8JG5: GI.4 Chiba VLP

Name: PDB 8JG5: Cryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1 Fv-clasp
Published: 2024-04-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of the GI.4 Chiba VLP complexed with the CV-1A1 Fv-clasp. Determined by electron microscopy at 3.04 Å resolution. Released 17 Apr 2024.

Method: Electron microscopy
Resolution: 3.04 Å
Organisms: Chiba virus, Homo sapiens
Chains: 7
Atoms: 16,057
Mol. weight: 250.41 kDa
Released: 17 Apr 2024

Explore 8JG5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JG5 contains 72 α-helices and 171 β-strands across 7 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: 18 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	54-58	5
β-strand	61-70	10	1
β-strand	79-84	6	2
α-helix	87-89	3
α-helix	91-98	8
β-strand	100	1	3
β-strand	102-104	3	4
β-strand	107-114	8	1
β-strand	120-128	9	2
α-helix	129	1
α-helix	139-142	4
β-strand	147-151	5	2
β-strand	158-162	5	1
β-strand	171-172	2	4
β-strand	180-190	11	2
α-helix	197-200	4
β-strand	203-211	9	1
β-strand	216-217	2	4
β-strand	220	1	3
α-helix	230-232	3
α-helix	242	1
β-strand	243	1	5
α-helix	244	1
β-strand	250	1	5
β-strand	253-255	3	6
β-strand	264	1	7
β-strand	271	1	8
β-strand	277	1	8
α-helix	285-287	3
β-strand	290-295	6	9
β-strand	301-302	2	10
β-strand	303-305	3	9
β-strand	330-337	8	9
β-strand	349-353	5	9
β-strand	361	1	11
α-helix	362-364	3
β-strand	366	1	11
β-strand	367-368	2	10
β-strand	377-387	11	9
α-helix	388-389	2
α-helix	415-418	4
β-strand	419	1	7
β-strand	427-429	3	12
β-strand	430-432	3	6
β-strand	433-434	2	13
β-strand	446-447	2	13
α-helix	448	1
α-helix	453-461	9
α-helix	464-466	3
β-strand	470-477	8	12
β-strand	482-489	8	12
β-strand	495-497	3	12
β-strand	499	1	14
α-helix	506-508	3
β-strand	514-521	8	12
α-helix	527-529	3
β-strand	530	1	14

Chain B: 19 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	15-18	4
α-helix	54-58	5
β-strand	61-70	10	15
α-helix	74-75	2
β-strand	79-84	6	16
α-helix	87-89	3
α-helix	91-97	7
β-strand	100	1	17
β-strand	102-104	3	18
β-strand	107-112	6	15
β-strand	122-128	7	16
α-helix	139-142	4
β-strand	147-151	5	16
β-strand	158-162	5	15
β-strand	171-172	2	18
β-strand	180-187	8	16
α-helix	199-201	3
α-helix	202	1
β-strand	203-211	9	15
β-strand	216-217	2	18
β-strand	220	1	17
α-helix	230-232	3
β-strand	243	1	19
β-strand	250	1	19
β-strand	253-255	3	20
β-strand	264	1	21
β-strand	271	1	22
β-strand	277	1	22
α-helix	285-287	3
β-strand	291-295	5	23
β-strand	299-302	4	24
β-strand	303-305	3	23
α-helix	310-312	3
α-helix	314-316	3
β-strand	330-337	8	23
β-strand	349-353	5	23
β-strand	361	1	25
α-helix	362-364	3
β-strand	366	1	25
β-strand	367-368	2	24
β-strand	369	1	23
β-strand	370-373	4	24
β-strand	377-387	11	23
α-helix	388-389	2
α-helix	415-418	4
β-strand	419	1	21
α-helix	420-422	3
β-strand	427-429	3	26
β-strand	430-434	5	20
β-strand	446-449	4	20
α-helix	453-461	9
β-strand	470-476	7	26
β-strand	483-489	7	26
β-strand	495-497	3	26
β-strand	499	1	27
α-helix	505-508	4
β-strand	514-521	8	26
α-helix	527-529	3
β-strand	530	1	27

Chain C: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	28
β-strand	12	1	29
β-strand	18-25	8	28
β-strand	34-40	7	30
β-strand	44-51	8	30
β-strand	59-60	2	30
α-helix	62-64	3
β-strand	68-73	6	28
β-strand	78-83	6	28
β-strand	92-99	8	30
β-strand	107-110	4	30
β-strand	114-116	3	30
β-strand	118	1	29
α-helix	124-128	5
α-helix	135-138	4
α-helix	142-159	18
α-helix	162-168	7

Chain D: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	31
β-strand	9-11	3	32
β-strand	18-23	6	31
α-helix	26-30	5
β-strand	35-40	6	32
β-strand	47-50	4	32
β-strand	52	1	33
β-strand	55	1	33
β-strand	64-69	6	31
β-strand	72-77	6	31
α-helix	82-84	3
β-strand	87-93	7	32
β-strand	99-101	3	32
β-strand	105-108	4	32
α-helix	116-120	5
α-helix	123-151	29
α-helix	153-160	8

