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- PDB-4agk: Crystal structure of capsid protein (110-267) from Aura virus -

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Basic information

Entry
Database: PDB / ID: 4agk
TitleCrystal structure of capsid protein (110-267) from Aura virus
ComponentsCAPSID PROTEINCapsid
KeywordsHYDROLASE / VIRAL PROTEIN
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / proteolysis / RNA binding / membrane
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. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesAURA VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsAggarwal, M. / Kumar, P. / Tomar, S.
Citation
Journal: Plos One / Year: 2012
Title: Crystal Structure of Aura Virus Capsid Protease and its Complex with Dioxane: New Insights Into Capsid-Glycoprotein Molecular Contacts
Authors: Aggarwal, M. / Tapas, S. / Preeti / Siwach, A. / Kumar, P. / Kuhn, R.J. / Tomar, S.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Crystallization, High-Resolution Data Collection and Preliminary Crystallographic Analysis of Aura Virus Capsid Protease and its Complex with Dioxane.
Authors: Aggarwal, M. / Dhindwal, S. / Pratap, S. / Kuhn, R.J. / Kumar, P. / Tomar, S.
History
DepositionJan 30, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,0081
Polymers17,0081
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.661, 35.262, 49.578
Angle α, β, γ (deg.)90.00, 102.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CAPSID PROTEIN / Capsid / COAT PROTEIN / C


Mass: 17008.246 Da / Num. of mol.: 1 / Fragment: RESIDUES 110-267
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AURA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q86925, togavirin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSOME RESIDUES ARE FOUND TO BE DIFFERENT IN OUR DATA

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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 Å3/Da / Density % sol: 38.56 % / Description: NONE
Crystal growDetails: 0.1 M BIS-TRIS AND POLYETHYLENE GLYCOL MONOMETHYL ETHER 2000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 11410 / % possible obs: 90.2 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.95 / % possible all: 42.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KXA

1kxa


Resolution: 1.81→48.45 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.379 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23151 548 4.8 %RANDOM
Rwork0.17645 ---
obs0.17898 10862 90.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å2-0.79 Å2
2--1.34 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.81→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 0 127 1279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021194
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9391617
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9735155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68623.7548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96715197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.38155
X-RAY DIFFRACTIONr_chiral_restr0.1050.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021908
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.805→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 24 -
Rwork0.344 477 -
obs--54.87 %
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)
12.2459-0.92861.5032.80910.93942.5776-0.0405-0.18520.0677-0.099-0.04870.2102-0.1065-0.4250.08930.05570.02620.00030.12450.01660.0591-20.33680.7825-15.8436
23.0276-1.31391.13470.98450.37893.5991-0.1903-0.00190.30240.0118-0.06290.0755-0.0457-0.57290.25320.1159-0.0258-0.0650.16140.06710.2162-23.26554.2588-19.0373
32.44090.35671.79271.2343-0.10922.3647-0.2127-0.23090.36040.0564-0.05060.1063-0.2995-0.26530.26320.08130.0442-0.00570.0619-0.03540.0707-12.07936.0722-9.3014
45.58011.71860.84351.66310.85974.39310.0889-0.0739-0.2030.0807-0.0112-0.19160.01650.4072-0.07770.01980.005100.04860.00860.02790.0598-4.4087-8.2114
52.10040.3537-0.48452.01431.41541.2755-0.0272-0.2221-0.027-0.0434-0.00290.06630.05020.10950.03010.35550.0979-0.07580.0521-0.01410.0233-1.9097-8.9804-8.6538
61.65980.09150.74791.17560.15942.26530.00120.0135-0.0333-0.05180.0301-0.05350.0294-0.0063-0.03140.01640.00510.01290.01240.00320.0117-6.4296-3.122-13.6294
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A136 - 150
2X-RAY DIFFRACTION2A151 - 165
3X-RAY DIFFRACTION3A166 - 195
4X-RAY DIFFRACTION4A196 - 205
5X-RAY DIFFRACTION5A206 - 210
6X-RAY DIFFRACTION6A211 - 267

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