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- PDB-3gb8: Crystal structure of CRM1/Snurportin-1 complex -

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Basic information

Entry
Database: PDB / ID: 3gb8
TitleCrystal structure of CRM1/Snurportin-1 complex
Components
  • Exportin-1
  • Snurportin-1
KeywordsTRANSPORT PROTEIN / Nuclear Transport Complex / Host-virus interaction / mRNA transport / Nucleus / Phosphoprotein / Protein transport / RNA-binding / Transport
Function / homology
Function and homology information


RNA import into nucleus / cellular response to triglyceride / cellular response to salt / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA cap binding / snRNA import into nucleus / nuclear export signal receptor activity / Rev-mediated nuclear export of HIV RNA ...RNA import into nucleus / cellular response to triglyceride / cellular response to salt / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA cap binding / snRNA import into nucleus / nuclear export signal receptor activity / Rev-mediated nuclear export of HIV RNA / NEP/NS2 Interacts with the Cellular Export Machinery / nucleocytoplasmic transport / nuclear import signal receptor activity / Maturation of hRSV A proteins / protein complex oligomerization / nuclear pore / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / ribosomal large subunit export from nucleus / protein export from nucleus / Cajal body / ribosomal subunit export from nucleus / mRNA export from nucleus / Cyclin A/B1/B2 associated events during G2/M transition / NPAS4 regulates expression of target genes / cytoskeleton organization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ribosomal small subunit export from nucleus / Transcriptional and post-translational regulation of MITF-M expression and activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein import into nucleus / Resolution of Sister Chromatid Cohesion / Downregulation of TGF-beta receptor signaling / Heme signaling / Maturation of DENV proteins / protein tetramerization / RHO GTPases Activate Formins / Deactivation of the beta-catenin transactivating complex / MAPK6/MAPK4 signaling / small GTPase binding / kinetochore / Separation of Sister Chromatids / nuclear envelope / ribosome biogenesis / snRNP Assembly / DNA-binding transcription factor binding / response to xenobiotic stimulus / ribonucleoprotein complex / protein domain specific binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #450 / Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Snurportin1, m3G cap-binding domain / DNA ligase/mRNA capping enzyme / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #450 / Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Snurportin1, m3G cap-binding domain / DNA ligase/mRNA capping enzyme / 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 / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / D-amino Acid Aminotransferase; Chain A, domain 1 / Helix non-globular / Special / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Exportin-1 / Snurportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsDong, X. / Biswas, A. / Suel, K.E. / Jackson, L.K. / Martinez, R. / Gu, H. / Chook, Y.M.
Citation
Journal: Nature / Year: 2009
Title: Structural basis for leucine-rich nuclear export signal recognition by CRM1.
Authors: Dong, X. / Biswas, A. / Suel, K.E. / Jackson, L.K. / Martinez, R. / Gu, H. / Chook, Y.M.
#1: Journal: To be Published / Year: 2009
Title: Structural basis of assembly and disassembly of the CRM1 nuclear export complex
Authors: Dong, X. / Biswas, A. / Chook, Y.M.
History
DepositionFeb 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exportin-1
B: Snurportin-1


Theoretical massNumber of molelcules
Total (without water)161,2852
Polymers161,2852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-11.8 kcal/mol
Surface area55120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.400, 250.400, 190.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Exportin-1 / Exp1 / Chromosome region maintenance 1 protein homolog


Mass: 123518.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRM1, XPO1 / Plasmid: pGEXTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14980
#2: Protein Snurportin-1 / RNA U transporter 1


Mass: 37766.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNUT1, SNUPN, SPN1 / Plasmid: pGEXTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95149

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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: 5.34 Å3/Da / Density % sol: 76.97 %
Description: The structure factor file contains Bijvoet pairs.
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 8% PEG 8000, 0.2M Magnesium chloride, 0.1M MES pH 6.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935, 0.97945, 0.97167
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2008
Details: LN2 cooled first crystal, sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.979451
30.971671
ReflectionResolution: 2.9→50 Å / Num. obs: 73476 / % possible obs: 99.1 % / Redundancy: 7.4 % / Rsym value: 0.083 / Net I/σ(I): 25
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.58 / % possible all: 99.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→47.67 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.996 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Bijvoet pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3667 5 %RANDOM
Rwork0.236 ---
obs0.238 69818 94.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.05 Å2 / Biso mean: 44.541 Å2 / Biso min: 4.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9750 0 0 0 9750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229960
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.95313517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21351216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32724.577461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.45151718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5661549
X-RAY DIFFRACTIONr_chiral_restr0.1020.21543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027481
X-RAY DIFFRACTIONr_nbd_refined0.2460.25051
X-RAY DIFFRACTIONr_nbtor_refined0.3160.26931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2358
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3180.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.22
X-RAY DIFFRACTIONr_mcbond_it0.6841.56240
X-RAY DIFFRACTIONr_mcangle_it1.24929904
X-RAY DIFFRACTIONr_scbond_it1.61834158
X-RAY DIFFRACTIONr_scangle_it2.7654.53613
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 236 -
Rwork0.306 4608 -
all-4844 -
obs--85.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29020.08770.07260.0302-0.02330.56430.0686-0.00520.0408-0.0745-0.04460.06120.1573-0.1551-0.0240.02920.0247-0.0630.22280.00420.0031-5.4843107.95456.8971
25.4897-1.5225-0.84710.50160.38550.41610.35090.7323-0.13220.1028-0.1999-0.06560.0204-0.2163-0.151-0.07020.1-0.0060.2305-0.0238-0.118645.5674109.367567.644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 1061
2X-RAY DIFFRACTION2B0 - 293

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