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- PDB-6e34: Capsid protein of PCV2 with N,O6-DISULFO-GLUCOSAMINE and 2-O-sulf... -

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Basic information

Entry
Database: PDB / ID: 6e34
TitleCapsid protein of PCV2 with N,O6-DISULFO-GLUCOSAMINE and 2-O-sulfo-alpha-L-idopyranuronic acid
ComponentsCapsid protein of PCV2
KeywordsVIRUS LIKE PARTICLE / viral jelly-roll
Function / homologyCircovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / viral capsid assembly / host cell nucleus / 27.9 kDa capsid protein
Function and homology information
Specimen sourcePorcine circovirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
Model detailsCryo-EM image reconstruction at 3.2Angstrom resolution
AuthorsKhayat, R. / Dhindwal, S.
CitationJournal: J. Virol. / Year: 2019
Title: Porcine circovirus 2 uses a multitude of weak binding sites to interact with heparan sulfate, and the interactions do not follow the symmetry of the capsid.
Authors: Sonali Dhindwal / Bryant Avila / Shanshan Feng / Reza Khayat
Abstract: Porcine circovirus 2 is the smallest pathogenic virus capable of autonomous replication within its host. Infections result in immunosuppression and subsequent death of the host, and are initiated via ...Porcine circovirus 2 is the smallest pathogenic virus capable of autonomous replication within its host. Infections result in immunosuppression and subsequent death of the host, and are initiated via the attachment of the PCV2 icosahedral capsid to heparan sulfate and chondroitin sulfate B glycosaminoglycans on the cell surface. However, the underlying mechanism of structural recognition remains to be explored. Using heparin, a routinely used analog of heparan sulfate, we demonstrate that increasing lengths of heparin exhibit greater affinity towards PCV2. Our competition assays indicate that dextra sulfate (8kDa) has higher affinity than heparin (12kDa), chondroitin sulfate B (41kDa) hyaluronic acid (1.6MDa), and dextran (6kDa) for PCV2. This suggests that polymers high in sulfate content are capable of competing with the PCV2-heparan sulfate interaction, and thus have the potential to inhibit PCV2 infection. Finally, we visualize the interaction between heparin and the PCV2 capsid using cryo-electron microscopy single particle analysis, symmetry expansion, and focused classification. The image reconstructions provide the first example of an asymmetric distribution of heparin on the surface of an icosahedral virus capsid. We demonstrate that each of the 60 capsid subunits that generate the 1 capsid can bind heparin via one of five binding sites. However, not all of the binding sites are occupied by heparin and only one- to two-thirds of the binding sites are occupied. The binding sites are defined by arginine, lysine, and polar amino acids. Mutating the arginine, lysine, and polar amino acids to alanine diminishes the binding capacity of PCV2 to heparin. It has been demonstrated that porcine circovirus 2 () attaches to cells via heparan sulfate () and chondroitin sulfate B () glycosaminoglycans; however, the underlying structural mechanism describing the HS/CSB recognition by PCV2 remains to be explored. We use cryo-electron microscopy with single particle analysis, symmetry expansion, and focused classification to visualize the interaction between the PCV2 capsid and heparin, an analog of heparan sulfate, to better than 3.6Å resolution. We observe that the interaction between the PCV2 and heparin does not adhere to the icosahedral symmetry of the capsid. To the best of our knowledge, this is the first example where the interaction between heparin and an icosahedral capsid does not follow the symmetry elements of the capsid. Our findings also suggest that anionic polymers such as dextran sulfate may act to inhibit PCV2 infection.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 13, 2018 / Release: Dec 26, 2018

