- PDB-8h2i: Near-atomic structure of five-fold averaged PBCV-1 capsid -
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Basic information
Entry
Database: PDB / ID: 8h2i
Title
Near-atomic structure of five-fold averaged PBCV-1 capsid
Components
MCPv1
MCPv2
MCPv3
MCPv4
MCPv5
Major capsid protein (MCP)
P11
P12
P13
P15
P16
P17
P18
P19
P1v1
P2
P20
P21
P22
P23
P3
P4
P5
P6
P8
P9
Keywords
VIRAL PROTEIN / giant virus / nucleocytoplasmic large DNA viruses (NCLDVs) / viral assembly / Paramecium bursaria chlorella virus 1 (PBCV-1) / chlorovirus / major capsid protein / minor capsid protein / VIRUS
Chlorovirus glycoprotein repeat / Domain of unknown function DUF5901 / Chlorovirus glycoprotein repeat / Family of unknown function (DUF5901) / Protein of unknown function DUF5762 / Protein of unknown function DUF5761 / Domain of unknown function DUF5899 / Family of unknown function (DUF5761) / Family of unknown function (DUF5762) / Family of unknown function (DUF5899) ...Chlorovirus glycoprotein repeat / Domain of unknown function DUF5901 / Chlorovirus glycoprotein repeat / Family of unknown function (DUF5901) / Protein of unknown function DUF5762 / Protein of unknown function DUF5761 / Domain of unknown function DUF5899 / Family of unknown function (DUF5761) / Family of unknown function (DUF5762) / Family of unknown function (DUF5899) / Peptidase G2, IMC autoproteolytic cleavage domain / Peptidase_G2, IMC autoproteolytic cleavage domain / Major capsid protein, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / Parallel beta-helix repeat / Parallel beta-helix repeats Similarity search - Domain/homology
Major capsid protein VP54 / DUF5901 domain-containing protein / Capsid protein / Uncharacterized protein / Capsid protein / Capsid protein / Major capsid protein / Peptidase_G2 domain-containing protein / Uncharacterized protein / PsbP C-terminal domain-containing protein ...Major capsid protein VP54 / DUF5901 domain-containing protein / Capsid protein / Uncharacterized protein / Capsid protein / Capsid protein / Major capsid protein / Peptidase_G2 domain-containing protein / Uncharacterized protein / PsbP C-terminal domain-containing protein / Transmembrane protein / A2M domain-containing protein / Uncharacterized protein / DUF5899 domain-containing protein / Uncharacterized protein / Capsid protein / Capsid protein / Chlorovirus glycoprotein repeat domain-containing protein / Peptidase S74 domain-containing protein / Chlorovirus glycoprotein repeat domain-containing protein / SAYSvFN domain-containing protein / Uncharacterized protein / Glycine-rich protein / Entry/fusion complex component / Capsid protein / Uncharacterized protein Similarity search - Component
Biological species
Paramecium bursaria Chlorella virus 1
Method
ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
AI011219
United States
Citation
Journal: Nat Commun / Year: 2022 Title: Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1. Authors: Qianqian Shao / Irina V Agarkova / Eric A Noel / David D Dunigan / Yunshu Liu / Aohan Wang / Mingcheng Guo / Linlin Xie / Xinyue Zhao / Michael G Rossmann / James L Van Etten / Thomas Klose / Qianglin Fang / Abstract: Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play ...Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play critical roles in the viral life cycles, identities and high-resolution structures of these components remain unknown. Here, by determining a near-atomic-resolution, five-fold averaged structure of Paramecium bursaria chlorella virus 1, we unexpectedly found the viral capsid possesses up to five major capsid protein variants and a penton protein variant. These variants create varied capsid microenvironments for the associations of fibers, a vesicle, and previously unresolved minor capsid proteins. Our structure reveals the identities and atomic models of the capsid components that do not obey the overall icosahedral symmetry and leads to a model for how these components are assembled and initiate capsid assembly, and this model might be applicable to many other giant viruses.
