9I9D: CP of RHDV virion

CP of RHDV virion (full particle). Determined by electron microscopy at 3.3 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Oryctolagus cuniculus
Chains: 3
Atoms: 12,123
Mol. weight: 180.03 kDa
Released: 26 Nov 2025

Explore 9I9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9I9D contains 45 α-helices and 150 β-strands across 3 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: 15 helices, 46 β-strands

Element	Residues	Length	Sheet
α-helix	46-52	7
α-helix	53-56	4
β-strand	60	1	1
β-strand	73-81	9	2
β-strand	89-94	6	3
α-helix	97-99	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	1	5
β-strand	132-138	7	3
α-helix	139	1
α-helix	150-152	3
β-strand	155-159	5	3
α-helix	165	1
β-strand	166-170	5	2
β-strand	179	1	1
β-strand	189-194	6	3
β-strand	199	1	5
β-strand	208-217	10	2
β-strand	222-223	2	1
β-strand	226	1	4
α-helix	259-260	2
β-strand	261-266	6	6
β-strand	294-297	4	7
β-strand	300	1	8
β-strand	301-303	3	7
β-strand	312	1	9
β-strand	315-319	5	7
β-strand	340	1	7
α-helix	341-342	2
α-helix	348-350	3
β-strand	355-362	8	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	9
β-strand	415	1	8
β-strand	416-421	6	7
β-strand	425	1	7
β-strand	426	1	11
β-strand	437	1	6
β-strand	445	1	10
α-helix	450-452	3
β-strand	459-460	2	12
β-strand	461-466	6	6
β-strand	469	1	11
α-helix	482-484	3
β-strand	485-488	4	6
α-helix	492-499	8
β-strand	511-518	8	12
β-strand	523-528	6	12
β-strand	534-536	3	12
β-strand	545-546	2	6
β-strand	552	1	12
β-strand	555-560	6	12
α-helix	564-566	3
β-strand	567-568	2	12

Chain B: 14 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	34-35	2	13
α-helix	43-50	8
α-helix	52-56	5
α-helix	59	1
β-strand	60	1	14
β-strand	73-81	9	13
α-helix	84-85	2
β-strand	89-94	6	15
α-helix	97-99	3
α-helix	101-107	7
β-strand	113-114	2	14
β-strand	117-124	8	13
β-strand	130	1	16
β-strand	132-138	7	15
β-strand	155-159	5	15
β-strand	166-170	5	13
β-strand	179	1	14
β-strand	189-194	6	15
α-helix	197-198	2
β-strand	199	1	16
β-strand	208-217	10	13
β-strand	222-223	2	14
β-strand	261-266	6	17
α-helix	267	1
β-strand	278	1	18
β-strand	284	1	18
β-strand	294-296	3	19
β-strand	300	1	20
β-strand	301-303	3	19
β-strand	312	1	21
β-strand	315-319	5	19
β-strand	339	1	22
β-strand	340	1	19
α-helix	349-350	2
β-strand	354-362	9	19
α-helix	367	1
β-strand	368-382	15	19
β-strand	389-390	2	19
β-strand	393	1	23
β-strand	398-403	6	19
β-strand	407	1	21
β-strand	415	1	20
β-strand	416-421	6	19
β-strand	425	1	19
β-strand	426	1	24
β-strand	437	1	17
β-strand	443	1	22
β-strand	445	1	23
β-strand	455	1	25
β-strand	458	1	25
β-strand	459-460	2	26
β-strand	461-466	6	17
β-strand	469	1	24
α-helix	482-484	3
β-strand	485-488	4	17
α-helix	492-498	7
β-strand	509	1	26
β-strand	511-518	8	26
β-strand	523-524	2	26
β-strand	526-528	3	26
β-strand	534-536	3	26
α-helix	543-544	2
β-strand	545-546	2	17
β-strand	552-560	9	26
α-helix	564-566	3
β-strand	567-568	2	26

Chain C: 16 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	34-36	3	27
α-helix	43-53	11
α-helix	54-56	3
β-strand	60	1	28
α-helix	67-70	4
β-strand	73-81	9	27
α-helix	84-85	2
β-strand	89-94	6	29
α-helix	103-106	4
β-strand	110	1	30
β-strand	112-114	3	28
β-strand	117-123	7	27
β-strand	130	1	31
β-strand	132-138	7	29
α-helix	139	1
α-helix	150-152	3
β-strand	155-159	5	29
β-strand	166-170	5	27
β-strand	179-180	2	28
β-strand	189-194	6	29
β-strand	199	1	31
β-strand	208-217	10	27
β-strand	222-223	2	28
β-strand	226	1	30
α-helix	234-237	4
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
α-helix	341-343	3
β-strand	353-361	9	37
α-helix	367	1
β-strand	368	1	37
α-helix	369	1
β-strand	374-381	8	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
α-helix	449-451	3
β-strand	452	1	35
β-strand	455	1	40
β-strand	458-460	3	40
β-strand	461-466	6	34
β-strand	469	1	37
β-strand	485-488	4	34
β-strand	491	1	33
α-helix	492-498	7
β-strand	511-518	8	40
β-strand	523-528	6	40
β-strand	534-537	4	40
α-helix	543-544	2
β-strand	545	1	34
β-strand	552-560	9	40
α-helix	564-566	3
β-strand	567-568	2	40

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP60	A, B, C	protein	577	Oryctolagus cuniculus	Q86119

Sequence of entity 1 (A, B, C), FASTA

>9I9D_1 Capsid protein VP60 (chains A, B, C)
GKARTAPQGEAAGTATTASVPGTTTDGMDPGVVATTSVVTAENSSASIATAGIGGPPQQV
DQQETWRTNFYYNDVFTWSVADAPGSILYTVQHSPQNNPFTAVLSQMYAGWAGGMQFRFI
VAGSGVFGGRLVAAVIPPGIEIGPGLEVRQFPHVVIDARSLEPVTITMPDLRPNMYHPTG
DPGLVPTLVLSVYNNLINPFGGSTSAIQVTVETRPSEDFEFVMIRAPSSKTVDSISPAGL
LTTPVLTGVGNDNRWNGQIVGLQPVPGGFSTCNRHWNLNGSTYGWSSPRFADIDHRRGSA
SYPGNNATNVLQFWYANAGSAIDNPISQVAPDGFPDMSFVPFNGPGIPAAGWVGFGAIWN
SNSGAPNVTTVQAYELGFATGAPGNLQPTTNTSGSQTVAKSIYAVVTGTAQNPAGLFVMA
SGVISTPSANAITYTPQPDRIVTTPGTPAAAPVGKNTPIMFASVVRRTGDVNATAGSANG
TQYGTGSQPLPVTIGLSLNNYSSALMPGQFFVWQLTFASGFMEIGLSVDGYFYAGTGAST
TLIDLTELIDVRPVGPRPSKSTLVFNLGGTANGFSYV

Primary citation

Structure of full RHDV virion at 3.3 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
9I3H 2.5 Å, CP of RHDV mutant - N15
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)
3ZUE 10.3 Å, Rabbit Hemorrhagic Disease Virus (RHDV)capsid protein

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