8YS4: Spike glycoprotein E1

Overall structure of Eastern Equine Encephalitis virus VLP in complex with the receptor VLDLR LA3-5. Determined by electron microscopy at 4.8 Å resolution. Released 28 Aug 2024.

Method: Electron microscopy
Resolution: 4.8 Å
Organisms: Eastern equine encephalitis virus, Homo sapiens
Chains: 20
Atoms: 33,820
Mol. weight: 533.01 kDa
Ligands: CA
Released: 28 Aug 2024

Explore 8YS4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YS4 contains 84 α-helices and 382 β-strands across 20 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: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	15-19	5	2
β-strand	24	1	3
β-strand	27-48	22	2
β-strand	51-54	4	4
α-helix	56-59	4
β-strand	60-61	2	5
β-strand	77	1	6
β-strand	81-82	2	5
β-strand	87	1	7
β-strand	92	1	7
β-strand	101-102	2	5
β-strand	106	1	6
β-strand	107-110	4	4
α-helix	112-115	4
β-strand	119-137	19	2
β-strand	140-148	9	2
β-strand	155	1	1
β-strand	162	1	1
α-helix	164-167	4
β-strand	177-181	5	2
β-strand	184-187	4	2
β-strand	204-205	2	8
β-strand	206	1	2
β-strand	215-216	2	8
β-strand	221-222	2	9
β-strand	229	1	7
β-strand	234-235	2	9
α-helix	240-244	5
α-helix	252-255	4
α-helix	257-259	3
β-strand	261	1	2
β-strand	270	1	2
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
β-strand	297-306	10	10
β-strand	308	1	11
β-strand	315-323	9	10
β-strand	328-330	3	12
β-strand	331-332	2	13
β-strand	338-340	3	10
β-strand	344-346	3	12
β-strand	352-359	8	10
β-strand	367-370	4	13
β-strand	373-376	4	13
β-strand	382	1	11
β-strand	388-389	2	14
α-helix	405-440	36

Chain B: 9 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	9-11	3
β-strand	12	1	15
β-strand	17-18	2	16
β-strand	28-29	2	16
β-strand	34-37	4	17
β-strand	44-53	10	17
β-strand	64-69	6	17
β-strand	72-77	6	17
β-strand	82-84	3	18
β-strand	88-89	2	18
β-strand	90-102	13	17
β-strand	106-112	7	18
β-strand	121-128	8	18
β-strand	136	1	19
β-strand	146-153	8	20
β-strand	163-164	2	21
β-strand	166-167	2	22
β-strand	178-180	3	23
β-strand	185-187	3	23
β-strand	196-199	4	24
β-strand	200	1	25
β-strand	204	1	25
β-strand	207-208	2	24
α-helix	220-222	3
β-strand	223-225	3	24
β-strand	233	1	15
β-strand	234-235	2	22
β-strand	252-253	2	21
α-helix	254	1
β-strand	258-265	8	20
α-helix	268-271	4
β-strand	272-275	4	26
β-strand	279-284	6	26
β-strand	290-296	7	19
β-strand	304-308	5	19
β-strand	312-317	6	26
β-strand	323-327	5	19
α-helix	331-332	2
β-strand	333-335	3	19
β-strand	336-337	2	14
α-helix	349-359	11
α-helix	366-394	29
α-helix	407-411	5

Chain C: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	113-118	6	27
β-strand	121-127	7	27
β-strand	128-129	2	28
β-strand	132-133	2	28
β-strand	142-143	2	27
α-helix	168-170	3
β-strand	175-176	2	29
α-helix	177	1
β-strand	186-188	3	30
β-strand	191-193	3	30
β-strand	202	1	31
β-strand	215-216	2	32
β-strand	222-223	2	29
β-strand	225-226	2	32
β-strand	227-229	3	33
β-strand	237	1	31
β-strand	240-241	2	33
β-strand	242-244	3	34
β-strand	250-252	3	34
β-strand	260	1	33