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Structure visualization

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Assembly

Deposited unit
A1: Capsid protein of PCV2
A2: Capsid protein of PCV2
A3: Capsid protein of PCV2
A4: Capsid protein of PCV2
A5: Capsid protein of PCV2
A6: Capsid protein of PCV2
A7: Capsid protein of PCV2
A8: Capsid protein of PCV2
A9: Capsid protein of PCV2
AA: Capsid protein of PCV2
AB: Capsid protein of PCV2
AC: Capsid protein of PCV2
AD: Capsid protein of PCV2
AE: Capsid protein of PCV2
AF: Capsid protein of PCV2
AG: Capsid protein of PCV2
AH: Capsid protein of PCV2
AI: Capsid protein of PCV2
AJ: Capsid protein of PCV2
AK: Capsid protein of PCV2
AL: Capsid protein of PCV2
AM: Capsid protein of PCV2
AN: Capsid protein of PCV2
AO: Capsid protein of PCV2
AP: Capsid protein of PCV2
AQ: Capsid protein of PCV2
AR: Capsid protein of PCV2
AS: Capsid protein of PCV2
AT: Capsid protein of PCV2
AU: Capsid protein of PCV2
AV: Capsid protein of PCV2
AW: Capsid protein of PCV2
AX: Capsid protein of PCV2
AY: Capsid protein of PCV2
AZ: Capsid protein of PCV2
Aa: Capsid protein of PCV2
Ab: Capsid protein of PCV2
Ac: Capsid protein of PCV2
Ad: Capsid protein of PCV2
Ae: Capsid protein of PCV2
Af: Capsid protein of PCV2
Ag: Capsid protein of PCV2
Ah: Capsid protein of PCV2
Ai: Capsid protein of PCV2
Aj: Capsid protein of PCV2
Ak: Capsid protein of PCV2
Al: Capsid protein of PCV2
Am: Capsid protein of PCV2
An: Capsid protein of PCV2
Ao: Capsid protein of PCV2
Ap: Capsid protein of PCV2
Aq: Capsid protein of PCV2
Ar: Capsid protein of PCV2
As: Capsid protein of PCV2
At: Capsid protein of PCV2
Au: Capsid protein of PCV2
Av: Capsid protein of PCV2
Aw: Capsid protein of PCV2
Ax: Capsid protein of PCV2
Ay: Capsid protein of PCV2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,674,94063
Polyers1,673,98860
Non-polymers9533
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: none
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)231580
ΔGint (kcal/M)-918
Surface area (Å2)406510

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Components

#1: Protein/peptide ...
Capsid protein of PCV2 /


Mass: 27899.795 Da / Num. of mol.: 60 / Source: (gene. exp.) Porcine circovirus 2 / Gene: cap, Cap, cp, ORF2, PCV2_gp3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q805N7
#2: Chemical ChemComp-SGN / N,O6-DISULFO-GLUCOSAMINE


Mass: 339.298 Da / Num. of mol.: 2 / Formula: C6H13NO11S2
#3: Chemical ChemComp-IDS / 2-O-sulfo-alpha-L-idopyranuronic acid / O2-SULFO-GLUCURONIC ACID


Mass: 274.203 Da / Num. of mol.: 1 / Formula: C6H10O10S

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSourceDetails
1Porcine circovirus 2VIRUS10RECOMBINANT
2PCV2 capsidCOMPLEX11NATURALA segment of heparin sulfate identified in the image reconstruction
3Heparin sulfateCOMPLEX1NATURAL
Molecular weight
IDValueEntity assembly IDExperimental value
11.5 MDa1NO
21.5 MDa1YES
31.4 kDa/nm1YES
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
2185708Porcine circovirus 2
329823Sus scrofa (pig)
439823Sus scrofa (pig)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
217111Trichoplusia ni (cabbage looper)
327111Trichoplusia ni (cabbage looper)
437111Trichoplusia ni (cabbage looper)
Details of virus
IDEntity assembly IDEmptyEnvelopedVirus isolateVirus type
11NONOSPECIESVIRUS-LIKE PARTICLE
22
33
Natural host
IDEntity assembly IDNcbi tax IDOrganism
119823Sus scrofa
12
13
Virus shell
IDNameEntity assembly IDDiameterTriangulation number (T number)
1Capsid protein12151
12
13
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer ID
120 mM(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)HEPES1
2250 mMSodium ChlorideNaCl1
30.1 mMTris(2-carboxyethyl)phosphineTCEP1
42 mMEthylenediaminetetraacetic acidEDTA1
SpecimenConc.: 0.718 mg/ml / Details: This sample was monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 kelvins

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / C2 aperture diameter: 100 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 5 sec. / Electron dose: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 3725
Image scansMovie frames/image: 25 / Used frames/image: 2-25

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Processing

EM software
IDNameVersionCategoryDetails
2Leginonimage acquisition
4GctfCTF correctionPer particle estimation
7Coot0.82model fitting
9PHENIX1.13model refinement
10RELION2.0initial Euler assignment
11RELIONfinal Euler assignment
12FREALIGN9,11classification
13FREALIGN9.113D reconstructionNo refinement of parameters
CTF correctionDetails: Per particle estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 166369
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 58599 / Symmetry type: POINT
Atomic model buildingDetails: Several iterations of refinement / Overall b value: 35.5 / Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Correlation coefficient

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