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

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Basic information

Entry
Database: PDB / ID: 3fey
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 / mRNA transport / Nucleus / Phosphoprotein / RNA-binding / 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 mRNA 3'-end processing / positive regulation of RNA export from nucleus / Sensing of DNA Double Strand Breaks / regulation of DNA recombination ...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 mRNA 3'-end processing / positive regulation of RNA export from nucleus / Sensing of DNA Double Strand Breaks / regulation of DNA recombination / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / RNA cap binding / alternative mRNA splicing, via spliceosome / entry of viral genome into host nucleus through nuclear pore complex via importin / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / regulation of mRNA processing / 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 / NLS-dependent protein nuclear import complex / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / RNA catabolic process / mRNA cis splicing, via spliceosome / Abortive elongation of HIV-1 transcript in the absence of Tat / Transport of Mature mRNA derived from an Intron-Containing Transcript / regulation of translational initiation / positive regulation of mRNA splicing, via spliceosome / FGFR2 alternative splicing / RNA Polymerase II Transcription Termination / Signaling by FGFR2 IIIa TM / nuclear import signal receptor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / DNA metabolic process / nuclear localization sequence binding / CaMK IV-mediated phosphorylation of CREB / NLS-bearing protein import into nucleus / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / spliceosomal complex assembly / positive regulation of type I interferon production / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 7-methylguanosine mRNA capping / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / histone deacetylase binding / Regulation of expression of SLITs and ROBOs / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / host cell / snRNP Assembly / positive regulation of cell growth / defense response to virus / nuclear membrane / Estrogen-dependent gene expression / molecular adaptor activity / 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 / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) ...Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / 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 / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / 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: 2.2 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: Advisory / 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

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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
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint2 kcal/mol
Surface area55980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.842, 104.505, 108.558
Angle α, β, γ (deg.)90.00, 109.04, 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6.0, and 8% PEG 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2007
Details: Triple striped vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 87239 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 2 / Rsym value: 0.572 / % possible all: 83.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N54 and 1IAL