aa: Major capsid protein (MCP) ab: Major capsid protein (MCP) ac: Major capsid protein (MCP) ad: Major capsid protein (MCP) ae: Major capsid protein (MCP) af: Major capsid protein (MCP) ag: Major capsid protein (MCP) ah: Major capsid protein (MCP) ai: Major capsid protein (MCP) aj: Major capsid protein (MCP) ak: Major capsid protein (MCP) al: Major capsid protein (MCP) am: Major capsid protein (MCP) an: Major capsid protein (MCP) ao: Major capsid protein (MCP) ap: Major capsid protein (MCP) aq: Major capsid protein (MCP) ar: Major capsid protein (MCP) as: Major capsid protein (MCP) at: Major capsid protein (MCP) au: Major capsid protein (MCP) av: Major capsid protein (MCP) aw: Major capsid protein (MCP) ax: Major capsid protein (MCP) ay: Major capsid protein (MCP) az: Major capsid protein (MCP) aA: Major capsid protein (MCP) aB: Major capsid protein (MCP) aC: Major capsid protein (MCP) aD: Major capsid protein (MCP) aE: Major capsid protein (MCP) aF: Major capsid protein (MCP) aG: Major capsid protein (MCP) aH: Major capsid protein (MCP) aI: Major capsid protein (MCP) aJ: Major capsid protein (MCP) aK: Major capsid protein (MCP) aL: Major capsid protein (MCP) aM: Major capsid protein (MCP) aN: Major capsid protein (MCP) aO: Major capsid protein (MCP) aP: Major capsid protein (MCP) aQ: Major capsid protein (MCP) aR: Major capsid protein (MCP) aS: Major capsid protein (MCP) aT: Major capsid protein (MCP) aU: Major capsid protein (MCP) aV: Major capsid protein (MCP) aW: Major capsid protein (MCP) aX: Major capsid protein (MCP) aY: Major capsid protein (MCP) aZ: Major capsid protein (MCP) ba: Major capsid protein (MCP) bb: Major capsid protein (MCP) bc: Major capsid protein (MCP) bd: Major capsid protein (MCP) be: Major capsid protein (MCP) bf: Major capsid protein (MCP) bg: Major capsid protein (MCP) bh: Major capsid protein (MCP) bi: Major capsid protein (MCP) bj: Major capsid protein (MCP) bk: Major capsid protein (MCP) bl: Major capsid protein (MCP) bm: Major capsid protein (MCP) bn: Major capsid protein (MCP) bo: Major capsid protein (MCP) bp: Major capsid protein (MCP) bq: Major capsid protein (MCP) br: Major capsid protein (MCP) bs: Major capsid protein (MCP) bt: Major capsid protein (MCP) bu: MCPv1 bv: MCPv1 bw: MCPv1 bx: MCPv1 by: MCPv1 bz: MCPv1 bA: MCPv1 bB: MCPv1 bC: MCPv2 bD: MCPv3 bE: MCPv4 bF: MCPv3 bG: P1v1 bH: P2 bI: P3 bJ: P3 bK: P3 bL: P4 bM: P4 bN: P4 bO: P4 bP: P5 bQ: P6 bR: P8 bS: P9 bT: P11 bU: P11 bV: P11 bW: P11 bX: P11 bY: P11 bZ: P11 ca: P11 cb: P11 cc: P11 cd: P11 ce: P11 cf: P12 cg: P13 ch: P15 ci: P16 cj: P17 ck: P17 cl: P17 cm: P17 cn: P18 co: P18 cp: P19 cq: P19 cr: P19 cs: P19 ct: P19 cu: P19 cv: P19 cw: P19 cx: P19 cy: P19 cz: P19 cA: P19 cB: P19 cC: P19 cD: P19 cE: P19 cF: P19 cG: P19 cH: P19 cI: P19 cJ: P19 cK: P19 cL: P19 cM: P19 cN: P19 cO: P20 cP: P21 cQ: P20 cR: MCPv5 cS: MCPv5 cT: MCPv5 cU: P22 cV: P22 cW: P22 cX: MCPv3 cY: MCPv4 cZ: MCPv3 da: P20 db: P21 dc: P20 dd: MCPv3 de: MCPv4 df: MCPv3 dg: P20 dh: P21 di: P20 dj: MCPv3 dk: MCPv3 dl: MCPv3 dm: P23 dn: P23 do: P23 dp: MCPv3 dq: MCPv4 dr: MCPv3 ds: P20 dt: P21 du: P20
