9I3H: CP of RHDV mutant - N15

CP of RHDV mutant - N15. Determined by electron microscopy at 2.5 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Rabbit hemorrhagic disease virus-AST89, Oryctolagus cuniculus
Chains: 4
Atoms: 12,140
Mol. weight: 173.91 kDa
Released: 26 Nov 2025

Explore 9I3H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I3H contains 42 α-helices and 147 β-strands across 4 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: 13 helices, 47 β-strands

Element	Residues	Length	Sheet
α-helix	46-52	7
α-helix	53-56	4
β-strand	60	1	1
α-helix	67-70	4
β-strand	73-81	9	2
α-helix	84-85	2
β-strand	89-94	6	3
α-helix	103-106	4
α-helix	107-109	3
β-strand	110	1	4
β-strand	113-114	2	1
β-strand	117-123	7	2
β-strand	130-138	9	3
α-helix	139	1
α-helix	150-152	3
β-strand	155-159	5	3
β-strand	166-170	5	2
β-strand	179	1	1
β-strand	189-199	11	3
β-strand	208-217	10	2
β-strand	222-223	2	1
β-strand	226	1	4
α-helix	246-249	4
β-strand	261-266	6	5
β-strand	278	1	6
β-strand	284	1	6
β-strand	294-296	3	7
β-strand	301-303	3	7
β-strand	312	1	8
β-strand	315-319	5	7
β-strand	339	1	9
β-strand	340	1	7
α-helix	348-350	3
β-strand	354-362	9	7
β-strand	368-382	15	7
β-strand	389-390	2	7
β-strand	393	1	10
β-strand	398-403	6	7
β-strand	407	1	8
β-strand	416-421	6	7
β-strand	425	1	7
β-strand	426	1	11
β-strand	437	1	5
β-strand	443	1	9
β-strand	445	1	10
β-strand	455	1	12
β-strand	458	1	12
β-strand	459-460	2	13
β-strand	461-466	6	5
β-strand	469	1	11
α-helix	482-484	3
β-strand	485-488	4	5
α-helix	492-498	7
β-strand	511-518	8	14
β-strand	523-526	4	14
β-strand	527-528	2	13
β-strand	534-536	3	13
β-strand	545-546	2	5
β-strand	552-560	9	14
α-helix	564-566	3

Chain B: 15 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	34-36	3	15
α-helix	43-52	10
α-helix	53-56	4
β-strand	60	1	16
α-helix	67-69	3
β-strand	73-81	9	15
α-helix	84-85	2
β-strand	89-94	6	17
α-helix	97-99	3
α-helix	101-106	6
α-helix	107-109	3
β-strand	113-114	2	16
β-strand	117-124	8	15
β-strand	130-138	9	17
α-helix	150-152	3
β-strand	155-159	5	17
β-strand	166-170	5	15
β-strand	179	1	16
β-strand	189-199	11	17
β-strand	208-217	10	15
β-strand	222-223	2	16
α-helix	245-248	4
β-strand	261-266	6	18
β-strand	278	1	19
β-strand	284	1	19
β-strand	294-296	3	20
β-strand	300	1	21
β-strand	301-303	3	20
β-strand	312	1	22
β-strand	315-319	5	20
β-strand	339	1	23
β-strand	340	1	20
α-helix	341-343	3
α-helix	349-350	2
β-strand	354-362	9	20
α-helix	367	1
β-strand	368-381	14	20
β-strand	382	1	24
β-strand	389	1	24
β-strand	393	1	25
β-strand	398-403	6	20
β-strand	407	1	22
β-strand	415	1	21
β-strand	416-421	6	20
β-strand	425	1	20
β-strand	426	1	26
β-strand	437	1	18
β-strand	443	1	23
β-strand	445	1	25
α-helix	450-452	3
β-strand	459-466	8	18
β-strand	469	1	26
β-strand	485-488	4	18
α-helix	492-499	8
β-strand	511-514	4	18
β-strand	517-518	2	27
β-strand	523-524	2	27
β-strand	526-528	3	18
β-strand	534-536	3	18
β-strand	545-546	2	18
β-strand	552-553	2	27
β-strand	557-560	4	18
α-helix	564-566	3
β-strand	567-568	2	27

