spanning six C-terminal HEAT repeats
ComponentsCRM1 PROTEIN
KeywordsNUCLEAR PROTEIN / EXPORTIN 1 / NUCLEAR EXPORT COMPLEX
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of centrosome duplication / nuclear export signal receptor activity / regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / NEP/NS2 Interacts with the Cellular Export Machinery / nucleocytoplasmic transport / Maturation of hRSV A proteins ...HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of centrosome duplication / nuclear export signal receptor activity / regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / NEP/NS2 Interacts with the Cellular Export Machinery / nucleocytoplasmic transport / Maturation of hRSV A proteins / protein localization to nucleus / ribosomal large subunit export from nucleus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / mRNA export from nucleus / ribosomal subunit export from nucleus / Cyclin A/B1/B2 associated events during G2/M transition / Cajal body / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / NPAS4 regulates expression of target genes / protein export from nucleus / Downregulation of TGF-beta receptor signaling / Deactivation of the beta-catenin transactivating complex / RHO GTPases Activate Formins / Heme signaling / MAPK6/MAPK4 signaling / kinetochore / small GTPase binding / Separation of Sister Chromatids / ribosome biogenesis / nuclear envelope / nuclear membrane / ribonucleoprotein complex / intracellular membrane-bounded organelle / nucleolus / protein-containing complex / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
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 / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsPetosa, C. / Schoehn, G. / Askjaer, P. / Bauer, U. / Moulin, M. / Steuerwald, U. / Soler-Lopez, M. / Baudin, F. / Mattaj, I.W. / Muller, C.W.
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 8, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2004Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Nov 13, 2019Group: Data collection / Database references / Other / Category: pdbx_database_related / pdbx_database_status
Item: _pdbx_database_related.content_type / _pdbx_database_status.status_code_sf
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRM1 PROTEIN
B: CRM1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)72,5442
Polymers72,5442
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)118.870, 62.870, 114.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, 0.002, 0.005), (0.002, -1, -0.005), (0.005, 0.005, -1)
Vector: -0.27684, -50.4442, 57.18188)

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Components

#1: Protein CRM1 PROTEIN / EXPORTIN 1


Mass: 36271.750 Da / Num. of mol.: 2 / Fragment: C-TERMINAL SIX HEAT REPEATS, RESIDUES 707-1027
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O14980
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 35395 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.6 / % possible all: 73.3

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.3→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1788 5.1 %RANDOM
Rwork0.229 ---
obs0.229 35395 90.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.3285 Å2 / ksol: 0.356663 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-10.55 Å20 Å20 Å2
2---5.51 Å20 Å2
3----5.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 0 192 5300
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.441.5
X-RAY DIFFRACTIONc_mcangle_it5.162
X-RAY DIFFRACTIONc_scbond_it5.782
X-RAY DIFFRACTIONc_scangle_it7.822.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 199 4.9 %
Rwork0.362 3860 -
obs--63.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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