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- PDB-3fex: Crystal structure of the CBC-importin alpha complex. -

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Basic information

Entry
Database: PDB / ID: 3fex
TitleCrystal structure of the CBC-importin alpha complex.
Components
  • Importin subunit alpha-2
  • Nuclear cap-binding protein subunit 1
  • Nuclear cap-binding protein subunit 2
KeywordsTRANSLATION / PROTEIN TRANSPORT / Cap binding complex / importin alpha / nuclear transport / Coiled coil / mRNA transport / Nucleus / Phosphoprotein / RNA-binding / Acetylation / Cytoplasm / Host-virus interaction
Function / homology
Function and homology information


positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / positive regulation of RNA export from nucleus / Sensing of DNA Double Strand Breaks / regulation of DNA recombination / cap-dependent translational initiation ...positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / positive regulation of RNA export from nucleus / Sensing of DNA Double Strand Breaks / regulation of DNA recombination / cap-dependent translational initiation / positive regulation of mRNA 3'-end processing / Processing of Intronless Pre-mRNAs / RNA cap binding / snRNA binding / entry of viral genome into host nucleus through nuclear pore complex via importin / regulation of mRNA processing / primary miRNA processing / miRNA-mediated post-transcriptional gene silencing / SLBP independent Processing of Histone Pre-mRNAs / positive regulation of viral life cycle / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulatory ncRNA-mediated post-transcriptional gene silencing / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / alternative mRNA splicing, via spliceosome / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / mRNA 3'-end processing / nuclear localization sequence binding / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA catabolic process / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / nuclear import signal receptor activity / regulation of translational initiation / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Signaling by FGFR2 IIIa TM / CaMK IV-mediated phosphorylation of CREB / DNA metabolic process / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / 7-methylguanosine mRNA capping / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of type I interferon production / mRNA export from nucleus / Formation of HIV-1 elongation complex containing HIV-1 Tat / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of HIV elongation complex in the absence of HIV Tat / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / ISG15 antiviral mechanism / Regulation of expression of SLITs and ROBOs / histone deacetylase binding / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / host cell / positive regulation of cell growth / snRNP Assembly / nuclear membrane / defense response to virus / molecular adaptor activity / Estrogen-dependent gene expression / ciliary basal body / ribonucleoprotein complex / Golgi membrane / mRNA binding / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) ...MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Importin subunit alpha-1 / Nuclear cap-binding protein subunit 2 / Nuclear cap-binding protein subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.549 Å
AuthorsDias, S.M.G. / Ambrosio, A.L.B. / Cerione, R.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: The molecular basis for the regulation of the cap-binding complex by the importins.
Authors: Dias, S.M. / Wilson, K.F. / Rojas, K.S. / Ambrosio, A.L. / Cerione, R.A.
History
DepositionDec 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Nuclear cap-binding protein subunit 1
B: Nuclear cap-binding protein subunit 2
C: Importin subunit alpha-2


Theoretical massNumber of molelcules
Total (without water)160,7683
Polymers160,7683
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nuclear cap-binding protein subunit 1
B: Nuclear cap-binding protein subunit 2


Theoretical massNumber of molelcules
Total (without water)109,9882
Polymers109,9882
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-2 kcal/mol
Surface area38450 Å2
MethodPISA
3
C: Importin subunit alpha-2


Theoretical massNumber of molelcules
Total (without water)50,7801
Polymers50,7801
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.508, 102.051, 107.878
Angle α, β, γ (deg.)90.00, 108.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nuclear cap-binding protein subunit 1 / Cap binding protein 80 / 80 kDa nuclear cap-binding protein / NCBP 80 kDa subunit / CBP80


Mass: 91960.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBP80, NCBP, NCBP1 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: Q09161
#2: Protein Nuclear cap-binding protein subunit 2 / Cap binding protein 20 / 20 kDa nuclear cap-binding protein / NCBP 20 kDa subunit / CBP20 / NCBP- ...Cap binding protein 20 / 20 kDa nuclear cap-binding protein / NCBP 20 kDa subunit / CBP20 / NCBP-interacting protein 1 / NIP1 / Cell proliferation-inducing gene 55 protein


Mass: 18028.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBP20, NCBP2, PIG55 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: P52298
#3: Protein Importin subunit alpha-2 / Importin alpha 1 / Karyopherin subunit alpha-2 / SRP1-alpha / RAG cohort protein 1


Mass: 50779.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA2, RCH1, SRP1 / Plasmid: PET 30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52292

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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: 2.71 Å3/Da / Density % sol: 54.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM KCl, 12% PEG 8000, 100 mM Tris-HCl pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 4, 2007 / Details: Mirror
RadiationMonochromator: Horizontal bHorizontal bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 3.5→15.652 Å / Num. all: 19814 / Num. obs: 18110 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 74.05 Å2 / Rmerge(I) obs: 0.161 / Rsym value: 0.161 / Net I/σ(I): 12.3
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.58 / Rsym value: 0.428 / % possible all: 92.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FEY

3fey


Resolution: 3.549→15.652 Å / SU ML: 0.54 / Isotropic thermal model: Group ADP / σ(F): 1.34 / Phase error: 30.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2924 927 5.13 %
Rwork0.2173 --
obs0.2212 18063 87.5 %
all-20643 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.202 Å2 / ksol: 0.252 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.4226 Å20 Å2-4.846 Å2
2---0.9607 Å20 Å2
3----7.4619 Å2
Refinement stepCycle: LAST / Resolution: 3.549→15.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10051 0 0 0 10051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510269
X-RAY DIFFRACTIONf_angle_d0.54913937
X-RAY DIFFRACTIONf_dihedral_angle_d12.4773760
X-RAY DIFFRACTIONf_chiral_restr0.0321595
X-RAY DIFFRACTIONf_plane_restr0.0021776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.549-3.73410.31251030.25931884X-RAY DIFFRACTION68
3.7341-3.96450.34191350.23522558X-RAY DIFFRACTION92
3.9645-4.26490.29811190.21722583X-RAY DIFFRACTION92
4.2649-4.68360.28441390.19152545X-RAY DIFFRACTION91
4.6836-5.33770.26571520.18672505X-RAY DIFFRACTION91
5.3377-6.63840.33221430.23352544X-RAY DIFFRACTION90
6.6384-15.65250.23871360.19472517X-RAY DIFFRACTION88

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