8UA4: Eastern equine encephalitis virus VLP

Structure of eastern equine encephalitis virus VLP in complex with VLDLR LA1. Determined by electron microscopy at 3.58 Å resolution. Released 14 Aug 2024.

Method: Electron microscopy
Resolution: 3.58 Å
Organisms: Eastern equine encephalitis virus, Homo sapiens
Chains: 17
Atoms: 33,292
Mol. weight: 532.43 kDa
Ligands: CA, NAG
Released: 14 Aug 2024

Explore 8UA4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UA4 contains 113 α-helices and 399 β-strands across 17 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: 12 helices, 40 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	27-39	13	2
β-strand	42-46	5	4
β-strand	47	1	5
β-strand	51-54	4	6
α-helix	56-58	3
β-strand	59-63	5	7
β-strand	77	1	8
β-strand	80-82	3	7
β-strand	100-103	4	7
β-strand	106	1	8
β-strand	107-110	4	6
α-helix	112-115	4
β-strand	120-124	5	4
β-strand	128-137	10	2
β-strand	143-148	6	2
β-strand	157	1	9
β-strand	160	1	9
β-strand	161-164	4	1
α-helix	165-167	3
β-strand	177-181	5	4
β-strand	184-186	3	4
β-strand	206	1	5
β-strand	214	1	5
β-strand	221-222	2	10
α-helix	226-228	3
β-strand	234-235	2	10
α-helix	237-239	3
α-helix	240-246	7
α-helix	252-254	3
β-strand	261-263	3	2
β-strand	268-270	3	2
β-strand	276-282	7	1
β-strand	290	1	3
α-helix	291-293	3
α-helix	295-296	2
β-strand	297-307	11	11
β-strand	315-323	9	11
β-strand	327-330	4	12
β-strand	331-332	2	13
β-strand	339-340	2	11
β-strand	344-347	4	12
β-strand	351-358	8	11
β-strand	365-367	3	14
β-strand	369-370	2	13
β-strand	376-378	3	14
β-strand	388-389	2	15
α-helix	396-397	2
α-helix	407-431	25
α-helix	432-436	5

Chain B: 8 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	8-10	3
β-strand	12	1	16
α-helix	14-16	3
β-strand	17-20	4	17
β-strand	21	1	18
β-strand	22	1	17
β-strand	25-29	5	17
β-strand	34-37	4	19
β-strand	44-48	5	19
β-strand	67-68	2	20
β-strand	73-74	2	20
β-strand	82-84	3	18
β-strand	88	1	18
β-strand	90-94	5	19
β-strand	99-102	4	19
β-strand	106-112	7	18
β-strand	121-128	8	18
β-strand	136	1	21
β-strand	147-153	7	22
β-strand	163	1	23
β-strand	166-167	2	24
β-strand	172-173	2	25
β-strand	178-181	4	26
β-strand	184-187	4	26
β-strand	194-198	5	25
β-strand	206-209	4	25
β-strand	213-214	2	26
β-strand	226-228	3	25
β-strand	233	1	16
β-strand	234-235	2	24
β-strand	249-250	2	24
β-strand	253	1	23
β-strand	258-264	7	22
α-helix	268-271	4
β-strand	272-276	5	27
β-strand	279-284	6	27
β-strand	290-296	7	21
β-strand	304-308	5	21
β-strand	312-317	6	27
β-strand	323-327	5	21
α-helix	331-332	2
β-strand	333-335	3	21
β-strand	336-337	2	15
α-helix	349-358	10
α-helix	365-399	35
α-helix	407-412	6

Chain C: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	109-112	4
β-strand	113-118	6	28
β-strand	121-129	9	28
β-strand	132-135	4	28
β-strand	142-143	2	28
α-helix	146-149	4
α-helix	152-153	2
β-strand	154	1	28
α-helix	155	1
α-helix	157-159	3
β-strand	162-165	4	28
α-helix	166-167	2
α-helix	168-170	3
β-strand	175	1	28
β-strand	176-177	2	29
β-strand	201	1	29
β-strand	215-217	3	29
β-strand	222-231	10	29
β-strand	238-244	7	29
β-strand	250-253	4	29
β-strand	259-260	2	29

