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- PDB-5j37: Crystal structure of 60-mer BFDV Capsid Protein in complex with s... -

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Basic information

Entry
Database: PDB / ID: 5j37
TitleCrystal structure of 60-mer BFDV Capsid Protein in complex with single stranded DNA
Components
  • Beak and feather disease virus capsid protein
  • single stranded DNA
KeywordsVIRUS/DNA / BFDV Virus Capsid Jelly Roll / VIRAL PROTEIN / VIRUS-DNA complex
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 / virion attachment to host cell / host cell nucleus
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 / DNA / DNA (> 10) / Capsid protein
Similarity search - Component
Biological speciesBeak and feather disease virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / citation_author ...audit_author / citation_author / database_2 / diffrn_source / pdbx_struct_oper_list
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 25, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
E: Beak and feather disease virus capsid protein
F: single stranded DNA
A: Beak and feather disease virus capsid protein
G: single stranded DNA
B: Beak and feather disease virus capsid protein
H: single stranded DNA
C: Beak and feather disease virus capsid protein
I: single stranded DNA
D: Beak and feather disease virus capsid protein
J: single stranded DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,19115
Polymers196,71610
Non-polymers4755
Water11,440635
1
E: Beak and feather disease virus capsid protein
F: single stranded DNA
A: Beak and feather disease virus capsid protein
G: single stranded DNA
B: Beak and feather disease virus capsid protein
H: single stranded DNA
C: Beak and feather disease virus capsid protein
I: single stranded DNA
D: Beak and feather disease virus capsid protein
J: single stranded DNA
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)2,366,288180
Polymers2,360,590120
Non-polymers5,69860
Water1,946108
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 area445100 Å2
ΔGint-1959 kcal/mol
Surface area369860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)377.280, 377.280, 377.280
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: DNA chain
single stranded DNA


Mass: 9105.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.84 Å3/Da / Density % sol: 56.75 %
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: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→40.218 Å / Num. obs: 101384 / % possible obs: 100 % / Redundancy: 8.6 % / Net I/σ(I): 7.5

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Processing

SoftwareName: PHENIX / Version: (1.10pre_2104: ???) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J09

5j09


Resolution: 2.3→40.218 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1969 5030 4.97 %
Rwork0.1735 --
obs0.1747 101168 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→40.218 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8615 0 25 635 9275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028890
X-RAY DIFFRACTIONf_angle_d0.64212140
X-RAY DIFFRACTIONf_dihedral_angle_d14.5725195
X-RAY DIFFRACTIONf_chiral_restr0.0441330
X-RAY DIFFRACTIONf_plane_restr0.0031525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.32630.27771550.25033156X-RAY DIFFRACTION100
2.3263-2.35360.26721500.23843180X-RAY DIFFRACTION100
2.3536-2.38230.27581870.23463157X-RAY DIFFRACTION100
2.3823-2.41250.23611520.23743133X-RAY DIFFRACTION100
2.4125-2.44420.2631540.22233192X-RAY DIFFRACTION100
2.4442-2.47770.27281980.22763117X-RAY DIFFRACTION100
2.4777-2.51310.22892000.21993134X-RAY DIFFRACTION100
2.5131-2.55060.23451510.21623170X-RAY DIFFRACTION100
2.5506-2.59050.26771740.21183149X-RAY DIFFRACTION100
2.5905-2.63290.23371860.20483123X-RAY DIFFRACTION100
2.6329-2.67830.23181730.20213196X-RAY DIFFRACTION100
2.6783-2.7270.22681360.20283168X-RAY DIFFRACTION100
2.727-2.77940.24781610.18673197X-RAY DIFFRACTION100
2.7794-2.83620.20661620.18453205X-RAY DIFFRACTION100
2.8362-2.89780.23711660.18763151X-RAY DIFFRACTION100
2.8978-2.96520.19871780.1733177X-RAY DIFFRACTION100
2.9652-3.03930.1951720.1753187X-RAY DIFFRACTION100
3.0393-3.12150.21461650.18913187X-RAY DIFFRACTION100
3.1215-3.21330.20851590.17633185X-RAY DIFFRACTION100
3.2133-3.3170.19991430.16553221X-RAY DIFFRACTION100
3.317-3.43550.18561770.16583172X-RAY DIFFRACTION100
3.4355-3.57290.19891560.15893243X-RAY DIFFRACTION100
3.5729-3.73540.19451600.16393217X-RAY DIFFRACTION100
3.7354-3.93220.18421680.15483215X-RAY DIFFRACTION100
3.9322-4.17830.16011730.13723233X-RAY DIFFRACTION100
4.1783-4.50060.12031540.123256X-RAY DIFFRACTION100
4.5006-4.95270.131780.12013266X-RAY DIFFRACTION100
4.9527-5.66770.14351770.14123284X-RAY DIFFRACTION100
5.6677-7.13420.2061760.18983332X-RAY DIFFRACTION100
7.1342-40.22430.23011890.21643535X-RAY DIFFRACTION99

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