Chain D: 8 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	35
β-strand	15-19	5	36
β-strand	24	1	37
β-strand	27-48	22	36
β-strand	51-54	4	38
α-helix	57-59	3
β-strand	60-61	2	39
β-strand	77	1	40
β-strand	81-82	2	39
β-strand	87	1	41
β-strand	92	1	41
β-strand	101-102	2	39
β-strand	106	1	40
β-strand	107-110	4	38
β-strand	119-137	19	36
β-strand	143-148	6	36
β-strand	155	1	35
β-strand	162	1	35
α-helix	164-167	4
β-strand	177-181	5	36
β-strand	184-186	3	36
β-strand	205-206	2	36
β-strand	214-215	2	36
β-strand	221-222	2	42
β-strand	234-235	2	42
α-helix	237-239	3
α-helix	240-247	8
α-helix	252-254	3
β-strand	261-262	2	36
β-strand	269-270	2	36
β-strand	276-282	7	35
α-helix	285-287	3
β-strand	290	1	37
α-helix	291-293	3
β-strand	297-306	10	43
β-strand	308	1	44
β-strand	315-323	9	43
β-strand	327-330	4	45
β-strand	331-332	2	46
β-strand	339-340	2	43
β-strand	344-347	4	45
β-strand	352-358	7	43
β-strand	367-370	4	46
β-strand	374-376	3	46
β-strand	382	1	44
β-strand	388-389	2	47
α-helix	405-439	35

Chain E: 7 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	12	1	48
β-strand	17-18	2	49
β-strand	28-29	2	49
β-strand	34-37	4	50
β-strand	44-55	12	50
β-strand	60-69	10	50
β-strand	72-77	6	50
β-strand	81-84	4	51
β-strand	88	1	51
β-strand	90-102	13	50
β-strand	106	1	52
β-strand	109-113	5	51
β-strand	121-124	4	51
β-strand	128	1	52
β-strand	136	1	53
β-strand	146-153	8	54
β-strand	163-165	3	55
β-strand	166-167	2	56
β-strand	178-180	3	57
β-strand	185-187	3	57
β-strand	196-199	4	58
β-strand	200	1	59
β-strand	204	1	59
β-strand	207-208	2	58
α-helix	220-222	3
β-strand	223-225	3	58
β-strand	233	1	48
β-strand	234-235	2	56
β-strand	251-253	3	55
β-strand	258-265	8	54
α-helix	268-271	4
β-strand	272-276	5	60
β-strand	279-284	6	60
β-strand	290-295	6	53
β-strand	304-308	5	53
β-strand	312-316	5	60
β-strand	323-327	5	53
α-helix	331-332	2
β-strand	333-335	3	53
β-strand	336-337	2	47
α-helix	349-357	9
α-helix	363-394	32
α-helix	408-411	4

Chain F: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	113-118	6	61
β-strand	121-127	7	61
β-strand	128-129	2	62
β-strand	132-133	2	62
β-strand	142-143	2	61
α-helix	168-170	3
β-strand	176	1	63
β-strand	186-187	2	63
β-strand	192-193	2	63
β-strand	202	1	64
β-strand	215-217	3	63
β-strand	223-229	7	63
β-strand	237	1	64
β-strand	240-244	5	63
β-strand	250-253	4	63
β-strand	260	1	63

Chain G: 10 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	65
β-strand	8	1	66
β-strand	15-19	5	67
β-strand	24	1	68
β-strand	27-48	22	67
β-strand	51-54	4	69
α-helix	56-59	4
β-strand	60-61	2	70
β-strand	77	1	71
β-strand	81-82	2	70
β-strand	87	1	72
β-strand	92	1	72
β-strand	101-102	2	70
β-strand	106	1	71
β-strand	107-110	4	69
α-helix	112-115	4
β-strand	119-137	19	67
β-strand	140-148	9	67
β-strand	155-157	3	65
β-strand	160-164	5	65
α-helix	165-167	3
β-strand	177-181	5	67
β-strand	184-186	3	67
β-strand	205-206	2	67
β-strand	215	1	67
β-strand	221-222	2	73
β-strand	234-235	2	73
α-helix	240-246	7
α-helix	252-254	3
β-strand	261-262	2	67
β-strand	269-270	2	67
β-strand	276	1	66
β-strand	279-282	4	65
α-helix	285-287	3
β-strand	290	1	68
α-helix	295-296	2
β-strand	297-307	11	74
β-strand	308	1	75
β-strand	315-323	9	74
β-strand	331-332	2	76
β-strand	338-340	3	74
β-strand	352-359	8	74
β-strand	367-370	4	76
β-strand	374-376	3	76
β-strand	382	1	75
β-strand	388-389	2	77
α-helix	400-402	3
α-helix	405-410	6
α-helix	417-437	21

