7VY5: Capsid protein VP1
Coxsackievirus B3 (VP3-234Q) incubation with CD55 at pH7.4. Determined by electron microscopy at 3.15 Å resolution. Released 19 Jan 2022.
- Method
- Electron microscopy
- Resolution
- 3.15 Å
- Organisms
- Coxsackievirus B3, Homo sapiens
- Chains
- 5
- Atoms
- 7,341
- Mol. weight
- 105.61 kDa
- Ligands
- PLM
- Released
- 19 Jan 2022
Explore 7VY5 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7VY5 contains 31 α-helices and 79 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 9 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-16 | 3 | |
| β-strand | 17 | 1 | 1 |
| β-strand | 32 | 1 | 2 |
| α-helix | 34-36 | 3 | |
| α-helix | 44-46 | 3 | |
| β-strand | 53 | 1 | 1 |
| α-helix | 64-68 | 5 | |
| β-strand | 72-80 | 9 | 3 |
| β-strand | 87-91 | 5 | 4 |
| α-helix | 99-104 | 6 | |
| β-strand | 107-124 | 18 | 3 |
| β-strand | 138-144 | 7 | 4 |
| α-helix | 158-160 | 3 | |
| β-strand | 166-170 | 5 | 4 |
| α-helix | 175-176 | 2 | |
| β-strand | 177-180 | 4 | 3 |
| β-strand | 189-190 | 2 | 3 |
| β-strand | 195 | 1 | 5 |
| β-strand | 196 | 1 | 6 |
| β-strand | 205 | 1 | 6 |
| α-helix | 207-209 | 3 | |
| β-strand | 215-220 | 6 | 4 |
| β-strand | 229-247 | 19 | 3 |
| α-helix | 249-250 | 2 | |
| β-strand | 251 | 1 | 7 |
Chain B: 9 helices, 24 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 15-18 | 4 | 8 |
| β-strand | 21-24 | 4 | 8 |
| α-helix | 29-31 | 3 | |
| β-strand | 32-33 | 2 | 9 |
| α-helix | 52-53 | 2 | |
| β-strand | 54 | 1 | 10 |
| β-strand | 64-65 | 2 | 9 |
| α-helix | 66-68 | 3 | |
| β-strand | 69-70 | 2 | 11 |
| β-strand | 78-81 | 4 | 12 |
| α-helix | 82-85 | 4 | |
| α-helix | 90-98 | 9 | |
| β-strand | 99-105 | 7 | 10 |
| β-strand | 106-111 | 6 | 9 |
| β-strand | 119-128 | 10 | 12 |
| β-strand | 134 | 1 | 13 |
| α-helix | 140-142 | 3 | |
| α-helix | 143-146 | 4 | |
| β-strand | 153-154 | 2 | 12 |
| β-strand | 156 | 1 | 14 |
| α-helix | 159-162 | 4 | |
| β-strand | 168 | 1 | 13 |
| β-strand | 171 | 1 | 14 |
| β-strand | 179 | 1 | 7 |
| α-helix | 181-184 | 4 | |
| β-strand | 189-193 | 5 | 12 |
| β-strand | 199-204 | 6 | 9 |
| β-strand | 213 | 1 | 10 |
| β-strand | 218 | 1 | 5 |
| β-strand | 221-232 | 12 | 12 |
| β-strand | 242-243 | 2 | 11 |
| β-strand | 244-247 | 4 | 9 |
| β-strand | 250-257 | 8 | 10 |
Chain C: 6 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23 | 1 | 3 |
| α-helix | 30-32 | 3 | |
| β-strand | 39-40 | 2 | 3 |
| α-helix | 43-47 | 5 | |
| β-strand | 51-52 | 2 | 2 |
| α-helix | 59-63 | 5 | |
| α-helix | 66-68 | 3 | |
| β-strand | 70-72 | 3 | 2 |
| β-strand | 81-86 | 6 | 15 |
| α-helix | 99-104 | 6 | |
| β-strand | 107 | 1 | 16 |
| β-strand | 109-111 | 3 | 17 |
| β-strand | 114-120 | 7 | 2 |
| β-strand | 127 | 1 | 18 |
| β-strand | 129-135 | 7 | 15 |
| α-helix | 145-149 | 5 | |
| β-strand | 152-157 | 6 | 15 |
| β-strand | 163-168 | 6 | 2 |
| β-strand | 177-178 | 2 | 17 |
| β-strand | 189-194 | 6 | 15 |
| β-strand | 199 | 1 | 18 |
| β-strand | 208-216 | 9 | 2 |
| β-strand | 221-222 | 2 | 17 |
| β-strand | 225 | 1 | 16 |
Chain D: 1 helix, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-7 | 4 | 19 |
| β-strand | 26-29 | 4 | 19 |
| α-helix | 40-41 | 2 | |
| β-strand | 57 | 1 | 9 |
Chain E: 6 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 69-71 | 3 | |
| β-strand | 75-77 | 3 | 20 |
| α-helix | 79-83 | 5 | |
| β-strand | 92-94 | 3 | 21 |
| β-strand | 95-97 | 3 | 20 |
| α-helix | 98 | 1 | |
| β-strand | 101-103 | 3 | 22 |
| α-helix | 104 | 1 | |
| β-strand | 110-112 | 3 | 21 |
| β-strand | 113 | 1 | 23 |
