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- PDB-3ve6: Crystal Structure Analysis of Venezuelan Equine Encephalitis Viru... -

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Basic information

Entry
Database: PDB / ID: 3ve6
TitleCrystal Structure Analysis of Venezuelan Equine Encephalitis Virus Capsid Protein NLS and Importin Alpha
Components
  • Importin subunit alpha-2
  • Venezuelan equine encephalitis virus capsid protein NLS
KeywordsPROTEIN BINDING / importin / importin alpha / Venezuelan equine encephalitis virus / capsid protein NLS
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / togavirin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / T=4 icosahedral viral capsid / nuclear import signal receptor activity / nuclear localization sequence binding ...symbiont-mediated suppression of host transcription / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / togavirin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / T=4 icosahedral viral capsid / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / symbiont-mediated suppression of host mRNA export from nucleus / cytoplasmic stress granule / protein import into nucleus / symbiont-mediated suppression of host gene expression / clathrin-dependent endocytosis of virus by host cell / DNA-binding transcription factor binding / host cell cytoplasm / membrane => GO:0016020 / postsynaptic density / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / glutamatergic synapse / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / 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 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Armadillo-like helical / Alpha Horseshoe / Immunoglobulin E-set / Armadillo-type fold / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Mainly Alpha
Similarity search - Domain/homology
Structural polyprotein / Importin subunit alpha-1 / Togavirin
Similarity search - Component
Biological speciesMus musculus (house mouse)
Venezuelan equine encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.829 Å
AuthorsFan, F.
CitationJournal: To be Published
Title: Crystal Structure Analysis of Venezuelan Equine Encephalitis Virus Capsid Protein NLS and Importin Alpha
Authors: Fan, F.
History
DepositionJan 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Mar 28, 2012Group: Source and taxonomy
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit alpha-2
B: Venezuelan equine encephalitis virus capsid protein NLS


Theoretical massNumber of molelcules
Total (without water)47,4582
Polymers47,4582
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1613.2 Å2
ΔGint-1 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.950, 89.750, 99.580
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-2 / / 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: 46184.875 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) / Strain (production host): BL21(DE3) / References: UniProt: P52293
#2: Protein/peptide Venezuelan equine encephalitis virus capsid protein NLS


Mass: 1273.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Venezuelan equine encephalitis virus / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WCF8, UniProt: P09592*PLUS

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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: 3.72 Å3/Da / Density % sol: 66.91 %
Crystal growMethod: vapor diffusion, hanging drop / Details: vapor diffusion, hanging drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953692
DetectorDate: Oct 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953692 Å / Relative weight: 1
ReflectionResolution: 2.829→50.937 Å / Num. obs: 17446 / Biso Wilson estimate: 53.2 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX2011_12_24_0706refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.829→50.937 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.85 / SU ML: 0.38 / σ(F): 1.37 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2702 882 5.06 %
Rwork0.2263 --
obs0.2285 17446 99.98 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.903 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 161.01 Å2 / Biso mean: 61.043 Å2 / Biso min: 16.73 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.829→50.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 0 0 3336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013395
X-RAY DIFFRACTIONf_angle_d0.4624622
X-RAY DIFFRACTIONf_chiral_restr0.03555
X-RAY DIFFRACTIONf_plane_restr0.002593
X-RAY DIFFRACTIONf_dihedral_angle_d10.7571249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.829-3.00640.30981530.281726882841
3.0064-3.23840.35131370.264327262863
3.2384-3.56430.2851570.253527092866
3.5643-4.07980.31081330.223127582891
4.0798-5.13940.22591580.200827612919
5.1394-50.94490.23631440.207329223066

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