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- PDB-4bsm: Crystal structure of the Nuclear Export Receptor CRM1 (exportin-1... -

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Basic information

Entry
Database: PDB / ID: 4bsm
TitleCrystal structure of the Nuclear Export Receptor CRM1 (exportin-1) lacking the C-terminal helical extension at 4.5A
ComponentsEXPORTIN-1
KeywordsPROTEIN TRANSPORT / HEAT REPEAT PROTEIN / IMPORTIN-BETA SUPERFAMILY / NUCLEOCYTOPLASMIC TRANSPORT OF PROTEIN AND RNP CARGOES
Function / homology
Function and homology information


cellular response to triglyceride / cellular response to salt / 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 ...cellular response to triglyceride / cellular response to salt / 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 / ribosomal large subunit export from nucleus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / protein localization to nucleus / mRNA export from nucleus / ribosomal subunit export from nucleus / Cajal body / Cyclin A/B1/B2 associated events during G2/M transition / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / NPAS4 regulates expression of target genes / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Transcriptional and post-translational regulation of MITF-M expression and activity / protein export from nucleus / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / Deactivation of the beta-catenin transactivating complex / Heme signaling / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / kinetochore / small GTPase binding / Separation of Sister Chromatids / nuclear envelope / ribosome biogenesis / nuclear membrane / DNA-binding transcription factor binding / response to xenobiotic stimulus / ribonucleoprotein complex / protein domain specific binding / intracellular membrane-bounded organelle / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 ...Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsDian, C. / Bernaudat, F. / Langer, K. / Oliva, M.F. / Fornerod, M. / Schoehn, G. / Muller, C.W. / Petosa, C.
CitationJournal: Structure / Year: 2013
Title: Structure of a Truncation Mutant of the Nuclear Export Factor Crm1 Provides Insights Into the Auto-Inhibitory Role of its C-Terminal Helix.
Authors: Dian, C. / Bernaudat, F. / Langer, K. / Oliva, M.F. / Fornerod, M. / Schoehn, G. / Muller, C.W. / Petosa, C.
History
DepositionJun 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXPORTIN-1


Theoretical massNumber of molelcules
Total (without water)118,8631
Polymers118,8631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.640, 248.330, 107.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein EXPORTIN-1 / HUMAN NUCLEAR EXPORT RECEPTOR CRM1 / EXP1 / CHROMOSOME REGION MAINTENANCE 1 PROTEIN HOMOLOG / EXPORTIN1


Mass: 118863.172 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-1032
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQE60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 / References: UniProt: O14980

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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: 4.26 Å3/Da / Density % sol: 71.15 % / Description: NONE
Crystal growpH: 8
Details: BY MIXING EQUAL VOLUMES OF PROTEIN (8-10 MG/ML) AND RESERVOIR SOLUTION 0.5 M DISODIUM TARTRATE, 50 MM TRIS PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9754
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 4.5→48.59 Å / Num. obs: 12112 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 145.78 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.1
Reflection shellResolution: 4.5→4.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1056)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GB8

3gb8


Resolution: 4.5→48.589 Å / SU ML: 0.5 / σ(F): 1.33 / Phase error: 26.69 / Stereochemistry target values: ML
Details: RESIDUES 3-19 AND 932-1017 WERE MODELED AS POLYALANINE OR POLYGLYCINE DUE TO AMBIGUOUS DENSITY
RfactorNum. reflection% reflection
Rfree0.2692 1212 10.03 %
Rwork0.229 --
obs0.2329 12089 99.79 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.5→48.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6854 0 0 0 6854
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036978
X-RAY DIFFRACTIONf_angle_d0.7419473
X-RAY DIFFRACTIONf_dihedral_angle_d14.5132458
X-RAY DIFFRACTIONf_chiral_restr0.0541113
X-RAY DIFFRACTIONf_plane_restr0.0031207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5001-4.68010.3051330.25451169X-RAY DIFFRACTION100
4.6801-4.89290.27711300.21641189X-RAY DIFFRACTION100
4.8929-5.15060.27241320.22121200X-RAY DIFFRACTION100
5.1506-5.47290.30591310.23791183X-RAY DIFFRACTION100
5.4729-5.89480.27091350.24741202X-RAY DIFFRACTION100
5.8948-6.48680.31811400.26981197X-RAY DIFFRACTION100
6.4868-7.42260.28811290.24941226X-RAY DIFFRACTION100
7.4226-9.34080.25561350.19711231X-RAY DIFFRACTION100
9.3408-48.59180.24041470.22421280X-RAY DIFFRACTION99

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