aa: Major capsid protein (MCP) ab: Major capsid protein (MCP) ac: Major capsid protein (MCP) ad: Major capsid protein (MCP) ae: Major capsid protein (MCP) af: Major capsid protein (MCP) ag: Major capsid protein (MCP) ah: Major capsid protein (MCP) ai: Major capsid protein (MCP) aj: Major capsid protein (MCP) ak: Major capsid protein (MCP) al: Major capsid protein (MCP) am: Major capsid protein (MCP) an: Major capsid protein (MCP) ao: Major capsid protein (MCP) ap: Major capsid protein (MCP) aq: Major capsid protein (MCP) ar: Major capsid protein (MCP) as: Major capsid protein (MCP) at: Major capsid protein (MCP) au: Major capsid protein (MCP) av: Major capsid protein (MCP) aw: Major capsid protein (MCP) ax: Major capsid protein (MCP) ay: Major capsid protein (MCP) az: Major capsid protein (MCP) aA: Major capsid protein (MCP) aB: Major capsid protein (MCP) aC: Major capsid protein (MCP) aD: Major capsid protein (MCP) aE: Major capsid protein (MCP) aF: Major capsid protein (MCP) aG: Major capsid protein (MCP) aH: Major capsid protein (MCP) aI: Major capsid protein (MCP) aJ: Major capsid protein (MCP) aK: Major capsid protein (MCP) aL: Major capsid protein (MCP) aM: Major capsid protein (MCP) aN: Major capsid protein (MCP) aO: Major capsid protein (MCP) aP: Major capsid protein (MCP) aQ: Major capsid protein (MCP) aR: Major capsid protein (MCP) aS: Major capsid protein (MCP) aT: Major capsid protein (MCP) aU: Major capsid protein (MCP) aV: Major capsid protein (MCP) aW: Major capsid protein (MCP) aX: Major capsid protein (MCP) aY: Major capsid protein (MCP) aZ: Major capsid protein (MCP) ba: Major capsid protein (MCP) bb: Major capsid protein (MCP) bc: Major capsid protein (MCP) bd: Major capsid protein (MCP) be: Major capsid protein (MCP) bf: Major capsid protein (MCP) bg: Major capsid protein (MCP) bh: Major capsid protein (MCP) bi: Major capsid protein (MCP) bj: Major capsid protein (MCP) bk: Major capsid protein (MCP) bl: Major capsid protein (MCP) bm: Major capsid protein (MCP) bn: Major capsid protein (MCP) bo: Major capsid protein (MCP) bp: Major capsid protein (MCP) bq: Major capsid protein (MCP) br: Major capsid protein (MCP) bs: Major capsid protein (MCP) bt: Major capsid protein (MCP) bu: MCPv1 bv: MCPv1 bw: MCPv1 bx: MCPv1 by: MCPv1 bz: MCPv1 bA: MCPv1 bB: MCPv1 bC: MCPv2 bD: MCPv3 bE: MCPv4 bF: MCPv3 bG: P1v1 bH: P2 bI: P3 bJ: P3 bK: P3 bL: P4 bM: P4 bN: P4 bO: P4 bP: P5 bQ: P6 bR: P8 bS: P9 bT: P11 bU: P11 bV: P11 bW: P11 bX: P11 bY: P11 bZ: P11 ca: P11 cb: P11 cc: P11 cd: P11 ce: P11 cf: P12 cg: P13 ch: P15 ci: P16 cj: P17 ck: P17 cl: P17 cm: P17 cn: P18 co: P18 cp: P19 cq: P19 cr: P19 cs: P19 ct: P19 cu: P19 cv: P19 cw: P19 cx: P19 cy: P19 cz: P19 cA: P19 cB: P19 cC: P19 cD: P19 cE: P19 cF: P19 cG: P19 cH: P19 cI: P19 cJ: P19 cK: P19 cL: P19 cM: P19 cN: P19 cO: P20 cP: P21 cQ: P20 cR: MCPv5 cS: MCPv5 cT: MCPv5 cU: P22 cV: P22 cW: P22 cX: MCPv3 cY: MCPv4 cZ: MCPv3 da: P20 db: P21 dc: P20 dd: MCPv3 de: MCPv4 df: MCPv3 dg: P20 dh: P21 di: P20 dj: MCPv3 dk: MCPv3 dl: MCPv3 dm: P23 dn: P23 do: P23 dp: MCPv3 dq: MCPv4 dr: MCPv3 ds: P20 dt: P21 du: P20
x 5
complete point assembly
Evidence: microscopy
45.7 MDa, 885 polymers
Theoretical mass
Number of molelcules
Total (without water)
45,669,943
885
Polymers
45,669,943
885
Non-polymers
0
0
Water
0
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
point symmetry operation
4
2
Idetical with deposited unit
point asymmetric unit
Type
Name
Symmetry operation
Number
identity operation
1_555
x,y,z
1
3
Idetical with deposited unit in distinct coordinate
point asymmetric unit, std point frame
Type
Name
Symmetry operation
Number
transform to point frame
1
Symmetry
Point symmetry: (Schoenflies symbol: C5 (5 fold cyclic))
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Components
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Protein , 26 types, 177 molecules aaabacadaeafagahaiajakalamanaoapaqarasatauavawaxayazaAaBaCaD...
#1: Protein
