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- PDB-5svz: HIV-1 Tat NLS in complex with importin alpha -

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Basic information

Entry
Database: PDB / ID: 5svz
TitleHIV-1 Tat NLS in complex with importin alpha
Components
  • Importin subunit alpha-1
  • Tat
KeywordsTransport Protein/Viral Protein / HIV-1 / Tat / Importin alpha / Virus / Complex / Transport Protein-Viral Protein complex
Function / homology
Function and homology information


trans-activation response element binding / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / symbiont-mediated perturbation of host chromatin organization / Sensing of DNA Double Strand Breaks / symbiont-mediated suppression of host translation initiation / regulation of transcription by glucose / entry of viral genome into host nucleus through nuclear pore complex via importin / : / positive regulation of viral life cycle ...trans-activation response element binding / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / symbiont-mediated perturbation of host chromatin organization / Sensing of DNA Double Strand Breaks / symbiont-mediated suppression of host translation initiation / regulation of transcription by glucose / entry of viral genome into host nucleus through nuclear pore complex via importin / : / positive regulation of viral life cycle / negative regulation of peptidyl-threonine phosphorylation / host cell nucleolus / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / actinin binding / NLS-bearing protein import into nucleus / nuclear import signal receptor activity / nuclear localization sequence binding / non-canonical NF-kappaB signal transduction / RNA-binding transcription regulator activity / positive regulation of type I interferon production / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / histone deacetylase binding / protein import into nucleus / cytoplasmic stress granule / host cell / nuclear membrane / DNA-binding transcription factor binding / host cell cytoplasm / postsynaptic density / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / protein domain specific binding / apoptotic process / DNA-templated transcription / positive regulation of DNA-templated transcription / glutamatergic synapse / extracellular region / nucleoplasm / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / 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. ...Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Protein Tat / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSmith, K.M. / Himiari, Z. / Forwood, J.K.
CitationJournal: Sci Rep / Year: 2017
Title: Structural Basis for Importin-alpha Binding of the Human Immunodeficiency Virus Tat.
Authors: Smith, K.M. / Himiari, Z. / Tsimbalyuk, S. / Forwood, J.K.
History
DepositionAug 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Oct 4, 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
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: Tat


Theoretical massNumber of molelcules
Total (without water)57,1712
Polymers57,1712
Non-polymers00
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint2 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.000, 89.831, 99.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 55268.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52293
#2: Protein/peptide Tat


Mass: 1902.220 Da / Num. of mol.: 1 / Fragment: NLS motif
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04326*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1.25 M sodium citrate pH 7 and 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→29.662 Å / Num. obs: 46564 / % possible obs: 96.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 27.42 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2-2.054.61.0570.65198.2
8.94-29.664.30.0280.999188.6

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FC8

5fc8


Resolution: 2→29.662 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.37
RfactorNum. reflection% reflection
Rfree0.1924 2333 5.02 %
Rwork0.1743 --
obs0.1752 46516 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.04 Å2 / Biso mean: 40.434 Å2 / Biso min: 16.39 Å2
Refinement stepCycle: final / Resolution: 2→29.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 0 314 3633
Biso mean---41.24 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033376
X-RAY DIFFRACTIONf_angle_d0.6534592
X-RAY DIFFRACTIONf_chiral_restr0.04551
X-RAY DIFFRACTIONf_plane_restr0.004588
X-RAY DIFFRACTIONf_dihedral_angle_d18.8971244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.04090.26911360.25852582271898
2.0409-2.08520.26271280.23872622275098
2.0852-2.13370.27111340.22172640277498
2.1337-2.18710.25551480.21622579272798
2.1871-2.24620.22161380.20052612275097
2.2462-2.31220.2291250.18962634275998
2.3122-2.38680.24821490.19692593274297
2.3868-2.47210.19581410.19032590273197
2.4721-2.5710.1781120.18412600271297
2.571-2.6880.20731450.19052603274897
2.688-2.82960.21991360.18142605274196
2.8296-3.00670.19211540.19042565271996
3.0067-3.23860.23591380.18462590272895
3.2386-3.5640.18581270.16592590271795
3.564-4.07860.13771400.13832586272694
4.0786-5.13430.13431370.12992590272794
5.1343-29.66480.18021450.16582602274790

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