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Nakamichi Y, Miyazaki N, Tsutsumi K, Higashiura A, Narita H, Murata K, Nakagawa A. An Assembly Intermediate Structure of Rice Dwarf Virus Reveals a Hierarchical Outer Capsid Shell Assembly Mechanism. Structure 2018; 27:439-448.e3. [PMID: 30581044 DOI: 10.1016/j.str.2018.10.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 08/29/2018] [Accepted: 10/26/2018] [Indexed: 10/27/2022]
Abstract
Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric protein) exhibiting icosahedral T = 13 symmetry. Here we describe the construction and structural evaluation of an assembly intermediate of the Rice dwarf virus of the family Reoviridae stalled at the second capsid layer via targeted disruption of the trimer-trimer interaction interface in the second-layer capsid protein. Structural determination was performed by conventional and Zernike/Volta phase-contrast cryoelectron microscopy. The assembly defect second-layer capsid trimers bound exclusively to the outer surface of the innermost capsid layer at the icosahedral 3-fold axis. Furthermore, the second-layer assembly could not proceed without specific inter-trimer interactions. Our results suggest that the correct assembly pathway for second-layer capsid formation is highly controlled at the inter-layer and inter-trimer interactions.
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Affiliation(s)
- Yusuke Nakamichi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan; Institute for Sustainable Chemistry, National Institute of Advanced Industrial Science and Technology, Higashi-Hiroshima, Hiroshima 739-0046 Japan
| | - Naoyuki Miyazaki
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan; National Institute for Physiological Sciences, Okazaki, Aichi 444-8787 Japan
| | - Kenta Tsutsumi
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan
| | - Akifumi Higashiura
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan; Department of Virology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Hiroshima 734-8551 Japan
| | - Hirotaka Narita
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8787 Japan
| | - Atsushi Nakagawa
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 Japan.
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Mathieu M, Petitpas I, Navaza J, Lepault J, Kohli E, Pothier P, Prasad B, Cohen J, Rey FA. Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion. EMBO J 2001; 20:1485-97. [PMID: 11285213 PMCID: PMC145492 DOI: 10.1093/emboj/20.7.1485] [Citation(s) in RCA: 155] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The structural protein VP6 of rotavirus, an important pathogen responsible for severe gastroenteritis in children, forms the middle layer in the triple-layered viral capsid. Here we present the crystal structure of VP6 determined to 2 A resolution and describe its interactions with other capsid proteins by fitting the atomic model into electron cryomicroscopic reconstructions of viral particles. VP6, which forms a tight trimer, has two distinct domains: a distal beta-barrel domain and a proximal alpha-helical domain, which interact with the outer and inner layer of the virion, respectively. The overall fold is similar to that of protein VP7 from bluetongue virus, with the subunits wrapping about a central 3-fold axis. A distinguishing feature of the VP6 trimer is a central Zn(2+) ion located on the 3-fold molecular axis. The crude atomic model of the middle layer derived from the fit shows that quasi-equivalence is only partially obeyed by VP6 in the T = 13 middle layer and suggests a model for the assembly of the 260 VP6 trimers onto the T = 1 viral inner layer.
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Affiliation(s)
- Magali Mathieu
- Laboratoire de Génétique des Virus, CNRS–UPR 9053 1, Avenue de la Terrasse Bâtiment 14C, 91198 Gif-sur-Yvette Cedex, Laboratoire de Microbiologie Médicale et Moléculaire, UFR Médecine et Pharmacie, Université de Bourgogne, Boulevard Jeanne d’Arc, F-21000 Dijon, Virologie Moléculaire et Cellulaire, INRA–CRJ, Domaine de Vilvert, F-78350 Jouy-en-Josas, France and Department of Biochemistry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA Present address: Aventis Pharma, 13 quai Jules Guesde, F-94403 Vitry-sur-Seine Cedex, France Present address: Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK Corresponding authors e-mail: or
M.Mathieu and I.Petitpas contributed equally to this work
| | - Isabelle Petitpas
- Laboratoire de Génétique des Virus, CNRS–UPR 9053 1, Avenue de la Terrasse Bâtiment 14C, 91198 Gif-sur-Yvette Cedex, Laboratoire de Microbiologie Médicale et Moléculaire, UFR Médecine et Pharmacie, Université de Bourgogne, Boulevard Jeanne d’Arc, F-21000 Dijon, Virologie Moléculaire et Cellulaire, INRA–CRJ, Domaine de Vilvert, F-78350 Jouy-en-Josas, France and Department of Biochemistry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA Present address: Aventis Pharma, 13 quai Jules Guesde, F-94403 Vitry-sur-Seine Cedex, France Present address: Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK Corresponding authors e-mail: or
M.Mathieu and I.Petitpas contributed equally to this work
