8DWO: Eastern Equine Encephalitis Virus

Cryo-EM Structure of Eastern Equine Encephalitis Virus in complex with SKE26 Fab. Determined by electron microscopy at 3.5 Å resolution. Released 19 Jul 2023.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Eastern equine encephalitis virus, Macaca fascicularis
Chains: 12
Atoms: 22,572
Mol. weight: 431.73 kDa
Released: 19 Jul 2023

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

Secondary structure: helices and β-sheets

8DWO contains 53 α-helices and 279 β-strands across 12 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: 7 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	14-19	6	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	77	1	5
β-strand	80	1	6
β-strand	103	1	6
β-strand	106	1	5
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	149	1	1
β-strand	155-157	3	1
β-strand	160-164	5	1
β-strand	177-181	5	2
β-strand	184-186	3	2
β-strand	204-206	3	2
β-strand	214-216	3	2
β-strand	221-222	2	7
α-helix	224-225	2
β-strand	234-235	2	7
α-helix	237-239	3
α-helix	240-247	8
β-strand	261	1	8
β-strand	270	1	8
β-strand	276-282	7	1
α-helix	285-287	3
β-strand	290	1	3
α-helix	295-296	2
β-strand	298-307	10	9
β-strand	315-322	8	9
β-strand	327-330	4	10
β-strand	331-332	2	11
β-strand	338-340	3	12
β-strand	344-347	4	10
β-strand	353-356	4	9
β-strand	357-359	3	12
β-strand	367-370	4	11
β-strand	373-376	4	11

Chain B: 6 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
β-strand	12	1	13
β-strand	17-19	3	14
β-strand	27-29	3	14
β-strand	33-37	5	15
β-strand	44-53	10	15
β-strand	64-69	6	15
β-strand	72-77	6	15
β-strand	81-84	4	16
β-strand	88	1	16
β-strand	90-102	13	15
β-strand	106	1	17
β-strand	109-113	5	16
β-strand	121-124	4	16
β-strand	128	1	17
β-strand	136	1	18
β-strand	146-153	8	19
β-strand	163-166	4	20
β-strand	167	1	21
α-helix	168	1
β-strand	169	1	22
α-helix	170-171	2
β-strand	172-174	3	23
β-strand	178-180	3	24
β-strand	185-187	3	24
β-strand	196-199	4	23
β-strand	212	1	24
α-helix	220-222	3
β-strand	223-227	5	23
β-strand	233	1	13
β-strand	234	1	21
β-strand	242	1	22
β-strand	250-253	4	20
β-strand	258-265	8	19
α-helix	268-271	4
β-strand	272-274	3	25
β-strand	280-284	5	25
β-strand	290-296	7	18
β-strand	304-308	5	18
β-strand	312-316	5	25
β-strand	323-327	5	18
α-helix	331-332	2
β-strand	333-335	3	18

Chain F: 7 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	26
β-strand	14-19	6	27
β-strand	24	1	28
β-strand	27-39	13	27
β-strand	44-48	5	29
β-strand	51-54	4	30
β-strand	77	1	31
β-strand	88	1	32
β-strand	91	1	32
β-strand	106	1	31
β-strand	107-110	4	30
α-helix	113-115	3
β-strand	119-123	5	29
β-strand	128-137	10	27
β-strand	143-148	6	27
β-strand	149-157	9	26
β-strand	160-164	5	26
β-strand	177-181	5	29
β-strand	184-186	3	29
β-strand	206	1	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	257-259	3
β-strand	269-270	2	27
β-strand	276-282	7	26
α-helix	285-287	3
β-strand	290	1	28
α-helix	291-293	3
β-strand	297-307	11	34
β-strand	315-323	9	34
β-strand	327-330	4	35
β-strand	331-332	2	36
β-strand	339-340	2	37
β-strand	344-347	4	35
β-strand	352-356	5	34
β-strand	357-358	2	37
β-strand	366-370	5	36
β-strand	374-377	4	36

Chain G: 7 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
β-strand	12	1	38
β-strand	19-22	4	39
β-strand	25-27	3	39
β-strand	37	1	40
β-strand	44-53	10	40
β-strand	64-68	5	40
β-strand	73-77	5	40
β-strand	81-84	4	41
β-strand	88	1	41
β-strand	90-102	13	40
α-helix	103-104	2
β-strand	106	1	42
β-strand	109-113	5	41
β-strand	121-124	4	41
β-strand	128	1	42
β-strand	136	1	43
β-strand	146-153	8	44
β-strand	163-167	5	45
β-strand	169	1	46
β-strand	172-174	3	47
β-strand	178-180	3	48
β-strand	185-187	3	48
β-strand	196-198	3	47
β-strand	213-214	2	48
α-helix	220-222	3
β-strand	224-227	4	47
β-strand	233	1	38
β-strand	234-235	2	45
α-helix	241	1
β-strand	242	1	46
α-helix	243	1
β-strand	250-253	4	45
β-strand	258-265	8	44
α-helix	266-271	6
β-strand	272-274	3	49
β-strand	280-284	5	49
β-strand	290-296	7	43
β-strand	304-308	5	43
β-strand	312-316	5	49
β-strand	323-327	5	43
α-helix	331-332	2
β-strand	333-335	3	43

Chain H: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	50
α-helix	7-9	3
β-strand	10-12	3	51
β-strand	18-25	8	50
β-strand	33-39	7	51
β-strand	45-52	8	51
β-strand	57-59	3	51
β-strand	64	1	52
β-strand	67	1	52
β-strand	68-72	5	50
β-strand	77-82	6	50
α-helix	84-86	3
β-strand	88-95	8	51
β-strand	102-103	2	51
β-strand	107-111	5	51

