8I5L: P domain from norovirus GI.4 capsid protein

Crystal structure of P domain from norovirus GI.4 capsid protein in complex with broad specificity antibody single-chain Fv fragment CV-2F5. Determined by X-ray diffraction at 2.7 Å resolution. Released 31 Jan 2024.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: Chiba virus, Homo sapiens
Chains: 5
Atoms: 10,615
Mol. weight: 156.36 kDa
Released: 31 Jan 2024

Explore 8I5L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I5L contains 38 α-helices and 129 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: 11 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	230-232	3
α-helix	239-241	3
β-strand	243	1	1
β-strand	250	1	1
β-strand	253-255	3	2
β-strand	264	1	3
β-strand	271	1	4
β-strand	277	1	4
α-helix	285-287	3
β-strand	290-295	6	5
β-strand	301-304	4	5
β-strand	305	1	6
β-strand	311	1	6
β-strand	330-337	8	5
β-strand	349-353	5	5
β-strand	361	1	5
α-helix	362-364	3
β-strand	366-368	3	5
β-strand	377-387	11	5
α-helix	388-389	2
α-helix	395-397	3
α-helix	415-418	4
β-strand	419	1	3
β-strand	427-429	3	7
β-strand	430-434	5	2
β-strand	446-449	4	2
α-helix	453-462	10
α-helix	464-466	3
β-strand	470-477	8	7
β-strand	482-490	9	7
β-strand	494-497	4	7
β-strand	499	1	8
α-helix	506-508	3
β-strand	514-521	8	7
β-strand	525	1	9
α-helix	527-529	3
β-strand	530	1	8

Chain B: 10 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	238	1	10
α-helix	239-241	3
β-strand	243	1	11
β-strand	250	1	11
β-strand	253-255	3	12
β-strand	264	1	13
β-strand	271	1	14
β-strand	277	1	14
α-helix	285-287	3
β-strand	290-295	6	15
β-strand	299-304	6	15
β-strand	305	1	16
β-strand	311	1	16
β-strand	330-337	8	15
β-strand	349-353	5	15
β-strand	361	1	15
α-helix	362-364	3
β-strand	366-373	8	15
β-strand	377-387	11	15
α-helix	388-389	2
α-helix	395-397	3
β-strand	408	1	17
β-strand	411	1	17
α-helix	415-418	4
β-strand	419	1	13
β-strand	427-428	2	10
β-strand	430-432	3	12
β-strand	433-434	2	18
β-strand	446-447	2	18
α-helix	453-462	10
α-helix	464-466	3
β-strand	470-476	7	10
β-strand	483-490	8	10
β-strand	494-497	4	10
β-strand	499	1	19
α-helix	506-508	3
β-strand	514-521	8	10
β-strand	525	1	20
α-helix	527-529	3
β-strand	530	1	19

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	239-241	3
β-strand	243	1	21
β-strand	250	1	21
β-strand	253-255	3	22
β-strand	264	1	23
β-strand	271	1	24
β-strand	277	1	24
α-helix	285-287	3
β-strand	290-295	6	25
β-strand	301-305	5	25
β-strand	330-337	8	25
β-strand	349-353	5	25
β-strand	361	1	25
α-helix	362-364	3
β-strand	366-368	3	25
β-strand	377-387	11	25
α-helix	388-389	2
α-helix	395-397	3
α-helix	415-418	4
β-strand	419	1	23
β-strand	427-428	2	26
β-strand	430-434	5	22
β-strand	446-449	4	22
α-helix	453-462	10
β-strand	470-477	8	26
β-strand	482-489	8	26
β-strand	495-497	3	26
α-helix	506-508	3
β-strand	514-521	8	26