Chain D: 14 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	30
β-strand	15-19	5	31
β-strand	24	1	32
α-helix	25-26	2
β-strand	27-39	13	31
β-strand	42-48	7	33
β-strand	51-54	4	34
α-helix	56-58	3
β-strand	59	1	35
β-strand	60-61	2	36
β-strand	64	1	37
β-strand	77	1	38
α-helix	80	1
β-strand	81-82	2	36
β-strand	87	1	39
β-strand	92	1	39
β-strand	100	1	37
β-strand	101-102	2	36
β-strand	106	1	38
β-strand	107-110	4	34
β-strand	119-124	6	33
β-strand	128-137	10	31
β-strand	140-148	9	31
β-strand	154-157	4	30
β-strand	160-164	5	30
β-strand	177-181	5	33
β-strand	184-186	3	33
α-helix	190-192	3
β-strand	204-205	2	40
β-strand	206	1	33
β-strand	215-216	2	40
β-strand	221-222	2	41
α-helix	223-225	3
β-strand	234-235	2	41
α-helix	237-239	3
α-helix	240-246	7
α-helix	252-255	4
β-strand	261-262	2	31
α-helix	263	1
β-strand	269-270	2	31
β-strand	276-282	7	30
α-helix	285-287	3
β-strand	290	1	32
α-helix	291-293	3
β-strand	297-307	11	42
β-strand	308	1	43
β-strand	315-323	9	42
β-strand	327-330	4	44
β-strand	331-332	2	45
β-strand	338-340	3	42
β-strand	344-347	4	44
β-strand	352-359	8	42
β-strand	366-370	5	45
β-strand	374-377	4	45
β-strand	382	1	43
β-strand	388-389	2	46
α-helix	392-393	2
α-helix	399-401	3
α-helix	407-437	31

Chain E: 9 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12	1	47
β-strand	17-20	4	48
β-strand	21	1	49
β-strand	22	1	48
β-strand	25-29	5	48
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	82-84	3	49
β-strand	88	1	49
β-strand	90-102	13	50
β-strand	106	1	51
β-strand	109-112	4	49
β-strand	121-124	4	49
β-strand	128	1	51
β-strand	136	1	52
β-strand	147-153	7	53
β-strand	163-164	2	54
β-strand	166-167	2	55
β-strand	172-173	2	56
β-strand	178-181	4	57
β-strand	184-187	4	57
α-helix	190-192	3
β-strand	195-199	5	56
β-strand	205-209	5	56
β-strand	213-214	2	57
β-strand	223-227	5	56
β-strand	233	1	47
β-strand	234-235	2	55
α-helix	241	1
β-strand	242	1	35
α-helix	243	1
β-strand	252-253	2	54
β-strand	258-264	7	53
α-helix	268-271	4
β-strand	272-276	5	58
β-strand	279-284	6	58
β-strand	290-296	7	52
β-strand	304-308	5	52
β-strand	312-317	6	58
β-strand	323-327	5	52
α-helix	331-332	2
β-strand	333-335	3	52
β-strand	336-337	2	46
α-helix	349-359	11
α-helix	361-399	39
α-helix	407-412	6

Chain F: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	109-112	4
β-strand	113-118	6	59
β-strand	121-129	9	59
β-strand	132-136	5	59
β-strand	142-143	2	59
α-helix	147-150	4
α-helix	152-153	2
β-strand	154-156	3	59
α-helix	157-159	3
β-strand	161-165	5	59
α-helix	168-170	3
β-strand	175	1	59
β-strand	177	1	60
β-strand	184-188	5	60
β-strand	191-196	6	60
β-strand	199-203	5	60
β-strand	215-217	3	60
β-strand	223-233	11	60
β-strand	236-244	9	60
β-strand	250-253	4	60
β-strand	259-260	2	60

Chain G: 12 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	61
β-strand	15-19	5	62
β-strand	24	1	63
β-strand	27-39	13	62
β-strand	42-48	7	64
β-strand	51-54	4	65
α-helix	56-58	3
β-strand	59	1	66
β-strand	77	1	67
β-strand	81	1	68
β-strand	87	1	69
β-strand	92	1	69
β-strand	102	1	68
β-strand	106	1	67
β-strand	107-110	4	65
α-helix	112-115	4
β-strand	119-124	6	64
β-strand	128-137	10	62
β-strand	143-148	6	62
β-strand	155-157	3	61
β-strand	160-164	5	61
β-strand	177-181	5	64
β-strand	184-186	3	64
α-helix	190-192	3
β-strand	204-206	3	64
β-strand	214-216	3	64
β-strand	221-222	2	70
β-strand	234-235	2	70
α-helix	237-239	3
α-helix	240-246	7
α-helix	252-254	3
β-strand	261-262	2	62
β-strand	269-270	2	62
β-strand	276-282	7	61
α-helix	285-287	3
β-strand	290	1	63
α-helix	291-293	3
α-helix	295-296	2
β-strand	298-307	10	71
β-strand	308	1	72
β-strand	315-322	8	71
β-strand	327-330	4	73
β-strand	331-332	2	74
β-strand	338-340	3	71
β-strand	344-347	4	73
β-strand	352-359	8	71
β-strand	367-370	4	74
β-strand	373-376	4	74
β-strand	382	1	72
β-strand	388-389	2	75
α-helix	392-393	2
α-helix	399-401	3
α-helix	407-437	31