Chain J: 8 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	53
β-strand	14-21	8	54
β-strand	24-48	25	54
β-strand	51-54	4	55
α-helix	56-58	3
β-strand	59	1	56
β-strand	77-80	4	57
β-strand	87	1	58
β-strand	103-106	4	57
β-strand	107-110	4	55
α-helix	113-115	3
β-strand	119-137	19	54
β-strand	143-148	6	54
β-strand	150-157	8	53
β-strand	160-164	5	53
β-strand	177-181	5	54
β-strand	184-186	3	54
β-strand	205-206	2	54
β-strand	221-222	2	59
α-helix	223-226	4
β-strand	229	1	58
β-strand	234-235	2	59
α-helix	237-239	3
α-helix	240-247	8
β-strand	270	1	54
β-strand	276-282	7	53
α-helix	285-287	3
β-strand	290	1	54
α-helix	291-293	3
α-helix	295-296	2
β-strand	297-307	11	60
β-strand	315-323	9	60
β-strand	327-330	4	61
β-strand	331-332	2	62
β-strand	338-340	3	60
β-strand	344-347	4	61
β-strand	352-359	8	60
β-strand	367-370	4	62
β-strand	374-376	3	62

Chain K: 6 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
β-strand	12	1	63
β-strand	17-22	6	64
β-strand	25-29	5	64
β-strand	34-37	4	65
β-strand	44-54	11	65
β-strand	64-68	5	65
β-strand	73-77	5	65
β-strand	82-84	3	66
β-strand	88-89	2	66
β-strand	90-102	13	65
β-strand	109-112	4	66
β-strand	121-124	4	66
β-strand	136	1	67
β-strand	146-153	8	68
β-strand	163-164	2	69
β-strand	166-167	2	70
β-strand	169	1	56
β-strand	172-174	3	71
β-strand	178-180	3	72
β-strand	185-187	3	72
β-strand	195-198	4	71
β-strand	208	1	71
β-strand	212-214	3	72
α-helix	220-222	3
β-strand	224-227	4	71
β-strand	233	1	63
β-strand	234-235	2	70
α-helix	241	1
β-strand	242	1	56
α-helix	243	1
β-strand	252-253	2	69
β-strand	258-265	8	68
α-helix	268-271	4
β-strand	272-274	3	73
β-strand	280-284	5	73
β-strand	290-296	7	67
β-strand	304-308	5	67
β-strand	312-316	5	73
β-strand	323-327	5	67
α-helix	331-332	2
β-strand	333-335	3	67

Chain L: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	74
β-strand	10-12	3	75
β-strand	19-25	7	74
β-strand	27C	1	76
β-strand	31	1	76
β-strand	33-38	6	75
β-strand	44-49	6	75
β-strand	53-54	2	75
β-strand	62-67	6	74
β-strand	70-75	6	74
α-helix	80-82	3
β-strand	84-90	7	75
α-helix	96	1
β-strand	102-105	4	75

4 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, F, J	protein	441	Eastern equine encephalitis virus	P08768
Envelope glycoprotein E2	B, G, K	protein	420	Eastern equine encephalitis virus	P08768
SKE26 Fab Heavy Chain	H, S, U	protein	233	Macaca fascicularis
SKE26 Fab Light Chain	L, T, V	protein	219	Macaca fascicularis

Sequence of entity 1 (A, F, J), FASTA

>8DWO_1 Envelope glycoprotein E1 (chains A, F, J)
YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVV
KCCGATQCTSKPHPDYQCQVFSGVYPFMYGGAYCFCDTENTQMSEAYVERSEECSIDHAK
AYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVV
YGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQVPSG
FERWKKDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDL
ECKITECTYAFDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTA
NIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWIKVLVGGTSA
FIVLGLIATAVVALVLFFHRH

Sequence of entity 2 (B, G, K), FASTA

>8DWO_2 Envelope glycoprotein E2 (chains B, G, K)
DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGV
DLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRH
TCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSI
HSAKVKITVPSGAQVKYYCKCPDVRKGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRL
PRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSD
ANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRY
PLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPTRA

Sequence of entity 3 (H, S, U), FASTA

>8DWO_3 SKE26 Fab Heavy Chain (chains H, S, U)
VVQLVQSGAEVKRPGESLRISCKTSGYRFTDIWINWVRQRPGKGLEWMGSIYLDDSDIRF
NPSFQGHVTISADKSTSTTYLQWSSLKASDTATYFCARSVWSGYYIGWFDVWGPGVLVTV
SSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGGLEVLFQ

Sequence of entity 4 (L, T, V), FASTA

>8DWO_4 SKE26 Fab Light Chain (chains L, T, V)
DVVMTQTPLSLPVTPGEPASISCRSSQSLLDSNGNTYLHWYLQKPGQSPQLLIYGGSNRA
SGVPDRFSGSGSGTDFTLTINNVEAGDVGTYYCMQVIQVPLTFGGGTKVDIKRTVAAPSV
FIFPPSEDQVKSGTVSVVCLLNNFYPREASVKWKVDGALKTGNSQESVTEQDSKDNTYSL
SSTLTLSSTEYQSHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Vaccine elicitation and structural basis for antibody protection against alphaviruses. Sutton, M.S., Pletnev, S., Callahan, V. et al. Cell (2023) 186:2672-2689.e25. DOI 10.1016/j.cell.2023.05.019 · 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…
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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