8UA9: Envelope glycoprotein E1

Structure of eastern equine encephalitis virus VLP unliganded quasi-threefold spike protein. Determined by electron microscopy at 3.0 Å resolution. Released 14 Aug 2024.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Eastern equine encephalitis virus
Chains: 16
Atoms: 33,106
Mol. weight: 522.64 kDa
Ligands: NAG
Released: 14 Aug 2024

Explore 8UA9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UA9 contains 99 α-helices and 392 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: 11 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	15-21	7	2
β-strand	24-39	16	2
β-strand	42-48	7	3
β-strand	51-54	4	4
α-helix	56-58	3
β-strand	59-61	3	5
β-strand	77-79	3	6
β-strand	82	1	5
β-strand	101-103	3	5
β-strand	104-106	3	6
β-strand	107-110	4	4
α-helix	112-115	4
β-strand	119-124	6	3
β-strand	128-137	10	2
β-strand	145-148	4	2
β-strand	155-157	3	1
β-strand	160-162	3	1
β-strand	177-181	5	3
β-strand	184-186	3	3
α-helix	190-192	3
β-strand	204-206	3	3
β-strand	215-216	2	3
β-strand	221-222	2	7
α-helix	224-226	3
β-strand	234-235	2	7
α-helix	237-239	3
α-helix	240-247	8
α-helix	252-255	4
α-helix	257-259	3
β-strand	261-264	4	2
β-strand	267-270	4	2
β-strand	276-282	7	1
β-strand	290	1	2
α-helix	291-293	3
β-strand	300-307	8	8
β-strand	308	1	9
β-strand	315-321	7	8
β-strand	327-330	4	10
β-strand	331-332	2	11
β-strand	338-340	3	8
β-strand	344-347	4	10
β-strand	352-359	8	8
β-strand	366-370	5	11
β-strand	374-377	4	11
β-strand	382	1	9
α-helix	383-384	2
β-strand	388-389	2	12
α-helix	404-440	37

Chain B: 10 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6
α-helix	8-11	4
β-strand	12	1	13
β-strand	17-19	3	14
β-strand	21	1	15
β-strand	27-29	3	14
β-strand	35-37	3	16
β-strand	44-55	12	16
β-strand	60-67	8	16
β-strand	74-77	4	16
β-strand	82-84	3	15
β-strand	88	1	15
β-strand	90-102	13	16
β-strand	106	1	17
β-strand	109-115	7	15
β-strand	118-124	7	15
α-helix	126-127	2
β-strand	128	1	17
β-strand	136	1	18
β-strand	146-153	8	19
β-strand	163-164	2	20
β-strand	166-167	2	21
β-strand	172-173	2	22
β-strand	178-181	4	23
β-strand	184-187	4	23
β-strand	194-201	8	22
β-strand	203-209	7	22
β-strand	213-214	2	23
α-helix	220-222	3
β-strand	223-228	6	22
β-strand	233	1	13
β-strand	234-235	2	21
β-strand	242	1	5
β-strand	252-253	2	20
α-helix	254	1
β-strand	258-265	8	19
α-helix	268-271	4
β-strand	272-276	5	24
β-strand	279-284	6	24
β-strand	290-296	7	18
β-strand	304-308	5	18
β-strand	312-314	3	24
β-strand	323-327	5	18
α-helix	331-332	2
β-strand	333-335	3	18
β-strand	336-337	2	12
α-helix	349-359	11
α-helix	361-399	39
α-helix	407-412	6

Chains C, G, K and O: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	25
β-strand	12-15	4	25
α-helix	30-39	10
α-helix	46-54	9

Chain D: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	113-118	6	26
β-strand	121-129	9	26
β-strand	132-136	5	26
β-strand	142	1	26
α-helix	148-150	3
α-helix	153	1
β-strand	154-156	3	26
β-strand	161-165	5	26
α-helix	166-167	2
α-helix	168-170	3
β-strand	175	1	26
β-strand	177	1	27
β-strand	184-188	5	27
β-strand	191-196	6	27
β-strand	199-203	5	27
β-strand	215-217	3	27
β-strand	223-233	11	27
β-strand	236-244	9	27
β-strand	250-253	4	27