Chain H: 9 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	8-10	3
β-strand	12	1	76
β-strand	19	1	77
β-strand	21	1	78
β-strand	27	1	77
β-strand	34-37	4	79
β-strand	44-55	12	79
β-strand	60-68	9	79
β-strand	73-77	5	79
β-strand	82-84	3	78
β-strand	88	1	78
β-strand	90-102	13	79
β-strand	106	1	80
β-strand	109-112	4	78
β-strand	121-124	4	78
β-strand	128	1	80
β-strand	136	1	81
β-strand	146-153	8	82
β-strand	163-164	2	83
β-strand	166-167	2	84
α-helix	168-171	4
β-strand	172-174	3	85
β-strand	178-181	4	86
β-strand	184-187	4	86
α-helix	188-189	2
β-strand	194-199	6	85
β-strand	205-209	5	85
β-strand	213-214	2	86
β-strand	223-228	6	85
β-strand	233	1	76
β-strand	234-235	2	84
β-strand	242	1	66
β-strand	252-253	2	83
β-strand	258-265	8	82
α-helix	268-271	4
β-strand	272-276	5	87
β-strand	279-284	6	87
β-strand	290-296	7	81
β-strand	304-308	5	81
β-strand	312-316	5	87
β-strand	323-327	5	81
α-helix	331-332	2
β-strand	333-335	3	81
β-strand	336-337	2	75
α-helix	349-359	11
α-helix	361-394	34
α-helix	408-411	4

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
Envelope glycoprotein E1	A, D, G, J	protein	441	Eastern equine encephalitis virus	P08768
Envelope glycoprotein E2	B, E, H, K	protein	420	Eastern equine encephalitis virus	P08768
Capsid protein	C, F, I, L	protein	261	Eastern equine encephalitis virus	P08768
Envelope glycoprotein E3	M, N, O, P	protein	63	Eastern equine encephalitis virus	P08768
Very low-density lipoprotein receptor	R	protein	36	Homo sapiens	P98155 (AlphaFold model)

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

>8UA4_1 Envelope glycoprotein E1 (chains A, D, G, J)
YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVV
KCCGATQCTSKPHPDYQCQVFSGVYPFMWGGAYCFCDTENTQMSEAYVERSEECSIDHAK
AYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVV
YGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQVPSG
FERWKKDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDL
ECKITECTYAFDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTA
NIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWIKVLVGGTSA
FIVLGLIATAVVALVLFFHRH

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

>8UA4_2 Envelope glycoprotein E2 (chains B, E, H, K)
DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGV
DLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRH
TCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSI
HSAKVKITVPSGAQVKYYCKCPDVRKGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRL
PRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSD
ANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRY
PLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPTRA

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

>8UA4_3 Capsid protein (chains C, F, I, L)
MFPYPTLNYPPMAPINPMAYRDPNPPRRRWRPFRPPLAAQIEDLRRSIASLTLKQRAPNP
PAGPPANRKKPAPKPKPAQAKKKRPPPPAKKQKRKPKPGKRQRMCMKLESDKTFPIMLNG
QVNGYACVVGGRVFKPLHVEGRIDNEQLAAIKLKKASIYDLEYGDVPQCMKSDTLQYTSD
KPPGFYNWHHGAVQYENNRFTVPRGVGGKGDSGRPILDNKGRVVAIVLGGVNEGSRTALS
VVTWNQKGVTVKDTPEGSEPW

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

>8UA4_4 Envelope glycoprotein E3 (chains M, N, O, P)
SLATVMCVLANITFPCDQPPCMPCCYEKNPHETLTMLEQNYDSRAYDQLLDAAVKCNARR
TRR

Sequence of entity 5 (R), FASTA

>8UA4_5 Very low-density lipoprotein receptor (chains R)
CEPSQFQCTNGRCITLLWKCDGDEDCVDGSDEKNCV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Structural basis for VLDLR recognition by eastern equine encephalitis virus. Yang, P., Li, W., Fan, X. et al. Nat Commun (2024) 15:6548-6548. DOI 10.1038/s41467-024-50887-9 · PubMed

Other PDB entries of the same protein (UniProt P08768), best resolution first:

8UFA 2.86 Å, Eastern equine encephalitis virus (PE-6) VLP (asymmetric unit)
8UA9 3.0 Å, Structure of eastern equine encephalitis virus VLP unliganded quasi-threefold spike…
8UFC 3.09 Å, Eastern equine encephalitis virus (PE-6) VLP in complex with VLDLR LA(1-2) (asymmetric…
8DWO 3.5 Å, Cryo-EM Structure of Eastern Equine Encephalitis Virus in complex with SKE26 Fab
8UFB 3.89 Å, Eastern equine encephalitis virus (PE-6) VLP in complex with full-length VLDLR…
6XO4 4.2 Å, CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP
6XOB 8.5 Å, CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP with Fab EEEV-143.

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