7V0P: SINV/EEEV

Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a potently neutralizing human antibody IgG-106. Determined by electron microscopy at 5.2 Å resolution. Released 5 Apr 2023.

Method: Electron microscopy
Resolution: 5.2 Å
Organisms: Eastern equine encephalitis virus, Homo sapiens
Chains: 16
Atoms: 30,072
Mol. weight: 477.91 kDa
Released: 5 Apr 2023

Explore 7V0P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V0P contains 124 α-helices and 496 β-strands across 16 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: 5 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	12	1	108
β-strand	22	1	109
β-strand	25	1	109
β-strand	33-37	5	110
β-strand	44-49	6	110
β-strand	54	1	111
β-strand	64-69	6	111
β-strand	72-77	6	111
β-strand	82-84	3	112
β-strand	88	1	112
β-strand	90-95	6	110
β-strand	98-102	5	110
β-strand	106-112	7	112
β-strand	121-128	8	112
α-helix	131-132	2
β-strand	136	1	113
β-strand	147-149	3	114
β-strand	152-153	2	115
β-strand	163-165	3	116
β-strand	173	1	117
β-strand	179-180	2	118
β-strand	185-186	2	118
β-strand	194	1	119
β-strand	199	1	120
α-helix	220-222	3
β-strand	223	1	120
β-strand	226	1	117
β-strand	228	1	119
β-strand	233	1	108
β-strand	251-253	3	116
β-strand	258-259	2	115
β-strand	262-264	3	114
α-helix	268-271	4
β-strand	272-276	5	121
β-strand	279-284	6	121
β-strand	290-294	5	113
β-strand	304-308	5	113
β-strand	312-314	3	121
β-strand	317	1	121
β-strand	323-325	3	113
α-helix	331-332	2
β-strand	333-335	3	113
β-strand	336	1	16

Chains A, B and C: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
β-strand	18-19	2	2
β-strand	24	1	3
β-strand	27-28	2	2
β-strand	31-32	2	4
β-strand	44-48	5	5
β-strand	51-52	2	6
α-helix	55-58	4
β-strand	59-61	3	7
β-strand	77-82	6	7
β-strand	87	1	8
β-strand	101-106	6	7
β-strand	109-110	2	6
α-helix	113-115	3
β-strand	119-123	5	5
β-strand	131	1	9
β-strand	134-135	2	4
β-strand	144	1	4
β-strand	147	1	9
β-strand	161-163	3	1
β-strand	177-181	5	5
β-strand	184-186	3	5
α-helix	196-197	2
β-strand	204-206	3	5
β-strand	214-216	3	5
β-strand	221-222	2	10
α-helix	224-225	2
β-strand	229	1	8
β-strand	234-235	2	10
α-helix	237-239	3
α-helix	252-255	4
β-strand	261-262	2	11
β-strand	269-270	2	11
β-strand	276-282	7	1
α-helix	285-287	3
α-helix	288-289	2
β-strand	290	1	3
α-helix	291-293	3
α-helix	295-296	2
β-strand	301-306	6	12
β-strand	307-308	2	13
β-strand	315-320	6	12
β-strand	327-330	4	14
β-strand	339-340	2	12
β-strand	344-347	4	14
β-strand	352	1	12
β-strand	355-358	4	12
β-strand	367	1	15
β-strand	376	1	15
β-strand	381-382	2	13
β-strand	389	1	16

