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- PDB-4wv6: Heterodimer of Importin alpha 1 with nuclear localization signal ... -

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Basic information

Entry
Database: PDB / ID: 4wv6
TitleHeterodimer of Importin alpha 1 with nuclear localization signal of TAF8
Components
  • Importin subunit alpha-1
  • Transcription initiation factor TFIID subunit 8
KeywordsTRANSPORT PROTEIN / Nuclear import / Armadillo repeats / NLS
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / regulation of DNA recombination / DNA-templated transcription open complex formation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / maintenance of protein location in nucleus / regulation of fat cell differentiation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde ...Sensing of DNA Double Strand Breaks / regulation of DNA recombination / DNA-templated transcription open complex formation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / maintenance of protein location in nucleus / regulation of fat cell differentiation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / inner cell mass cell proliferation / nuclear import signal receptor activity / CaMK IV-mediated phosphorylation of CREB / DNA metabolic process / nuclear localization sequence binding / NLS-bearing protein import into nucleus / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / positive regulation of type I interferon production / positive regulation of transcription initiation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription initiation at RNA polymerase II promoter / mRNA transcription by RNA polymerase II / ISG15 antiviral mechanism / histone deacetylase binding / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / host cell / nuclear membrane / Estrogen-dependent gene expression / cell differentiation / protein heterodimerization activity / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / RNA binding / nucleoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / 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 / Histone-fold / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTrowitzsch, S.
Funding support France, 1items
OrganizationGrant numberCountry
European Commission (EC) Research Executive Agency (REA)254671 France
CitationJournal: Nat Commun / Year: 2015
Title: Cytoplasmic TAF2-TAF8-TAF10 complex provides evidence for nuclear holo-TFIID assembly from preformed submodules.
Authors: Trowitzsch, S. / Viola, C. / Scheer, E. / Conic, S. / Chavant, V. / Fournier, M. / Papai, G. / Ebong, I.O. / Schaffitzel, C. / Zou, J. / Haffke, M. / Rappsilber, J. / Robinson, C.V. / ...Authors: Trowitzsch, S. / Viola, C. / Scheer, E. / Conic, S. / Chavant, V. / Fournier, M. / Papai, G. / Ebong, I.O. / Schaffitzel, C. / Zou, J. / Haffke, M. / Rappsilber, J. / Robinson, C.V. / Schultz, P. / Tora, L. / Berger, I.
History
DepositionNov 4, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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
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: Importin subunit alpha-1
B: Transcription initiation factor TFIID subunit 8
C: Transcription initiation factor TFIID subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,07815
Polymers54,3333
Non-polymers74512
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint27 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.270, 77.720, 128.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-1 / Karyopherin subunit alpha-2 / RAG cohort protein 1 / SRP1-alpha


Mass: 50988.684 Da / Num. of mol.: 1 / Fragment: UNP residues 60-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA2, RCH1, SRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52292
#2: Protein/peptide Transcription initiation factor TFIID subunit 8 / Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8 / Transcription ...Protein taube nuss / TBP-associated factor 43 kDa / TBP-associated factor 8 / Transcription initiation factor TFIID 43 kDa subunit / hTAFII43


Mass: 1672.133 Da / Num. of mol.: 2 / Fragment: UNP residues 297-310 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z7C8
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: HEPES-NaOH, polyethylene glycole 3350, L-proline

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.75→49.54 Å / Num. obs: 55423 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.18
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.7745 / Mean I/σ(I) obs: 2.03 / Num. measured obs: 5436 / % possible all: 99.14