Chain E: 12 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	28
β-strand	15-21	7	29
β-strand	24-48	25	29
β-strand	51-54	4	30
α-helix	56-58	3
β-strand	59-61	3	31
β-strand	77-79	3	32
β-strand	82	1	31
β-strand	101-103	3	31
β-strand	104-106	3	32
β-strand	107-110	4	30
α-helix	112-115	4
β-strand	119-137	19	29
β-strand	140	1	29
β-strand	145-148	4	29
β-strand	155-157	3	28
β-strand	160-162	3	28
α-helix	164-167	4
β-strand	177-181	5	29
β-strand	184-186	3	29
α-helix	190-192	3
β-strand	204-206	3	29
β-strand	215-216	2	29
β-strand	221-222	2	33
α-helix	224-226	3
β-strand	234-235	2	33
α-helix	237-239	3
α-helix	240-247	8
α-helix	252-255	4
α-helix	257-259	3
β-strand	261-263	3	29
β-strand	268-270	3	29
β-strand	276-282	7	28
β-strand	290	1	29
α-helix	291-293	3
β-strand	297-307	11	34
β-strand	308	1	35
β-strand	315-323	9	34
β-strand	327-330	4	36
β-strand	331-332	2	37
β-strand	338-340	3	34
β-strand	344-347	4	36
β-strand	352-359	8	34
β-strand	366-370	5	37
β-strand	374-377	4	37
β-strand	382	1	35
α-helix	383-384	2
β-strand	388-389	2	38
α-helix	404-440	37

Chain F: 8 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	9-11	3
β-strand	12	1	39
β-strand	17-19	3	40
β-strand	21	1	41
β-strand	27-29	3	40
β-strand	35-37	3	42
β-strand	44-55	12	42
β-strand	60-67	8	42
β-strand	74-77	4	42
β-strand	82-84	3	41
β-strand	88	1	41
β-strand	90-102	13	42
β-strand	106	1	43
β-strand	109-115	7	41
β-strand	118-124	7	41
β-strand	128	1	43
β-strand	136	1	44
β-strand	146-153	8	45
β-strand	163-164	2	46
β-strand	166-167	2	47
β-strand	172-173	2	48
β-strand	178-181	4	49
β-strand	184-187	4	49
β-strand	194-200	7	48
β-strand	204-209	6	48
β-strand	213-214	2	49
β-strand	223-228	6	48
β-strand	233	1	39
β-strand	234-235	2	47
β-strand	242	1	31
β-strand	252-253	2	46
α-helix	254	1
β-strand	258-265	8	45
α-helix	268-271	4
β-strand	272-276	5	50
β-strand	279-284	6	50
β-strand	290-296	7	44
β-strand	304-308	5	44
β-strand	312-317	6	50
β-strand	323-327	5	44
α-helix	331-332	2
β-strand	333-335	3	44
β-strand	336-337	2	38
α-helix	349-359	11
α-helix	365-399	35
α-helix	407-412	6

Chain H: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	114-117	4	52
β-strand	122-126	5	52
β-strand	127-129	3	53
β-strand	132-136	5	53
β-strand	142	1	52
α-helix	146-149	4
α-helix	153	1
β-strand	154-156	3	53
β-strand	161-165	5	53
α-helix	166-167	2
α-helix	168-170	3
β-strand	175	1	53
β-strand	177	1	54
β-strand	184-188	5	54
β-strand	191-196	6	54
β-strand	199-203	5	54
β-strand	215-217	3	54
β-strand	223-233	11	54
β-strand	236-244	9	54
β-strand	250-253	4	54
β-strand	259-260	2	54