... Majorcapsidprotein (MCP) / Major capsid protein
Mass: 48199.625 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: P30328
#2: Protein
MCPv1 / Major capsid protein variant 1 (MCPv1)
Mass: 58136.645 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41104
#3: Protein
MCPv2 / Major capsid protein variant 2 (MCPv2)
Mass: 55733.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: M1I493
#4: Protein
MCPv3 / Major capsid protein variant 3 (MCPv3)
Mass: 45115.641 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q89346
#5: Protein
MCPv4 / Major capsid protein variant 4 (MCPv4)
Mass: 45034.797 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q89345
#6: Protein
P1v1 / DUF5901 domain-containing protein / Penton protein variant 1 (P1v1)
Mass: 57555.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: M1I677
#7: Protein
P2 / DUF5899 domain-containing protein
Mass: 63888.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84656
#8: Protein
P3 / Reductive dehalogenase subunit A
Mass: 19116.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98573
#9: Protein
P4 / DUF2268 domain-containing protein
Mass: 20637.311 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41054
#10: Protein
P5 / NADH-ubiquinone oxidoreductase subunit
Mass: 16455.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98576
#11: Protein
P6 / PsbP domain-containing protein
Mass: 24036.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84523
#12: Protein
P8 / Copine domain-containing protein
Mass: 19226.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41126
#13: Protein
P9 / Transmembrane protein
Mass: 23407.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98459
#14: Protein
P11 / Secreted protein
Mass: 23322.656 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84666
#15: Protein
P12
Mass: 17715.475 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84459
#16: Protein
P13 / NVEALA family protein
Mass: 11070.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98473
#17: Protein
P15 / Entry/fusion complex component
Mass: 18627.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98534
#18: Protein
P16 / Glycine-rich protein
Mass: 9844.584 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q98530
#19: Protein
P17
Mass: 9122.370 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84629
#20: Protein
P18 / Transmembrane protein
Mass: 16497.771 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84533
#21: Protein
... P19 / A2M domain-containing protein
Mass: 43094.387 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84602
#22: Protein
P20 / Peptidase S74 domain-containing protein
Mass: 137671.312 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q89353
#23: Protein
P21
Mass: 141414.188 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q89349
#24: Protein
MCPv5 / Capsid protein
Mass: 45585.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: O41040
#25: Protein
P22 / Peptidase_G2 domain-containing protein
Mass: 137927.828 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q84443
#26: Protein
P23 / Chlorovirus glycoprotein repeat domain-containing protein
Mass: 140121.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Paramecium bursaria Chlorella virus 1 / References: UniProt: Q89360
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Experimental details
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Experiment
Experiment
Method: ELECTRON MICROSCOPY
EM experiment
Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction
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