Chains b and c: 5 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	12	1	122
β-strand	22	1	123
β-strand	25	1	123
β-strand	33-37	5	124
β-strand	44-53	10	124
β-strand	54	1	125
β-strand	64-69	6	125
β-strand	72-77	6	125
β-strand	82-84	3	126
β-strand	88	1	126
β-strand	90-102	13	124
β-strand	106-112	7	126
β-strand	121-128	8	126
α-helix	131-132	2
β-strand	136	1	127
β-strand	147-149	3	128
β-strand	152-153	2	129
β-strand	163-165	3	130
β-strand	173	1	131
β-strand	179-180	2	132
β-strand	185-186	2	132
β-strand	194	1	133
β-strand	199	1	134
α-helix	220-222	3
β-strand	223	1	134
β-strand	226	1	131
β-strand	228	1	133
β-strand	233	1	122
β-strand	251-253	3	130
β-strand	258-259	2	129
β-strand	262-264	3	128
α-helix	268-271	4
β-strand	272-276	5	135
β-strand	279-284	6	135
β-strand	290-294	5	127
β-strand	304-308	5	127
β-strand	312-314	3	135
β-strand	317	1	135
β-strand	323-325	3	127
α-helix	331-332	2
β-strand	333-335	3	127
β-strand	336	1	32

Chain d: 5 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	12	1	150
β-strand	22	1	151
β-strand	25	1	151
β-strand	33-37	5	152
β-strand	44-49	6	152
β-strand	54	1	153
β-strand	64-69	6	153
β-strand	72-77	6	153
β-strand	82-84	3	154
β-strand	88	1	154
β-strand	90-95	6	152
β-strand	98-102	5	152
β-strand	106-112	7	154
β-strand	121-128	8	154
α-helix	131-132	2
β-strand	136	1	155
β-strand	147-149	3	156
β-strand	152-153	2	157
β-strand	163-165	3	158
β-strand	173	1	159
β-strand	179-180	2	160
β-strand	185-186	2	160
β-strand	194	1	161
β-strand	199	1	162
α-helix	220-222	3
β-strand	223	1	162
β-strand	226	1	159
β-strand	228	1	161
β-strand	233	1	150
β-strand	251-253	3	158
β-strand	258-259	2	157
β-strand	262-264	3	156
α-helix	268-271	4
β-strand	272-276	5	163
β-strand	279-284	6	163
β-strand	290-294	5	155
β-strand	304-308	5	155
β-strand	312-314	3	163
β-strand	317	1	163
β-strand	323-325	3	155
α-helix	331-332	2
β-strand	333-335	3	155

Chain D: 10 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	49
β-strand	18-19	2	50
β-strand	24	1	51
β-strand	27-28	2	50
β-strand	31-32	2	52
β-strand	44-48	5	53
β-strand	51-52	2	54
α-helix	55-58	4
β-strand	59-61	3	55
β-strand	77-82	6	55
β-strand	87	1	56
β-strand	101-106	6	55
β-strand	109-110	2	54
α-helix	113-115	3
β-strand	119-123	5	53
β-strand	131	1	57
β-strand	134-135	2	52
β-strand	144	1	52
β-strand	147	1	57
β-strand	161-163	3	49
β-strand	177-181	5	53
β-strand	184-186	3	53
α-helix	196-197	2
β-strand	204-206	3	53
β-strand	214-216	3	53
β-strand	221-222	2	58
α-helix	224-225	2
β-strand	229	1	56
β-strand	234-235	2	58
α-helix	237-239	3
α-helix	252-255	4
β-strand	261-262	2	59
β-strand	269-270	2	59
β-strand	276-282	7	49
α-helix	285-287	3
α-helix	288-289	2
β-strand	290	1	51
α-helix	291-293	3
α-helix	295-296	2
β-strand	301-306	6	60
β-strand	307-308	2	61
β-strand	315-320	6	60
β-strand	327-330	4	62
β-strand	339-340	2	60
β-strand	344-347	4	62
β-strand	352	1	60
β-strand	355-358	4	60
β-strand	367	1	63
β-strand	376	1	63
β-strand	381-382	2	61

