Fig 1.
Overall capsid structure of RnMBV1.
The RnMBV1 capsid comprises 60 MCP dimers (yellow: MCP_A, purple: MCP_B) and the CrP timers (in red, orange, and dark yellow). The red pentagon, triangle, and rectangle show the icosahedral 5-fold (5f), 3-fold (3f), and 2-fold (2f) axes, respectively.
Fig 2.
Extra-long C-terminal arms and the interlocking interface.
A) Superimposition of the MCP_A subunit (yellow) and B subunit (purple). B) Interactions of the C-terminal arm of MCP_A subunit (A1) with one adjacent MCP_B subunit (B1). Close-up view of the interactions between the C-terminal arm of A1 (Leu1126–Lys1193) and the amino acid residues in B1 (dotted yellow box). C) Interactions of the C-terminal arm of MCP_B subunit (B1) with two adjacent MCP_A subunits (A1, A2) and another MCP_B subunit (B0). Close-up view of the interactions between the C-terminal arm of B1 (Leu1126–Val1236) and the amino acid residues in the A2 (dotted light blue box), A1 (dotted red box), and B0 (dotted green box). D) Overall representation of C-terminal arms within a 5-fold complex made up with ten subunits. Both panels show the view inside the capsid. B, C, D) MCP_A and MCP_B subunits are colored yellow and purple, respectively, and are shown in surface representation. The C-terminal arms are colored by red and shown in cartoon representation. The interacting residues are found by contact distance restrictions of 3.8 Å in UCSF Chimera X. The interacting amino acid residues of the MCP_A and MCP_B subunits are labeled in yellow and magenta and represented in ball-and-stick mode.
Fig 3.
Unique protrusion domain of the RnMBV1 MCP.
A) Domain organization in the atomic model of the MCP. The protrusion domain, conserved domain, and extra-long C-terminal arm are colored red, gray, and dark blue, respectively. B) Superimposition of RnMBV1 MCP (colored by the domains corresponding to panel A) and ScV-L-A CP (orange). C) Locations of the protrusion domains on the capsid. The protrusion domains and conserved domains are colored red and gray, respectively. The green rectangle and yellow triangle display the protrusion domains formed by the MCP_A subunit dimer and the MCP_B subunit trimer, respectively.
Fig 4.
Atomic model, structural topology, and secondary structural elements of CrP.
A) Atomic model of one CrP trimer (red, orange, and dark yellow). The dashed lines indicate the exterior and interior sides of the CrP trimer. B) Structural topology diagram of the CrP. All ɑ-helices are colored red and numbered in order (assigned to be HA-G from the N- to C-terminus). C) Amino acid sequence organization of CrP. The amino acid sequence is a C-terminal portion of RnMBV1 ORF3. The amino acid residues of CrP are marked in black bold from Lys1292 to Gln1426. The orange boxes highlight ɑ-helices.
Fig 5.
CrPs and their interactions with MCPs.
A) Enlarged top view of the CrP trimer. Each trimer of the CrPs (red, orange, and dark yellow) is located on the top of the MCP_B subunits (purple, light purple, and dark purple) at the 3-fold axis. B) Close-up view of the interactions between CrP trimer and MCP_B subunit. The MCP_B subunit loop P548-K555 (dark blue) interacts with the CrP. The hydrogen bond between residues MCP_B subunit R533 and CrP G1341 is highlighted in a dashed-yellow circle.
Fig 6.
Reconstructed cryo-EM map after 3D focused classification on CrP trimers.
A) Overall central cross-section of the RnMBV1 cryo-EM map viewed along the icosahedral 3-fold axis (left panel). Enlarged views of the CrPs (right panels). The CrP trimer is surrounded by a red dotted line. The map intensity level in one CrP trimer (lower right panel) is weaker than that in the other regions, while the map intensity in another CrP trimer (upper right panel) is as strong as that in the other regions. B) Surface representation of reconstructed cryo-EM map. The intensity level in one CrP trimer is recovered as high after the 3D focused classification, which is deemed to be 100% occupancy (right upper panel). The map intensity in the other CrP trimers is low, which corresponds to approximately 30% occupancy (right bottom panel). The image is colored radially according to the distance from particle center.
Fig 7.
Number of CrP trimers on the particle and their distribution.
After the 3D focused classification of CrP trimers, the number of CrP trimers bound to the particle is counted and the distribution is plotted. The averaged numbers of presented CrP trimers per particle are 6.7 and 8.0 for full and empty particles, respectively.
Fig 8.
Structure of an obstructed pore and its properties.
A) Top view of the 5-fold obstructed pore. MCP_A and B subunits are colored yellow and purple, respectively. B) Close-up view (front view). The obstructing R140 and R141 residues of the MCP_A subunits are shown as stick representation. C) Electrostatics surface of the 5-fold pore. D) Backside view of the 5-fold pore. The C-terminal arm of the MCP_B subunits is colored purple. E) Cross-section of the obstructed pore. The dashed lines indicate the calculated pore size in diameter.