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RZ9

3rz9


Resolution: 1.75→49.536 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1799 2772 5 %
Rwork0.1533 --
obs0.1546 55419 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→49.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 0 48 463 3848
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083467
X-RAY DIFFRACTIONf_angle_d1.1584706
X-RAY DIFFRACTIONf_dihedral_angle_d12.8631283
X-RAY DIFFRACTIONf_chiral_restr0.045569
X-RAY DIFFRACTIONf_plane_restr0.006596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78020.26811350.2412547X-RAY DIFFRACTION99
1.7802-1.81260.27521370.23452616X-RAY DIFFRACTION99
1.8126-1.84740.29511360.21922584X-RAY DIFFRACTION100
1.8474-1.88510.24451370.20322591X-RAY DIFFRACTION99
1.8851-1.92610.24981360.19592585X-RAY DIFFRACTION99
1.9261-1.97090.25581370.18062605X-RAY DIFFRACTION100
1.9709-2.02020.1781360.16942598X-RAY DIFFRACTION100
2.0202-2.07480.18751370.15612599X-RAY DIFFRACTION100
2.0748-2.13590.16411370.14792600X-RAY DIFFRACTION100
2.1359-2.20480.17341380.14412628X-RAY DIFFRACTION100
2.2048-2.28360.16441390.13632628X-RAY DIFFRACTION100
2.2836-2.37510.16891380.13132627X-RAY DIFFRACTION100
2.3751-2.48320.15341380.13282615X-RAY DIFFRACTION100
2.4832-2.61410.18491390.13332655X-RAY DIFFRACTION100
2.6141-2.77780.14771390.13562626X-RAY DIFFRACTION100
2.7778-2.99230.17341400.14852666X-RAY DIFFRACTION100
2.9923-3.29340.1981390.15382644X-RAY DIFFRACTION100
3.2934-3.76980.17091420.15522693X-RAY DIFFRACTION100
3.7698-4.74890.14991430.12952712X-RAY DIFFRACTION100
4.7489-49.55560.17861490.16972828X-RAY DIFFRACTION99
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)
14.8369-1.61951.25835.06741.4382.9207-0.02930.1619-0.4010.10340.13670.07510.36530.4107-0.05660.290.06860.06590.1784-0.00070.2373-10.4768-32.854523.955
23.1681-1.13110.98512.1834-1.31992.536-0.076-0.2069-0.13570.04910.10380.19580.09-0.0953-0.05250.1681-0.00190.03260.10810.00770.1841-24.4319-19.46824.9185
30.51930.2062-0.25464.2391-1.71373.5453-0.02110.0544-0.03190.1913-0.0028-0.0547-0.0140.0830.02140.11350.0217-0.0030.14510.02480.1723-26.5475-0.12414.9012
41.61150.1446-0.77711.1097-1.01384.4342-0.005-0.0235-0.14010.0254-0.0092-0.0577-0.10280.1330.00510.12-0.01680.00090.1302-0.00210.1569-22.583213.6981-5.8999
56.962-5.50591.68175.8169-3.94366.5829-0.05690.1694-0.1630.06140.03030.45220.1733-0.5898-0.04160.1273-0.03130.00960.2204-0.03010.1296-27.640512.758-20.5341
63.90242.2752-0.4856.9472-0.59833.9518-0.25830.3797-0.1568-0.57850.1512-0.00380.5004-0.34460.09630.2939-0.01650.02430.2885-0.02610.1279-22.904512.2388-29.1505
76.11242.1002-1.13158.76942.42395.3775-0.10730.54550.87830.31720.1745-0.8846-1.18841.05660.27010.2539-0.06370.00090.28290.03680.3469-11.664-14.977720.1383
82.0597-0.24330.27968.665-2.44591.9986-0.57990.7796-1.26850.08330.19630.91621.2269-0.3178-0.0250.5547-0.14050.01040.50580.0230.449-30.10163.2556-4.2726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 120 )
2X-RAY DIFFRACTION2chain 'A' and (resid 121 through 222 )
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 322 )
4X-RAY DIFFRACTION4chain 'A' and (resid 323 through 433 )
5X-RAY DIFFRACTION5chain 'A' and (resid 434 through 454 )
6X-RAY DIFFRACTION6chain 'A' and (resid 455 through 497 )
7X-RAY DIFFRACTION7chain 'B' and (resid 297 through 305 )
8X-RAY DIFFRACTION8chain 'C' and (resid 306 through 308 )

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