Eukaryotic Viruses

Tomitake TsukiharaStructural organization of a double-shelled spherical virus, Rice dwarf virus

Mavis Agbandje-McKennaStructure to function correlation for the ssDNA parvoviruses

John J. JohnsonThe structural basis for a shared ancestry of viruses infecting eucaryota, bacteria and archaea

International School of CrystallographyStructure and Function of Large Molecular Assemblies

Structure organization of a double-shelled spherical viru

s, Rice dwarf virus

T. TsukiharaIPR, Osaka University, Japan

Motivation

Why are such complicated structures as RDV, cytochrome c oxidase, eukaryotic proteasome assembled correctly in the cell?

Hierarchy of assembly Accurate inter-molecular recognition

RDV(Nakagawa et al., 2003)

BTV(Grimes et al., 1998)

Reovirus(Reinisch et al., 2000)

RDV(Nakagawa et al., 2003)

12 genomesegments

10 genomesegments

Double stranded RNA Viruses Family: Reoviridae

10 genomesegments

Rice Dwarf Virus (RDV)Rice Dwarf Virus (RDV)

Non structural proteinsPns4 Pns6 Pns10Pns11Pns12

Guanylyltransferase

Diffraction data and structure refinement of RDVDiffraction data and structure refinement of RDV

Space group: I222 Cell constants (Å): a=770, b=795, c=814Resolution (Å) : 230.0-3.5Total film packs: 1477Observed reflections: 17,806,888Unique reflections: 3,001,937Completeness(%): 97.7Rmerge: 0.186

Rcryst : 0.303 Rfree : 0.306r.m.s. deviation bond lengths 0.010 Å bond angles 1.48°Ramachandran plots most favored region 85.2% disallowed region 0.1%

Electron density map of RDV refined by NCS averaging

25 Å resolution50 Å resolutionContour level is 1.0σ

3.5Å resolution electron density map3.5Å resolution electron density map

RNARNAP8P8 P3P3

BTV(Gouet et al., Cell, 1999)

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Transcription complex(Polymerase & Capping enzyme)dsRNA

BTV

P1,polymeraseP1,polymeraseP5,guanylyl transferaseP5,guanylyl transferaseP7,RNA binding proteinP7,RNA binding protein

RDV P7(289~300 SEPFSDKERSEL) P7(55KDa), an RNA binding protein directly interact with P3.

The electron density of P7 pentamer.

Outer shell Inner core

Inner core

Structure comparison of the inner capsid proteins Structure comparison of the inner capsid proteins of Reoviridaeof Reoviridae

RDV P3BRDV P3B BTV VP3ABTV VP3A Reovirus l1AReovirus l1ARDV P3ARDV P3A

P3AP3A

P3BP3B

P3 subunit structureP3 subunit structure

FE FG FR FS GE GK

Strong H-bond (<3.3Å) 11 17 0 13 3 0

Weak H-bond (3.3-3.6Å) 2 7 1 5 1 2

Strong Salt-bridge (<3.3Å) 4 9 2 5 0 0

Weak Salt-bridge (3.3-3.6Å) 3 5 1 3 2 0

Other interactions* 185 326 42 206 1 6

Total number of interactions 205 364 46 237 77 8

Estimated total energy (kcal/mol) 110.5 199.8 22.6 146.8 36.3 5.8

*Number of other atom pairs with distances less than 4Å*Number of other atom pairs with distances less than 4Å

FE FG FR FS GE GK

Strong H-bond (<3.3Å) 11 17 0 13 3 0

Weak H-bond (3.3-3.6Å) 2 7 1 5 1 2

Strong Salt-bridge (<3.3Å) 4 9 2 5 0 0

Weak Salt-bridge (3.3-3.6Å) 3 5 1 3 2 0

Other interactions* 185 326 42 206 1 6

Total number of interactions 205 364 46 237 77 8

Estimated total energy (kcal/mol) 110.5 199.8 22.6 146.8 36.3 5.8

FFG

RSS

K

E 1.G-F, strongest interaction --> Dimer

2. Circular E-F interaction --> Decamer

Intermolecular interactions

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The P3-decamer accepts a transcription complex and a genome segment in the viral inclusion.

1. Five P7 molecules combine with P3 decamers around five-fold axis. (Nakagawa et al., Structure, 2003)

2. P7 was included in a P3 core, when both proteins were co-expressed. ( Hagiwara et al., 2003, JGV)

3. A viral RNA tightly interacts with P1, P5 and P7 during the structural organization. (Zhong et al., Science China, 2004)

4. P1, P3, P5 and P7 are in the viral inclusion consisting of Pns6, Pns11 and Pns12. Viral RNAs are synthesized in the viral inclusion. (Wei et al., 2006, JGV)

Pns6 Pns11 Pns12

Immunogold labelling of electron-dense inclusions with Pns6, Pns11 and Pns12. Dark dots indicate these three proteins. The viral inclusions consist of these non-structural proteins. (Wei et al., 2006, JGV)

300 nm

Confocal fluorescence microscopy (Wei et al., 2006, JGV)

P1

P3

P5

P7

The inner core proteins, P1, P3, P5 and P7 coexist with Pns12 in viral inclusions.

P2

P8

P9

The outer shell proteins, P2, P8 and P9 are not in the viral inclusions.

The core particles were obtained by incubating virus particles in 1.4M MgCl solution. (Takahashi & Omura et al., 1994)

P3 can form the inner core without P8.

Simplified animation of assembly process of the inner core in the viral inclusion

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Proposed model for structure organization of

RDV particle (1) (Decamer model)

Structure organization of the outer shell

1. P8 trimers

2. Nucleation of trimers on the three-fold axes of the inner core.

3. Two dimensional growth on the inner core surface

P8 subunit structureP8 subunit structure

The P8 trimer is rigid.

FG

RS

E

K L

FG

RS

E

K L

FG

RS

E

K L TRQ

S

P

TRQ

S

P

TRQ

S

P

T S R Q P

P3B (F) P3B (L) P3B (R) P3A (G) P3B (F) P3B (F) P3A (G) P3B (F) P3A (G)

Strong H-bond (<3.3Å) 6 6 6 4 7 (1) 9 4 (2) 2 5

Weak H-bond (3.3-3.6Å) 6 6 6 4 4 5 3 (1) 1 3

Other interactions* 63 63 63 84 121 101 90 29 67

Total number of interactions 225 92 132 212 107

Estimated total energy (kcal/mol) 146.7 45.2 65.3 112.3 57.8

*Number of other atom pairs with distances less than 4Å*Number of other atom pairs with distances less than 4Å

P8 trimer - inner core interaction

T trimers are nucleation sites on the inner core surface.

Wu & Omura et al., 2000

0.8 M MgCl2 treated

P8-trimers tend to make a two-dimensional hexagonal array.

Zhu & Omura et al., 1997

Assembly of P8-trimerson the inner core surface

T

R

Q and S

The symmetry mismatch between the inner core and the outer shell is overcome by the sequential assembly following the nucleation.

Summary

Symmetry enable viruses to assemble by a few kinds of inter-molecular interactions.

Accurate inter-molecular recognition is achieved by accurate inter-atomic interactions.

Hierarchy of structural organization is achieved by protein sorting in the viral inclusion and ranking of inter-molecular interactions. It reduces the freedom of assembly process.