| | - Jorge Navaza
- Laboratoire de Génétique des Virus, CNRS–UPR 9053 1, Avenue de la Terrasse Bâtiment 14C, 91198 Gif-sur-Yvette Cedex, Laboratoire de Microbiologie Médicale et Moléculaire, UFR Médecine et Pharmacie, Université de Bourgogne, Boulevard Jeanne d’Arc, F-21000 Dijon, Virologie Moléculaire et Cellulaire, INRA–CRJ, Domaine de Vilvert, F-78350 Jouy-en-Josas, France and Department of Biochemistry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA Present address: Aventis Pharma, 13 quai Jules Guesde, F-94403 Vitry-sur-Seine Cedex, France Present address: Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK Corresponding authors e-mail: or
M.Mathieu and I.Petitpas contributed equally to this work
| | - Jean Lepault
- Laboratoire de Génétique des Virus, CNRS–UPR 9053 1, Avenue de la Terrasse Bâtiment 14C, 91198 Gif-sur-Yvette Cedex, Laboratoire de Microbiologie Médicale et Moléculaire, UFR Médecine et Pharmacie, Université de Bourgogne, Boulevard Jeanne d’Arc, F-21000 Dijon, Virologie Moléculaire et Cellulaire, INRA–CRJ, Domaine de Vilvert, F-78350 Jouy-en-Josas, France and Department of Biochemistry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA Present address: Aventis Pharma, 13 quai Jules Guesde, F-94403 Vitry-sur-Seine Cedex, France Present address: Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK Corresponding authors e-mail: or
M.Mathieu and I.Petitpas contributed equally to this work
| | - Evelyne Kohli
- Laboratoire de Génétique des Virus, CNRS–UPR 9053 1, Avenue de la Terrasse Bâtiment 14C, 91198 Gif-sur-Yvette Cedex, Laboratoire de Microbiologie Médicale et Moléculaire, UFR Médecine et Pharmacie, Université de Bourgogne, Boulevard Jeanne d’Arc, F-21000 Dijon, Virologie Moléculaire et Cellulaire, INRA–CRJ, Domaine de Vilvert, F-78350 Jouy-en-Josas, France and Department of Biochemistry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA Present address: Aventis Pharma, 13 quai Jules Guesde, F-94403 Vitry-sur-Seine Cedex, France Present address: Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK Corresponding authors e-mail: or
M.Mathieu and I.Petitpas contributed equally to this work
| | - Pierre Pothier
- Laboratoire de Génétique des Virus, CNRS–UPR 9053 1, Avenue de la Terrasse Bâtiment 14C, 91198 Gif-sur-Yvette Cedex, Laboratoire de Microbiologie Médicale et Moléculaire, UFR Médecine et Pharmacie, Université de Bourgogne, Boulevard Jeanne d’Arc, F-21000 Dijon, Virologie Moléculaire et Cellulaire, INRA–CRJ, Domaine de Vilvert, F-78350 Jouy-en-Josas, France and Department of Biochemistry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA Present address: Aventis Pharma, 13 quai Jules Guesde, F-94403 Vitry-sur-Seine Cedex, France Present address: Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK Corresponding authors e-mail: or
M.Mathieu and I.Petitpas contributed equally to this work
| | - B.V.Venkataram Prasad
- Laboratoire de Génétique des Virus, CNRS–UPR 9053 1, Avenue de la Terrasse Bâtiment 14C, 91198 Gif-sur-Yvette Cedex, Laboratoire de Microbiologie Médicale et Moléculaire, UFR Médecine et Pharmacie, Université de Bourgogne, Boulevard Jeanne d’Arc, F-21000 Dijon, Virologie Moléculaire et Cellulaire, INRA–CRJ, Domaine de Vilvert, F-78350 Jouy-en-Josas, France and Department of Biochemistry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA Present address: Aventis Pharma, 13 quai Jules Guesde, F-94403 Vitry-sur-Seine Cedex, France Present address: Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK Corresponding authors e-mail: or
M.Mathieu and I.Petitpas contributed equally to this work
| | - Jean Cohen
- Laboratoire de Génétique des Virus, CNRS–UPR 9053 1, Avenue de la Terrasse Bâtiment 14C, 91198 Gif-sur-Yvette Cedex, Laboratoire de Microbiologie Médicale et Moléculaire, UFR Médecine et Pharmacie, Université de Bourgogne, Boulevard Jeanne d’Arc, F-21000 Dijon, Virologie Moléculaire et Cellulaire, INRA–CRJ, Domaine de Vilvert, F-78350 Jouy-en-Josas, France and Department of Biochemistry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA Present address: Aventis Pharma, 13 quai Jules Guesde, F-94403 Vitry-sur-Seine Cedex, France Present address: Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK Corresponding authors e-mail: or
M.Mathieu and I.Petitpas contributed equally to this work
| | - Félix A. Rey
- Laboratoire de Génétique des Virus, CNRS–UPR 9053 1, Avenue de la Terrasse Bâtiment 14C, 91198 Gif-sur-Yvette Cedex, Laboratoire de Microbiologie Médicale et Moléculaire, UFR Médecine et Pharmacie, Université de Bourgogne, Boulevard Jeanne d’Arc, F-21000 Dijon, Virologie Moléculaire et Cellulaire, INRA–CRJ, Domaine de Vilvert, F-78350 Jouy-en-Josas, France and Department of Biochemistry, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA Present address: Aventis Pharma, 13 quai Jules Guesde, F-94403 Vitry-sur-Seine Cedex, France Present address: Blackett Laboratory, Imperial College, Prince Consort Road, London SW7 2BW, UK Corresponding authors e-mail: or
M.Mathieu and I.Petitpas contributed equally to this work
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