| β-strand | 119 | 1 | 23 |
| α-helix | 120-121 | 2 | |
| β-strand | 126-128 | 3 | 22 |
| β-strand | 130 | 1 | 24 |
| α-helix | 131-133 | 3 | |
| β-strand | 140-142 | 3 | 25 |
| β-strand | 149 | 1 | 24 |
| β-strand | 153-155 | 3 | 26 |
| β-strand | 156-158 | 3 | 25 |
| β-strand | 165 | 1 | 27 |
| β-strand | 169-171 | 3 | 26 |
| β-strand | 172-175 | 4 | 28 |
| β-strand | 178-181 | 4 | 28 |
| β-strand | 187 | 1 | 27 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Capsid protein VP1 | A | protein | 268 | Coxsackievirus B3 | P03313 |
| Capsid protein VP2 | B | protein | 256 | Coxsackievirus B3 | P03313 |
| Capsid protein VP3 | C | protein | 238 | Coxsackievirus B3 | P03313 |
| Genome polyprotein | D | protein | 68 | Coxsackievirus B3 | P03313 |
| Complement decay-accelerating factor | E | protein | 123 | Homo sapiens | P08174 (AlphaFold model) |
Sequence of entity 1 (A), FASTA
>7VY5_1 Capsid protein VP1 (chains A)
RVADTVGTGPTNSEAIPALTAAETGHTSQVVPGDTMQTRHVKNYHSRSESTIENFLCRSA
CVYFTEYENSGAKRYAEWVLTPRQAAQLRRKLEFFTYVRFDLELTFVITSTQQPSTTQNQ
DAQILTHQIMYVPPGGPVPDKVDSYVWQTSTNPSVFWTEGNAPPRMSIPFLSIGNAYSNF
YDGWSEFSRNGVYGINTLNNMGTLYARHVNAGSTGPIKSTIRIYFKPKHVKAWIPRPPRL
CQYEKAKNVNFQPSGVTTTRQSITTMTN
Sequence of entity 2 (B), FASTA
>7VY5_2 Capsid protein VP2 (chains B)
GYSDRARSITLGNSTITTQECANVVVGYGVWPDYLKDSEATAEDQPTQPDVATCRFYTLD
SVQWQKTSPGWWWKLPDALSNLGLFGQNMQYHYLGRTGYTVHVQCNASKFHQGCLLVVCV
PEAEMGCATLDNTPSSAELLGGDSAKEFADKPVASGSNKLVQRVVYNAGMGVGVGNLTIF
PHQWINLRTNNSATIVMPYTNSVPMDNMFRHNNVTLMVIPFVPLDYCPGSTTYVPITVTI
APMCAEYNGLRLAGHQ
Sequence of entity 3 (C), FASTA
>7VY5_3 Capsid protein VP3 (chains C)
GLPTMNTPGSCQFLTSDDFQSPSAMPQYDVTPEMRIPGEVKNLMEIAEVDSVVPVQNVGE
KVNSMEAYQIPVRSNEGSGTQVFGFPLQPGYSSVFSRTLLGEILNYYTHWSGSIKLTFMF
CGSAMATGKFLLAYSPPGAGAPTKRVDAMLGTHVVWDVGLQSSCVLCIPWISQTHYRYVT
SDEYTAGGFITCWYQTNIVVPADAQSSCYIMCFVSACNDFSVRLLKDTPFISQQNFFQ
Sequence of entity 4 (D), FASTA
>7VY5_4 Genome polyprotein (chains D)
GAQVSTQKTGAHETGLNASGNSIIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIM
IKSLPALN
Sequence of entity 5 (E), FASTA
>7VY5_5 Complement decay-accelerating factor (chains E)
CEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEF
CKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPL
PEC
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PLM | Palmitic acid | C16 H32 O2 | 1 |
Primary citation
Molecular basis of differential receptor usage for naturally occurring CD55-binding and -nonbinding coxsackievirus B3 strains. Wang, Q., Yang, Q., Liu, C. et al. Proc Natl Acad Sci U S A (2022) 119. DOI 10.1073/pnas.2118590119 · PubMed
Other PDB entries of the same protein (UniProt P03313), best resolution first:
- 7W0Q 1.1 Å, TRIM7 in complex with C-terminal peptide of 2C
- 2ZU1 1.38 Å, crystal structure of CVB3 3C protease mutant C147A
- 7W0S 1.4 Å, TRIM7 in complex with C-terminal peptide of 2C
- 6S3A 1.52 Å, Coxsackie B3 2C protein in complex with S-Fluoxetine
- 7W0T 1.57 Å, TRIM7 in complex with C-terminal peptide of 2C
- 7QUW 1.65 Å, CVB3-3Cpro in complex with inhibitor MG-78
- 2ZTX 1.72 Å, Complex structure of CVB3 3C protease with EPDTC
- 2ZTY 1.72 Å, crystal structure of 3C protease from CVB3 in space group C2
- 2ZU3 1.75 Å, Complex structure of CVB3 3C protease with TG-0204998
- 4WFZ 1.8 Å, Coxsackievirus B3 3Dpol RNA Dependent RNA Polymerase - NaCl Crystal Form
- 4WFX 1.81 Å, Coxsackievirus B3 Polymerase - F232L Mutant - NaCl Crystal Form
- 6T3W 1.82 Å, Coxsackie B3 2C protein in complex with S-Fluoxetine
Browse structure collections
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