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- PDB-5j36: Crystal structure of 60-mer BFDV Capsid Protein -

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Basic information

Entry
Database: PDB / ID: 5j36
TitleCrystal structure of 60-mer BFDV Capsid Protein
ComponentsBeak and feather disease virus capsid protein
KeywordsVIRUS / BFDV Virus Capsid Jelly Roll
Function / homology
Function and homology information


viral capsid assembly / T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell
Similarity search - Function
Circovirus capsid protein / Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Capsid protein
Similarity search - Component
Biological speciesBeak and feather disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsSarker, S. / Raidal, S. / Aragao, D. / Forwood, J.K.
CitationJournal: Nat Commun / Year: 2016
Title: Structural insights into the assembly and regulation of distinct viral capsid complexes.
Authors: Subir Sarker / María C Terrón / Yogesh Khandokar / David Aragão / Joshua M Hardy / Mazdak Radjainia / Manuel Jiménez-Zaragoza / Pedro J de Pablo / Fasséli Coulibaly / Daniel Luque / ...Authors: Subir Sarker / María C Terrón / Yogesh Khandokar / David Aragão / Joshua M Hardy / Mazdak Radjainia / Manuel Jiménez-Zaragoza / Pedro J de Pablo / Fasséli Coulibaly / Daniel Luque / Shane R Raidal / Jade K Forwood /
Abstract: The assembly and regulation of viral capsid proteins into highly ordered macromolecular complexes is essential for viral replication. Here, we utilize crystal structures of the capsid protein from ...The assembly and regulation of viral capsid proteins into highly ordered macromolecular complexes is essential for viral replication. Here, we utilize crystal structures of the capsid protein from the smallest and simplest known viruses capable of autonomously replicating in animal cells, circoviruses, to establish structural and mechanistic insights into capsid morphogenesis and regulation. The beak and feather disease virus, like many circoviruses, encode only two genes: a capsid protein and a replication initiation protein. The capsid protein forms distinct macromolecular assemblies during replication and here we elucidate these structures at high resolution, showing that these complexes reverse the exposure of the N-terminal arginine rich domain responsible for DNA binding and nuclear localization. We show that assembly of these complexes is regulated by single-stranded DNA (ssDNA), and provide a structural basis of capsid assembly around single-stranded DNA, highlighting novel binding interfaces distinct from the highly positively charged N-terminal ARM domain.
History
DepositionMar 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Mar 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / diffrn_source / pdbx_struct_oper_list
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Beak and feather disease virus capsid protein
A: Beak and feather disease virus capsid protein
B: Beak and feather disease virus capsid protein
C: Beak and feather disease virus capsid protein
D: Beak and feather disease virus capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,66110
Polymers151,1875
Non-polymers4755
Water5,891327
1
E: Beak and feather disease virus capsid protein
A: Beak and feather disease virus capsid protein
B: Beak and feather disease virus capsid protein
C: Beak and feather disease virus capsid protein
D: Beak and feather disease virus capsid protein
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)1,819,937120
Polymers1,814,23960
Non-polymers5,69860
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation28_544x,-y-1/2,-z-1/21
crystal symmetry operation30_544z,-x-1/2,-y-1/21
crystal symmetry operation35_544y,-z-1/2,-x-1/21
crystal symmetry operation51_454-x-1/2,y,-z-1/21
crystal symmetry operation56_454-z-1/2,x,-y-1/21
crystal symmetry operation58_454-y-1/2,z,-x-1/21
crystal symmetry operation74_445-x-1/2,-y-1/2,z1
crystal symmetry operation79_445-z-1/2,-x-1/2,y1
crystal symmetry operation84_445-y-1/2,-z-1/2,x1
Buried area380740 Å2
ΔGint-2238 kcal/mol
Surface area370720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)377.310, 377.310, 377.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: Protein
Beak and feather disease virus capsid protein


Mass: 30237.316 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beak and feather disease virus / Gene: Cap / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023R6W2
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 3.7 Å3/Da / Density % sol: 66.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.8 M Na/k hydrogen phosphate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→35 Å / Num. obs: 74754 / % possible obs: 99.9 % / Redundancy: 9.1 % / Net I/σ(I): 7.3

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Processing

SoftwareName: PHENIX / Version: (1.10pre_2104: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: J509

Resolution: 2.55→34.444 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 3730 5 %
Rwork0.1912 --
obs0.1925 74633 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→34.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8310 0 25 327 8662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028555
X-RAY DIFFRACTIONf_angle_d0.56111635
X-RAY DIFFRACTIONf_dihedral_angle_d13.5065060
X-RAY DIFFRACTIONf_chiral_restr0.0421270
X-RAY DIFFRACTIONf_plane_restr0.0031510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5501-2.58240.29311470.2582527X-RAY DIFFRACTION100
2.5824-2.61630.29581360.25472609X-RAY DIFFRACTION100
2.6163-2.65220.26441520.24642557X-RAY DIFFRACTION100
2.6522-2.690.28171410.25622574X-RAY DIFFRACTION100
2.69-2.73020.29081400.24352572X-RAY DIFFRACTION100
2.7302-2.77280.26651530.23252562X-RAY DIFFRACTION100
2.7728-2.81820.25661480.24042607X-RAY DIFFRACTION100
2.8182-2.86680.25661110.23232614X-RAY DIFFRACTION100
2.8668-2.91890.27311320.22852595X-RAY DIFFRACTION100
2.9189-2.9750.22981170.21412601X-RAY DIFFRACTION100
2.975-3.03570.27451200.21672613X-RAY DIFFRACTION100
3.0357-3.10170.2821110.22982647X-RAY DIFFRACTION100
3.1017-3.17380.26861390.22822587X-RAY DIFFRACTION100
3.1738-3.25310.24381670.21152585X-RAY DIFFRACTION100
3.2531-3.3410.26841570.20482583X-RAY DIFFRACTION100
3.341-3.43920.2541270.21052616X-RAY DIFFRACTION100
3.4392-3.55010.25011570.19922609X-RAY DIFFRACTION100
3.5501-3.67690.23711290.19032624X-RAY DIFFRACTION100
3.6769-3.82390.21051360.18942609X-RAY DIFFRACTION100
3.8239-3.99770.18951360.16612624X-RAY DIFFRACTION100
3.9977-4.20810.15361390.15382634X-RAY DIFFRACTION99
4.2081-4.47120.14271520.13342635X-RAY DIFFRACTION100
4.4712-4.81560.14671520.13012639X-RAY DIFFRACTION100
4.8156-5.29870.16251270.13422679X-RAY DIFFRACTION100
5.2987-6.06180.1661180.17242741X-RAY DIFFRACTION100
6.0618-7.62360.21131400.1992740X-RAY DIFFRACTION100
7.6236-34.44670.21311460.21192920X-RAY DIFFRACTION100

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