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- PDB-5huw: Structure of HSV-1 Large Terminase NLS bound to importin alpha -

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Basic information

Entry
Database: PDB / ID: 5huw
TitleStructure of HSV-1 Large Terminase NLS bound to importin alpha
Components
  • HSV1 large terminase NLS
  • Importin subunit alpha-1
Keywordstranport protein / viral protein / Nuclear Import / NLS / Importin alpha-1 / Herpes virus
Function / homology
Function and homology information


Sensing of DNA Double Strand Breaks / nuclease activity / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / viral release from host cell ...Sensing of DNA Double Strand Breaks / nuclease activity / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / viral release from host cell / chromosome organization / host cell / cytoplasmic stress granule / protein import into nucleus / DNA-binding transcription factor binding / Hydrolases; Acting on ester bonds / postsynaptic density / glutamatergic synapse / host cell nucleus / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Probable DNA packing protein, C-terminal / Probable DNA packing protein, N-terminal / Tripartite terminase subunit 3 / Probable DNA packing protein, C-terminal domain superfamily / Probable DNA packing protein, C-terminus / Probable DNA packing protein, N-terminus / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain ...Probable DNA packing protein, C-terminal / Probable DNA packing protein, N-terminal / Tripartite terminase subunit 3 / Probable DNA packing protein, C-terminal domain superfamily / Probable DNA packing protein, C-terminus / Probable DNA packing protein, N-terminus / 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Tripartite terminase subunit 3 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSankhala, R.S. / Lokareddy, R.K. / Cingolani, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100888 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Divergent Evolution of Nuclear Localization Signal Sequences in Herpesvirus Terminase Subunits.
Authors: Sankhala, R.S. / Lokareddy, R.K. / Cingolani, G.
History
DepositionJan 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
C: Importin subunit alpha-1
A: HSV1 large terminase NLS
B: HSV1 large terminase NLS


Theoretical massNumber of molelcules
Total (without water)60,3963
Polymers60,3963
Non-polymers00
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint0 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.260, 90.728, 97.659
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 / / 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: 57856.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Importin alpha-1 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide HSV1 large terminase NLS


Mass: 1269.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 1 (Herpes simplex virus type 1)
Production host: synthetic construct (others) / References: UniProt: P04295*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.87 Å3/Da / Density % sol: 57.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.6M sodium citrate, 100 mM Hepes, pH 6.0, and 10 mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 51772 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 27.2 Å2 / Rsym value: 0.087 / Net I/σ(I): 33.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.784 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000HKL-2000data reduction
HKL-2000HKL-2000data scaling
PHASERphaser-MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q5U

3q5u


Resolution: 1.95→14.943 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 1983 3.88 %Random selection
Rwork0.1727 ---
obs0.1736 51068 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→14.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 0 331 3682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083423
X-RAY DIFFRACTIONf_angle_d0.8874659
X-RAY DIFFRACTIONf_dihedral_angle_d16.4972091
X-RAY DIFFRACTIONf_chiral_restr0.049557
X-RAY DIFFRACTIONf_plane_restr0.006597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99870.33861330.32333462X-RAY DIFFRACTION99
1.9987-2.05260.28961400.28273462X-RAY DIFFRACTION100
2.0526-2.11280.25991390.25223442X-RAY DIFFRACTION99
2.1128-2.18080.25131410.23383473X-RAY DIFFRACTION100
2.1808-2.25850.26531510.21613441X-RAY DIFFRACTION100
2.2585-2.34860.23091260.18693479X-RAY DIFFRACTION100
2.3486-2.45510.19191530.17493498X-RAY DIFFRACTION100
2.4551-2.58390.20581360.17323462X-RAY DIFFRACTION100
2.5839-2.74480.18251480.16493500X-RAY DIFFRACTION100
2.7448-2.95520.20391370.16443513X-RAY DIFFRACTION100
2.9552-3.24990.17571490.16883524X-RAY DIFFRACTION100
3.2499-3.71380.18681410.16173540X-RAY DIFFRACTION100
3.7138-4.65540.15841410.13653590X-RAY DIFFRACTION100
4.6554-14.94370.17171480.15643699X-RAY DIFFRACTION100
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)
10.90880.08560.52651.98641.24450.96730.0404-0.0428-0.07270.10340.01610.02130.1203-0.04730.00010.2513-0.0196-0.01590.22370.00250.19196.421-2.8911-15.2147
20.7037-0.611-0.77920.77540.97871.25280.0607-0.04480.1046-0.0710.0017-0.0142-0.06960.017300.22550.00360.0040.2188-0.00010.2671-4.305727.9445-5.8191
30.6519-0.0471-0.55191.1450.20181.13760.0761-0.47080.15540.24690.0588-0.19260.04860.46150.00360.3332-0.0072-0.06910.5867-0.13710.3151-6.946540.056325.2896
44.2742-1.29890.52594.32981.29537.2534-0.05-0.10390.83870.4602-0.42810.9209-0.1034-0.3830.34820.2612-0.01140.06530.3567-0.01750.4143-2.70815.9865-7.5725
54.7358-0.2544-0.76911.0974-1.89953.6004-0.2662-0.67770.12650.5843-0.1524-0.5784-0.05140.44250.3550.89590.2636-0.12420.7918-0.20460.73432.833934.67518.0775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 75 through 202 )
2X-RAY DIFFRACTION2chain 'C' and (resid 203 through 390 )
3X-RAY DIFFRACTION3chain 'C' and (resid 391 through 497 )
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 190 )
5X-RAY DIFFRACTION5chain 'B' and (resid 182 through 187 )

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