Chain D: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	27
β-strand	18-25	8	27
α-helix	29-31	3
β-strand	34-39	6	28
β-strand	45-51	7	28
β-strand	58-60	3	28
β-strand	65	1	27
β-strand	68-73	6	27
β-strand	78-83	6	27
α-helix	88-90	3
β-strand	92-100	9	28
α-helix	101-103	3
β-strand	106-110	5	28
β-strand	114-116	3	28
β-strand	1004	1	29
β-strand	1005	1	30
β-strand	1009-1012	4	31
β-strand	1018-1023	6	30
β-strand	1032	1	9
β-strand	1035-1039	5	31
α-helix	1044	1
β-strand	1045-1049	5	31
β-strand	1050	1	32
β-strand	1054	1	32
β-strand	1063-1068	6	30
β-strand	1071-1076	6	30
α-helix	1081-1083	3
β-strand	1085-1093	9	31
β-strand	1098-1101	4	31
β-strand	1102	1	29
β-strand	1105-1109	5	31

Chain E: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	33
β-strand	10-12	3	34
β-strand	18-25	8	33
α-helix	29-31	3
β-strand	34-39	6	34
β-strand	45-51	7	34
β-strand	58-60	3	34
β-strand	68-73	6	33
β-strand	78-83	6	33
α-helix	88-90	3
β-strand	92-100	9	34
α-helix	101-103	3
β-strand	106-110	5	34
β-strand	114-118	5	34
β-strand	1004	1	35
β-strand	1005	1	36
β-strand	1009-1012	4	37
β-strand	1018-1023	6	36
β-strand	1032	1	20
β-strand	1034-1039	6	37
β-strand	1046-1049	4	37
β-strand	1050	1	38
β-strand	1054	1	38
β-strand	1063-1068	6	36
β-strand	1071-1076	6	36
α-helix	1081-1083	3
β-strand	1085-1093	9	37
β-strand	1098-1101	4	37
β-strand	1102	1	35
β-strand	1105-1109	5	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein	A, B, C	protein	314	Chiba virus	Q9DU46
scFv fragment	D, E	protein	263	Homo sapiens

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

>8I5L_1 Capsid protein (chains A, B, C)
QKTRPFTVPNIPLKYLSNSRIPNPIEGMSLSPDQTQNVQFQNGRCTIDGQPLGTTPVSVS
QLCKFRGRITSGQRVLNLTELDGSPFMAFAAPAPAGFPDLGSCDWHIEMSKIPNSSTQNN
PIVTNSVKPNSQQFVPHLSSITLDENVSSGGDYIGTIQWTSPPSDSGGANTNFWKIPDYG
SSLAEASQLAPAVYPPGFNEVIVYFMASIPGPNQSGSPNLVPCLLPQEYITHFISEQAPI
QGEAALLHYVDPDTNRNLGEFKLYPGGYLTCVPNSSSTGPQQLPLDGVFVFASWVSRFYQ
LKPVGTAGPARGRL

Sequence of entity 2 (D, E), FASTA

>8I5L_2 scFv fragment (chains D, E)
GSSGSSGMAEVQLVESGGGLVKPGGSLRLSCAASGFTFSSYNMNWVRQAPGKGLEWVSSI
STSSRYIYYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCAREEGSVDYGMDVWG
QGTTVTVSSGRGGSGGGGSGGGGSMAQSVLTQPPSASGTPGQRVTISCSGSSSNIGSNYV
YWYQQLPGTAPKLLIYRNNQRPSGVPDRFSGSKSGTSASLAISGLRSEDEADYYCAAWDD
SLSGWVFGGGTKLTVLGSARQSA

Primary citation

Structural analyses of the GI.4 norovirus by cryo-electron microscopy and X-ray crystallography revealing binding sites for human monoclonal antibodies. Kimura-Someya, T., Katsura, K., Kato-Murayama, M. et al. J Virol (2024) 98:e0019724-e0019724. DOI 10.1128/jvi.00197-24 · PubMed

Other PDB entries of the same protein (UniProt Q9DU46), best resolution first:

8JG5 3.04 Å, Cryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1 Fv-clasp

Browse structure collections

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