Chains E, G, I and K: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	64
β-strand	10-12	3	65
β-strand	18-25	8	64
β-strand	35-42	8	65
β-strand	47-53	7	65
β-strand	60-61	2	65
β-strand	69-74	6	64
β-strand	79-84	6	64
α-helix	89-91	3
β-strand	93-100	8	65
α-helix	109-111	3
β-strand	116	1	65
β-strand	120-124	5	65
β-strand	130	1	66
α-helix	131-132	2
β-strand	133-137	5	67
α-helix	138-140	3
α-helix	141-143	3
β-strand	145	1	67
β-strand	148-158	11	67
β-strand	159	1	66
β-strand	164-167	4	68
α-helix	168-170	3
β-strand	176-178	3	67
α-helix	179-181	3
β-strand	182-183	2	67
β-strand	189-198	10	67
α-helix	199-201	3
β-strand	202	1	69
β-strand	205	1	69
β-strand	207-213	7	68
α-helix	214-216	3
β-strand	218-224	7	68

Chains F, H, J and L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	70
β-strand	10-14	5	71
β-strand	19-25	7	70
β-strand	33-38	6	71
β-strand	45-49	5	71
β-strand	53-54	2	71
α-helix	55	1
β-strand	62-67	6	70
β-strand	70-75	6	70
β-strand	85-90	6	71
β-strand	97-98	2	71
β-strand	102-107	6	71
β-strand	111	1	72
α-helix	112-113	2
β-strand	114-118	5	73
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	73
β-strand	140	1	72
β-strand	145-150	6	74
β-strand	153-154	2	74
α-helix	155	1
β-strand	159-163	5	73
α-helix	164-167	4
β-strand	173-182	10	73
α-helix	183-186	4
β-strand	191-197	7	74
β-strand	205-210	6	74

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein E1	A, B, C, D	protein	400	Eastern equine encephalitis virus	Q4QXJ7
IgG 106 Fab heavy chain	E, G, I, K	protein	229	Homo sapiens
IgG 106 Fab light chain	F, H, J, L	protein	212	Homo sapiens
Spike glycoprotein E2	a, b, c, d	protein	342	Eastern equine encephalitis virus	Q4QXJ7

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

>7V0P_1 Spike glycoprotein E1 (chains A, B, C, D)
YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVV
KCCGATQCTSKPHPDYQCQVFTGVYPFMWGGAYCFCDTENTQMSEAYVERSEECSIDHAK
AYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVV
YGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQAPSG
FERWKRDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDL
ECKITECTYASDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTA
NIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFT

Sequence of entity 2 (E, G, I, K), FASTA

>7V0P_2 IgG 106 Fab heavy chain (chains E, G, I, K)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAAA

Sequence of entity 3 (F, H, J, L), FASTA

>7V0P_3 IgG 106 Fab light chain (chains F, H, J, L)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 4 (a, b, c, d), FASTA

>7V0P_4 Spike glycoprotein E2 (chains a, b, c, d)
DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGV
DLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRH
TCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSI
HSAKVKITVPSGAQVKYYCKCPDVREGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRL
PRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSD
ANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGE

Primary citation

Structural constraints link differences in neutralization potency of human anti-Eastern equine encephalitis virus monoclonal antibodies. Williamson, L.E., Bandyopadhyay, A., Bailey, K. et al. Proc Natl Acad Sci U S A (2023) 120:e2213690120-e2213690120. DOI 10.1073/pnas.2213690120 · PubMed

Other PDB entries of the same protein (UniProt Q4QXJ7), best resolution first:

8XI4 3.4 Å, Structure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA1-2
8XI5 3.4 Å, Structure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA3-5
6XO4 4.2 Å, CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP
6MX4 4.4 Å, CryoEM structure of chimeric Eastern Equine Encephalitis Virus
8YS4 4.8 Å, Overall structure of Eastern Equine Encephalitis virus VLP in complex with the receptor…
8YS2 5.2 Å, Overall structure of Eastern Equine Encephalitis virus VLP in complex with the receptor…
6ODF 5.8 Å, EEEV glycoproteins bound with heparan sulfate
7V0N 5.9 Å, Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a moderately/weakly…
7V0O 6.6 Å, Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a moderately/weakly…
6MW9 7.3 Å, CryoEM structure of chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-3 antibody
6MWV 7.3 Å, CryoEM structure of Chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-58…
6MWC 7.5 Å, CryoEM structure of chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-5 antibody

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