Chain E: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	34
β-strand	10-11	2	35
β-strand	17-25	9	34
α-helix	29-31	3
β-strand	34-39	6	35
β-strand	45-51	7	35
β-strand	58-59	2	35
α-helix	62-64	3
β-strand	68-73	6	34
β-strand	78-84	7	34
α-helix	88-90	3
β-strand	92-99	8	35
β-strand	107-110	4	35
β-strand	111	1	34
β-strand	114-117	4	35
α-helix	125-130	6
α-helix	132-167	36

Chain F: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	36
β-strand	5	1	37
β-strand	9	1	38
β-strand	18-23	6	37
α-helix	26-30	5
β-strand	35-40	6	39
α-helix	45-46	2
β-strand	47-50	4	39
β-strand	51	1	40
β-strand	55	1	40
β-strand	65-69	5	37
β-strand	72-77	6	37
α-helix	82-84	3
β-strand	87-93	7	39
β-strand	99-101	3	39
β-strand	102	1	36
β-strand	105	1	39
β-strand	106	1	38
α-helix	123-130	8
α-helix	135-160	26

Chain G: 15 helices, 41 β-strands

Element	Residues	Length	Sheet
α-helix	54-58	5
β-strand	61-70	10	41
β-strand	79-84	6	42
α-helix	87-89	3
α-helix	91-99	9
β-strand	100	1	43
β-strand	102-104	3	44
β-strand	107-113	7	41
β-strand	119-128	10	42
α-helix	129	1
α-helix	139-142	4
β-strand	147-151	5	42
α-helix	157	1
β-strand	158-162	5	41
β-strand	171-172	2	44
β-strand	180-191	12	42
β-strand	203-211	9	41
β-strand	216-217	2	44
β-strand	220	1	43
α-helix	227-229	3
β-strand	238	1	45
α-helix	239-241	3
β-strand	243	1	46
β-strand	250	1	46
β-strand	253-255	3	47
β-strand	264	1	48
β-strand	271	1	49
β-strand	277	1	49
β-strand	290-292	3	50
β-strand	302	1	51
α-helix	311-312	2
β-strand	328	1	52
β-strand	330-334	5	53
β-strand	336	1	50
β-strand	350-353	4	53
β-strand	367	1	51
β-strand	380-382	3	50
β-strand	383-387	5	53
β-strand	398	1	52
α-helix	402-404	3
α-helix	415-418	4
β-strand	419	1	48
β-strand	427-428	2	45
α-helix	429	1
β-strand	430-432	3	47
β-strand	433	1	54
β-strand	447	1	54
α-helix	453-461	9
β-strand	470-476	7	45
β-strand	483-490	8	45
β-strand	494-497	4	45
β-strand	499	1	55
α-helix	506-508	3
β-strand	514-521	8	45
α-helix	526-529	4
β-strand	530	1	55

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VP1	A, B, G	protein	542	Chiba virus	Q9DU46
Vh,sarah	C, E	protein	178	Homo sapiens	Q13043 (AlphaFold model)
Vl,sarah	D, F	protein	169	Homo sapiens	Q13043 (AlphaFold model)

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

>8JG5_1 VP1 (chains A, B, G)
MASKDATPSADGATGAGQLVPEVNTADPIPIDPVAGSSTAAPVAGQVNLIDPWIINNFVQ
APQGEFTISPNNTPGDVLFDLQLGPHLNPFLSHLSQMYNGWVGNMRVRVVLAGNAFTAGK
VIICCVPPGFQSRTLSIAQATLFPHVIADVRTLDPVEVPLEDVRNVLYHNNDTQPTMRLL
CMLYTPLRTGGASGGTDSFVVAGRVLTCPGPDFNFLFLVPPTVEQKTRPFTVPNIPLKYL
SNSRIPNPIEGMSLSPDQTQNVQFQNGRCTIDGQPLGTTPVSVSQLCKFRGRITSGQRVL
NLTELDGSPFMAFAAPAPAGFPDLGSCDWHIEMSKIPNSSTQNNPIVTNSVKPNSQQFVP
HLSSITLDENVSSGGDYIGTIQWTSPPSDSGGANTNFWKIPDYGSSLAEASQLAPAVYPP
GFNEVIVYFMASIPGPNQSGSPNLVPCLLPQEYITHFISEQAPIQGEAALLHYVDPDTNR
NLGEFKLYPGGYLTCVPNSSSTGPQQLPLDGVFVFASWVSRFYQLKPVGTAGPARGRLGV
RR

Sequence of entity 2 (C, E), FASTA

>8JG5_2 VH,SARAH (chains C, E)
GSSGSSGEVQLVESGAEVKKPGASVKVSCKASGYTFTSLYMHWVRQAPGQGLEWMGMINP
SGGGTWNAQKFQGRVTMTRDTSTSTVYMELRSLRSDDTAMYYCARDSDQYSQGLGYWGQG
TLVTVCSGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQSKRQPILDAIEAK

Sequence of entity 3 (D, F), FASTA

>8JG5_3 VL,SARAH (chains D, F)
GSSGSSGQSALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDV
SKRPSGVSNRFSGSKSGNTASLTISGLQAKDEADYYCSSYTSSSTWVFGGGTKLTVLGGS
DYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQCKRQPILDAIEAK

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:

8I5L 2.7 Å, Crystal structure of P domain from norovirus GI.4 capsid protein in complex with broad…

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