Chain C: 13 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	28
α-helix	43-53	11
α-helix	54-56	3
β-strand	60	1	29
α-helix	67-70	4
β-strand	73-81	9	28
α-helix	84-85	2
β-strand	89-94	6	30
α-helix	106-109	4
β-strand	110	1	31
β-strand	112-114	3	29
β-strand	117-124	8	28
β-strand	130-138	9	30
α-helix	139	1
β-strand	155-159	5	30
β-strand	166-170	5	28
β-strand	179-180	2	29
β-strand	189-199	11	30
β-strand	208-217	10	28
β-strand	222-223	2	29
β-strand	226	1	31
α-helix	245-246	2
α-helix	247-251	5
β-strand	253	1	32
β-strand	254	1	33
β-strand	260	1	32
β-strand	261-266	6	34
β-strand	271	1	35
β-strand	278	1	36
β-strand	284	1	36
β-strand	295-297	3	37
β-strand	301-303	3	37
β-strand	312	1	38
β-strand	315-319	5	37
β-strand	340	1	37
β-strand	353-361	9	37
α-helix	367	1
β-strand	368-381	14	37
β-strand	390	1	37
β-strand	393	1	39
β-strand	398-403	6	37
β-strand	407	1	38
β-strand	417-420	4	37
β-strand	425-427	3	37
β-strand	445	1	39
β-strand	452	1	35
β-strand	455	1	40
β-strand	458	1	40
β-strand	459-460	2	41
β-strand	461-466	6	34
β-strand	469	1	37
β-strand	472	1	37
β-strand	485-488	4	34
β-strand	491	1	33
α-helix	492-498	7
α-helix	504-506	3
β-strand	511-518	8	41
β-strand	523-528	6	41
β-strand	534-536	3	41
α-helix	543-544	2
β-strand	545	1	34
β-strand	552-560	9	41
α-helix	564-566	3
β-strand	567-568	2	41

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	174-181	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP60	A, C	protein	551	Rabbit hemorrhagic disease virus-AST89	Q86119
Capsid protein VP60	B	protein	551	Rabbit hemorrhagic disease virus-AST89	Q86119
Three-fold helix	D	protein	12	Oryctolagus cuniculus	P03311

Sequence of entity 1 (A, C), FASTA

>9I3H_1 Capsid protein VP60 (chains A, C)
SVPGTTTDGMDPGVVATTSVVTAENSSASIATAGIGGPPQQVDQQETWRTNFYYNDVFTW
SVADAPGSILYTVQHSPQNNPFTAVLSQMYAGWAGGMQFRFIVAGSGVFGGRLVAAVIPP
GIEIGPGLEVRQFPHVVIDARSLEPVTITMPDLRPNMYHPTGDPGLVPTLVLSVYNNLIN
PFGGSTSAIQVTVETRPSEDFEFVMIRAPSSKTVDSISPAGLLTTPVLTGVGNDNRWNGQ
IVGLQPVPGGFSTCNRHWNLNGSTYGWSSPRFADIDHRRGSASYPGNNATNVLQFWYANA
GSAIDNPISQVAPDGFPDMSFVPFNGPGIPAAGWVGFGAIWNSNSGAPNVTTVQAYELGF
ATGAPGNLQPTTNTSGSQTVAKSIYAVVTGTAQNPAGLFVMASGVISTPSANAITYTPQP
DRIVTTPGTPAAAPVGKNTPIMFASVVRRTGDVNATAGSANGTQYGTGSQPLPVTIGLSL
NNYSSALMPGQFFVWQLTFASGFMEIGLSVDGYFYAGTGASTTLIDLTELIDVRPVGPRP
SKSTLVFNLGG

Sequence of entity 2 (B), FASTA

>9I3H_2 Capsid protein VP60 (chains B)
SVPGTTTDGMDPGVVATTSVVTAENSSASVATAGIGGPPQQVDQQETWRTNFYYNDVFTW
SVADAPGSILYTVQHSPQNNPFTAVLSQMYAGWAGGMQFRFIVAGSGVFGGRLVAAVIPP
GIEIGPGLEVRQFPHVVIDARSLEPVTITMPDLRPNMYHPTGDPGLVPTLVLSVYNNLIN
PFGGSTSAIQVTVETRPSEDFEFVMIRAPSSKTVDSISPAGLLTTPVLTGVGNDNRWNGQ
IVGLQPVPGGFSTCNRHWNLNGSTYGWSSPRFADIDHRRGSASYPGNNATNVLQFWYANA
GSAIDNPISQVAPDGFPDMSFVPFNGPGIPAAGWVGFGAIWNSNSGAPNVTTVQAYELGF
ATGAPGNLQPTTNTSGSQTVAKSIYAVVTGTAQNPAGLFVMASGVISTPSANAITYTPQP
DRIVTTPGTPAAAPVGKNTPIMFASVVRRTGDVNATAGSANGTQYGTGSQPLPVTIGLSL
NNYSSALMPGQFFVWQLTFASGFMEIGLSVDGYFYAGTGASTTLIDLTELIDVRPVGPRP
SKSTLVFNLGG

Sequence of entity 3 (D), FASTA

>9I3H_3 Three-fold helix (chains D)
AAEFFEGMVHDS

Primary citation

Structure of RHDV mutant N15 at 2.5 Angstroms resolution. Novoa, G., Martinez-Romero, J.M., Perez-Mata, C. et al. To be published.

Other PDB entries of the same protein (UniProt Q86119), best resolution first:

8CYL 1.89 Å, Ast89 P domain
9I8J 2.9 Å, AB Spike of RHDV mutant N15
9I3E 3.0 Å, CP of RHDV mutant - 29N
9I90 3.2 Å, CP of empty RHDV virion
9I8R 3.3 Å, CP of RHDV VLP (VP1)
9I9D 3.3 Å, CP of RHDV virion (full particle)
3ZUE 10.3 Å, Rabbit Hemorrhagic Disease Virus (RHDV)capsid protein

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