1n54

1ial


Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 14.28 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.225 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23803 4376 5 %RANDOM
Rwork0.19159 ---
obs0.19395 82641 97.22 %-
all-89752 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.103 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å2-0.07 Å2
2--2.58 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10269 0 0 454 10723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210521
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.95814284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.98751286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85324.587484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.306151857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8021556
X-RAY DIFFRACTIONr_chiral_restr0.0830.21626
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217884
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.24997
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.27308
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2483
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5321.56443
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.024210468
X-RAY DIFFRACTIONr_scbond_it1.73634078
X-RAY DIFFRACTIONr_scangle_it2.7774.53812
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 263 -
Rwork0.305 4851 -
obs--79.2 %
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)
18.50588.5693.34718.87353.63531.6281-0.44370.7212-0.2787-0.5810.5953-0.3295-0.39520.163-0.15150.3808-0.0226-0.07130.1666-0.04490.331-11.3221-21.4994-2.5521
22.0995-0.6151-0.69383.08850.73355.0548-0.03640.3928-0.1057-0.30580.2511-0.03240.2375-0.2676-0.21470.1992-0.1173-0.07870.37460.07060.2535-6.829711.927721.5959
32.13170.22660.31070.73370.18123.92290.0769-0.33460.0626-0.01070.16310.39110.0429-1.007-0.240.1229-0.02260.01480.75090.21290.3262-20.532714.760839.3295
41.22480.15590.75580.945-0.26241.5672-0.0572-0.18680.10640.06530.13320.227-0.1834-0.5428-0.0760.15640.09040.05160.2510.06060.114-1.858723.720246.6356
51.7683-1.73120.66744.3112-0.98751.2988-0.1717-0.23450.03590.52640.1443-0.3443-0.10530.04260.02740.27480.0126-0.04340.2668-0.00520.076730.03157.276270.5572
60.7702-0.3641-0.12741.96160.69471.0278-0.02110.0562-0.18670.05110.05330.16910.1191-0.2621-0.03220.22120.03340.060.44460.12110.09875.37641.06567.688
740.300515.7669-18.87166.2391-8.359522.52981.87030.07152.75430.50930.01471.11512.30390.5032-1.8850.85540.2536-0.04060.5275-0.13670.241917.29421.918133.2265
80.1805-1.7823-0.567481.617524.3077.2485-0.31120.3879-0.221-0.22560.04610.73820.0124-0.09020.26510.925-0.71170.28091.9615-0.43110.474119.6425-6.627735.4715
92.49750.6709-1.19182.89051.12846.61210.0651-0.1589-0.16280.21520.0241-0.11870.3840.6952-0.08930.25010.07690.00250.23860.05640.13128.04567.957949.4388
109.91740.0304-5.01799.3215-2.39117.3981-0.0062-0.6247-0.06030.1407-0.2294-0.9430.65371.9240.23550.29430.21490.01750.61820.02470.21435.40642.829647.9265
115.4463-0.3116-1.49971.9552-1.01933.8138-0.0643-0.0127-0.0872-0.12720.06150.04940.34180.09420.00280.230.03460.01690.20080.00140.102322.58057.879143.9759
122.96480.49965.20252.86610.74219.28670.68480.7355-0.3377-0.1064-0.2022-0.39531.4741.4666-0.48260.65340.39950.16460.546-0.00250.388832.8666-3.748342.4122
135.31514.2403-1.49997.2537-0.59490.68920.3947-0.2249-0.59990.3529-0.3377-1.094-0.16590.1989-0.0570.2575-0.1483-0.13070.1926-0.04270.518714.6955-4.21455.6506
144.7242.62480.52296.1963-0.39413.4520.4405-0.3635-0.71480.565-0.2109-1.2801-0.2480.0774-0.22960.2468-0.106-0.21870.08350.03160.49714.0785-19.08799.9192
153.39111.79830.78682.91510.71072.22390.207-0.3169-0.1660.365-0.1119-0.4686-0.1386-0.0642-0.09510.354-0.0525-0.06930.1071-0.00220.2246-16.5146-27.86538.0167
167.99421.1352-2.31175.60231.61847.4575-0.1459-0.0440.4474-0.0042-0.0782-0.0537-0.738-0.25150.22410.38540.0607-0.04950.1688-0.03890.1842-30.1027-20.4766-2.8824
172.54450.41481.62941.78450.7253.0288-0.01-0.01920.1209-0.0266-0.00970.0575-0.2992-0.44640.01980.18810.01880.01890.174-0.03250.0942-36.2635-32.2629-9.4753
185.34891.4487-1.52581.9525-0.79136.9574-0.06320.164-0.1104-0.13550.11050.17490.2708-0.7424-0.04730.1781-0.014-0.02880.1512-0.03080.1507-39.6374-39.0859-25.329
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 23
2X-RAY DIFFRACTION2A24 - 93
3X-RAY DIFFRACTION3A94 - 196
4X-RAY DIFFRACTION4A197 - 426
5X-RAY DIFFRACTION5A427 - 606
6X-RAY DIFFRACTION6A607 - 790
7X-RAY DIFFRACTION7B12 - 32
8X-RAY DIFFRACTION8B33 - 39
9X-RAY DIFFRACTION9B40 - 66
10X-RAY DIFFRACTION10B67 - 84
11X-RAY DIFFRACTION11B85 - 114
12X-RAY DIFFRACTION12B115 - 126
13X-RAY DIFFRACTION13C69 - 135
14X-RAY DIFFRACTION14C136 - 224
15X-RAY DIFFRACTION15C225 - 339
16X-RAY DIFFRACTION16C340 - 354
17X-RAY DIFFRACTION17C355 - 434
18X-RAY DIFFRACTION18C435 - 499

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