Chain H: 10 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	12	1	78
β-strand	17-18	2	79
β-strand	28-29	2	79
β-strand	34-37	4	80
β-strand	44-53	10	80
β-strand	64-69	6	80
β-strand	72-77	6	80
β-strand	81-84	4	81
β-strand	88	1	81
β-strand	90-102	13	80
β-strand	106-113	8	81
β-strand	121-128	8	81
β-strand	136	1	82
β-strand	146-153	8	83
β-strand	163-167	5	84
α-helix	168-171	4
β-strand	178-180	3	85
β-strand	185-187	3	85
β-strand	196-199	4	86
β-strand	200	1	87
β-strand	204	1	87
β-strand	207-208	2	86
α-helix	220-222	3
β-strand	223-225	3	86
β-strand	233	1	78
β-strand	234-235	2	84
β-strand	250-253	4	84
β-strand	258-265	8	83
α-helix	268-271	4
β-strand	272-276	5	88
β-strand	279-284	6	88
β-strand	290-295	6	82
β-strand	304-308	5	82
β-strand	312-316	5	88
β-strand	323-327	5	82
α-helix	331-332	2
β-strand	333-335	3	82
β-strand	336-337	2	77
α-helix	349-359	11
α-helix	361-383	23
α-helix	386-398	13
α-helix	404-406	3
α-helix	407-411	5

9 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein E1	A, D, G, J	protein	441	Eastern equine encephalitis virus	Q4QXJ7
Spike glycoprotein E2	B, E, H, K	protein	420	Eastern equine encephalitis virus	Q4QXJ7
Capsid protein	C, F, I, L	protein	261	Eastern equine encephalitis virus	Q4QXJ7
Very low-density lipoprotein receptor	M, N, O, P	protein	41	Homo sapiens	P98155 (AlphaFold model)
Very low-density lipoprotein receptor	Q, R, S, T	protein	41	Homo sapiens	P98155 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>8YS4_1 Spike glycoprotein E1 (chains A, D, G, J)
YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVV
KCCGATQCTSKPHPDYQCQVFSGVYPFMWGGAYCFCDTENTQMSEAYVERSEECSIDHAK
AYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVV
YGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQVPSG
FERWKKDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDL
ECKITECTYAFDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTA
NIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWIKVLVGGTSA
FIVLGLIATAVVALVLFFHRH

Sequence of entity 2 (B, E, H, K), FASTA

>8YS4_2 Spike glycoprotein E2 (chains B, E, H, K)
DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGV
DLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRH
TCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSI
HSAKVKITVPSGAQVKYYCKCPDVRKGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRL
PRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSD
ANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRY
PLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPTRA

Sequence of entity 3 (C, F, I, L), FASTA

>8YS4_3 Capsid protein (chains C, F, I, L)
MFPYPTLNYPPMAPINPMAYRDPNPPRRRWRPFRPPLAAQIEDLRRSIASLTLKQRAPNP
PAGPPANRKKPAPKPKPAQAKKKRPPPPAKKQKRKPKPGKRQRMCMKLESDKTFPIMLNG
QVNGYACVVGGRVFKPLHVEGRIDNEQLAAIKLKKASIYDLEYGDVPQCMKSDTLQYTSD
KPPGFYNWHHGAVQYENNRFTVPRGVGGKGDSGRPILDNKGRVVAIVLGGVNEGSRTALS
VVTWNQKGVTVKDTPEGSEPW

Sequence of entity 4 (M, N, O, P), FASTA

>8YS4_4 Very low-density lipoprotein receptor (chains M, N, O, P)
PTCGAHEFQCSTSSCIPISWVCDDDADCSDQSDESLEQCGR

Sequence of entity 5 (Q, R, S, T), FASTA

>8YS4_5 Very low-density lipoprotein receptor (chains Q, R, S, T)
RTCRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENCGN

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	8

Primary citation

The receptor VLDLR binds Eastern Equine Encephalitis virus through multiple distinct modes. Cao, D., Ma, B., Cao, Z. et al. Nat Commun (2024) 15:6866-6866. DOI 10.1038/s41467-024-51293-x · 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
7V0P 5.2 Å, Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a potently neutralizing…
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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