Chain I: 11 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	55
β-strand	15-21	7	56
β-strand	24-39	16	56
β-strand	44-48	5	57
β-strand	51-54	4	58
α-helix	56-58	3
β-strand	59-61	3	59
β-strand	77-79	3	60
β-strand	82	1	59
β-strand	101-103	3	59
β-strand	104-106	3	60
β-strand	107-110	4	58
α-helix	112-115	4
β-strand	119-123	5	57
β-strand	128-137	10	56
β-strand	140	1	56
β-strand	145-148	4	56
β-strand	155-157	3	55
β-strand	160-164	5	55
β-strand	177-181	5	57
β-strand	184-186	3	57
α-helix	190-192	3
β-strand	204-205	2	61
β-strand	206	1	57
β-strand	215-216	2	61
β-strand	221-222	2	62
α-helix	224-226	3
β-strand	234-235	2	62
α-helix	237-239	3
α-helix	240-247	8
α-helix	252-255	4
α-helix	257-259	3
β-strand	261-264	4	56
β-strand	267-270	4	56
β-strand	276-282	7	55
β-strand	290	1	56
α-helix	291-293	3
β-strand	297-307	11	63
β-strand	308	1	64
β-strand	315-323	9	63
β-strand	327-330	4	65
β-strand	331-332	2	66
β-strand	338-340	3	63
β-strand	344-347	4	65
β-strand	352-359	8	63
β-strand	366-370	5	66
β-strand	374-377	4	66
β-strand	382	1	64
α-helix	383-384	2
β-strand	388-389	2	67
α-helix	404-440	37

5 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, E, I, M	protein	441	Eastern equine encephalitis virus	P08768
Structural polyprotein	B, F, J, N	protein	418	Eastern equine encephalitis virus	P08768
Structural polyprotein	C, G, K, O	protein	54	Eastern equine encephalitis virus	P08768
Capsid protein	D, H, L, P	protein	260	Eastern equine encephalitis virus	P08768

Sequence of entity 1 (A, E, I, M), FASTA

>8UA9_1 Envelope glycoprotein E1 (chains A, E, I, M)
YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVV
KCCGATQCTSKPHPDYQCQVFSGVYPFMWGGAYCFCDTENTQMSEAYVERSEECSIDHAK
AYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVV
YGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQVPSG
FERWKKDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDL
ECKITECTYAFDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTA
NIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWIKVLVGGTSA
FIVLGLIATAVVALVLFFHRH

Sequence of entity 2 (B, F, J, N), FASTA

>8UA9_2 Structural polyprotein (chains B, F, J, N)
DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGV
DLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRH
TCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSI
HSAKVKITVPSGAQVKYYCKCPDVRKGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRL
PRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSD
ANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRY
PLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPT

Sequence of entity 3 (C, G, K, O), FASTA

>8UA9_3 Structural polyprotein (chains C, G, K, O)
TVMCVLANITFPCDQPPCMPCCYEKNPHETLTMLEQNYDSRAYDQLLDAAVKCN

Sequence of entity 4 (D, H, L, P), FASTA

>8UA9_4 Capsid protein (chains D, H, L, P)
MFPYPTLNYPPMAPINPMAYRDPNPPRRRWRPFRPPLAAQIEDLRRSIANLTLKQRAPNP
PAGPPAKRKKPAPSLSLRRKKKRPPPPAKKQKRKPKPGKRQRMCMKLESDKTFPIMLNGQ
VNGYACVVGGRVFKPLHVEGRIDNEQLAAIKLKKASIYDLEYGDVPQCMKSDTLQYTSDK
PPGFYNWHHGAVQYENNRFTVPRGVGGKGDSGRPILDNKGRVVAIVLGGVNEGSRTALSV
VTWNQKGVTVKDTPEGSEPW

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

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)
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
8UA4 3.58 Å, Structure of eastern equine encephalitis virus VLP in complex with VLDLR LA1
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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