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- PDB-5huy: Structure of HCMV Small Terminase NLS bound to importin alpha -

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Basic information

Entry
Database: PDB / ID: 5huy
TitleStructure of HCMV Small Terminase NLS bound to importin alpha
Components
  • HCMV small terminase
  • Importin subunit alpha-1
Keywordstransport protein/viral protein / Nuclear Import / NLS / Importin alpha-1 / HCMV small terminase / VIRAL PROTEIN / transport protein-viral protein complex
Function / homology
Function and homology information


viral DNA genome packaging / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / viral capsid assembly / 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 DNA genome packaging / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / viral capsid assembly / 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 / protein processing / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / host cell nucleus / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Tripartite terminase subunit 1 / Herpesvirus processing and transport protein / 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. ...Tripartite terminase subunit 1 / Herpesvirus processing and transport protein / 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
Tripartite terminase subunit 1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human herpesvirus 5 strain Toledo
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.979 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 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 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
B: HCMV small terminase
A: HCMV small terminase


Theoretical massNumber of molelcules
Total (without water)61,7773
Polymers61,7773
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint7 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.254, 90.810, 96.934
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
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide HCMV small terminase


Mass: 1960.343 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 5 strain Toledo / Production host: synthetic construct (others) / References: UniProt: D3YRZ5*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 2.3 uL of deltaIBB-importin alpha concentrated to 20 mg/ml were mixed with 0.7 microlitre of a 2-fold molar excess of HCMV-NLS peptide; 3 uL of reservoir solution containing ~0.7 M sodium ...Details: 2.3 uL of deltaIBB-importin alpha concentrated to 20 mg/ml were mixed with 0.7 microlitre of a 2-fold molar excess of HCMV-NLS peptide; 3 uL of reservoir solution containing ~0.7 M sodium citrate, 100 mM Hepes, and 10 mM beta-mercaptoethanol were added to the drop, pH 6.0

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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: 50602 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 32.5 Å2 / Rsym value: 0.049 / Net I/σ(I): 48.1
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 3.8 / % possible all: 99.5

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Processing

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

3q5u


Resolution: 1.979→14.934 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 1999 4.17 %Random selection
Rwork0.1732 ---
obs0.1741 47920 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.979→14.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 0 196 3561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083423
X-RAY DIFFRACTIONf_angle_d1.0414656
X-RAY DIFFRACTIONf_dihedral_angle_d13.2872093
X-RAY DIFFRACTIONf_chiral_restr0.055558
X-RAY DIFFRACTIONf_plane_restr0.007597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9792-2.02860.34991330.27373207X-RAY DIFFRACTION99
2.0286-2.08330.29271580.25373218X-RAY DIFFRACTION100
2.0833-2.14440.23961380.2193286X-RAY DIFFRACTION100
2.1444-2.21340.21891340.19913259X-RAY DIFFRACTION100
2.2134-2.29230.18851470.18233232X-RAY DIFFRACTION100
2.2923-2.38370.20761450.17873239X-RAY DIFFRACTION100
2.3837-2.49170.2021300.17723288X-RAY DIFFRACTION100
2.4917-2.62240.21441500.17793246X-RAY DIFFRACTION100
2.6224-2.78570.1821430.17463283X-RAY DIFFRACTION100
2.7857-2.99920.18861410.17853286X-RAY DIFFRACTION100
2.9992-3.29810.21871410.18033307X-RAY DIFFRACTION100
3.2981-3.76860.20081430.17653314X-RAY DIFFRACTION100
3.7686-4.7230.18891470.14173349X-RAY DIFFRACTION100
4.723-14.93420.15931490.16643407X-RAY DIFFRACTION98
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)
11.72561.36991.25866.36862.34991.92620.138-0.0768-0.10090.26980.01280.04960.2799-0.0757-0.16420.2691-0.019-0.01480.29290.01530.26336.4764-2.9572-15.0172
21.2669-1.1951-1.2371.76931.43012.12130.041-0.11830.1734-0.12030.0467-0.047-0.11060.0416-0.08280.2526-0.0112-0.00040.2840.0130.3468-3.717528.0403-5.8247
32.22461.03421.20425.09620.12394.5409-0.0211-1.59710.4451.21130.2139-0.52810.04870.8577-0.13540.57710.0557-0.071.1834-0.22830.5498-5.963540.821225.3309
43.20431.73444.14872.00021.65456.0870.1964-0.6777-0.33321.21990.4807-1.9473-0.33011.2674-0.60220.49430.0414-0.0380.8372-0.1730.69243.845435.42228.6169
57.83470.73473.76456.30894.45584.50420.2793-1.0145-0.26561.0272-0.30690.52380.36-1.049-0.11340.4671-0.03280.02970.48120.04990.3963-1.29215.2205-7.5956
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 'B' and (resid 820 through 826 )
5X-RAY DIFFRACTION5chain 'A' and (resid 820 through 828 )

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