6XO4: Eastern Equine Encephalitis (EEEV) VLP

Name: PDB 6XO4: CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP
Published: 2020-12-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP. Determined by electron microscopy at 4.2 Å resolution. Released 23 Dec 2020.

Method: Electron microscopy
Resolution: 4.2 Å
Organism: Eastern equine encephalitis virus
Chains: 12
Atoms: 30,900
Mol. weight: 496.81 kDa
Released: 23 Dec 2020

Explore 6XO4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XO4 contains 72 α-helices and 342 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.

Chains A, D and G: 9 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	27-33	7	2
β-strand	37-38	2	2
β-strand	41-48	8	4
β-strand	51-54	4	5
α-helix	56-58	3
β-strand	77	1	6
β-strand	87	1	7
β-strand	106	1	6
β-strand	107-110	4	5
α-helix	112-115	4
β-strand	119-125	7	4
β-strand	129-137	9	2
β-strand	143-148	6	2
β-strand	155-157	3	1
β-strand	160-164	5	1
β-strand	177-181	5	4
β-strand	184-186	3	4
β-strand	205-206	2	4
β-strand	214	1	4
β-strand	221-222	2	8
β-strand	229	1	7
β-strand	234-235	2	8
α-helix	237-239	3
α-helix	240-246	7
α-helix	252-254	3
β-strand	269-270	2	2
β-strand	276-282	7	1
α-helix	285-287	3
β-strand	290	1	3
α-helix	291-293	3
α-helix	295-296	2
β-strand	297-307	11	9
β-strand	315-323	9	9
β-strand	327-330	4	10
β-strand	331-332	2	11
β-strand	338-340	3	9
β-strand	344-347	4	10
β-strand	352-359	8	9
β-strand	367-370	4	11
β-strand	374-376	3	11
α-helix	406-440	35

Chains B, E and H: 7 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
β-strand	12	1	12
β-strand	17-19	3	13
β-strand	27-29	3	13
β-strand	34-37	4	14
β-strand	44-54	11	14
β-strand	64-69	6	14
β-strand	72-77	6	14
β-strand	81-84	4	15
β-strand	88	1	15
β-strand	90-102	13	14
β-strand	106-113	8	15
β-strand	121-128	8	15
α-helix	131-133	3
β-strand	136	1	16
β-strand	146-153	8	17
β-strand	163-166	4	18
β-strand	167	1	19
β-strand	172-174	3	20
β-strand	178-180	3	21
β-strand	185-187	3	21
β-strand	195	1	22
β-strand	196-198	3	20
β-strand	208	1	22
β-strand	212	1	21
α-helix	220-222	3
β-strand	224-227	4	20
β-strand	233	1	12
β-strand	234	1	19
β-strand	250-253	4	18
β-strand	258-265	8	17
α-helix	266-271	6
β-strand	272-274	3	23
β-strand	280-284	5	23
β-strand	290	1	16
β-strand	292-296	5	24
β-strand	304-305	2	24
β-strand	308	1	16
β-strand	312-316	5	23
β-strand	323-327	5	24
β-strand	330-335	6	24
α-helix	349-358	10
α-helix	363-394	32
α-helix	395-402	8

Chains C, F, I and L: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	113-118	6	25
β-strand	121-127	7	25
β-strand	142-143	2	25
α-helix	148-150	3
β-strand	175	1	26
β-strand	185-188	4	27
β-strand	191-194	4	27
β-strand	202	1	28
α-helix	203	1
β-strand	215-217	3	29
β-strand	222	1	26
β-strand	223-227	5	29
β-strand	237	1	28
β-strand	241-244	4	29
β-strand	250-253	4	29

Chain J: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	88
β-strand	14-19	6	89
β-strand	24	1	90
β-strand	27-33	7	89
β-strand	37-38	2	89
β-strand	41-48	8	91
β-strand	51-54	4	92
α-helix	56-58	3
β-strand	59	1	93
β-strand	77	1	94
β-strand	87	1	95
β-strand	106	1	94
β-strand	107-110	4	92
α-helix	112-115	4
β-strand	119-125	7	91
β-strand	129-137	9	89
β-strand	143-148	6	89
β-strand	155-157	3	88
β-strand	160-164	5	88
β-strand	177-181	5	91
β-strand	184-186	3	91
β-strand	205-206	2	91
β-strand	214	1	91
β-strand	221-222	2	96
β-strand	229	1	95
β-strand	234-235	2	96
α-helix	237-239	3
α-helix	240-246	7
α-helix	252-254	3
β-strand	269-270	2	89
β-strand	276-282	7	88
α-helix	285-287	3
β-strand	290	1	90
α-helix	291-293	3
α-helix	295-296	2
β-strand	297-307	11	97
β-strand	315-323	9	97
β-strand	327-330	4	98
β-strand	331-332	2	99
β-strand	338-340	3	97
β-strand	344-347	4	98
β-strand	352-359	8	97
β-strand	367-370	4	99
β-strand	374-376	3	99
α-helix	406-440	35

Chain K: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	3-9	7
β-strand	12	1	100
β-strand	17-19	3	101
β-strand	27-29	3	101
β-strand	34-37	4	102
β-strand	44-54	11	102
β-strand	64-69	6	102
β-strand	72-77	6	102
β-strand	81-84	4	103
β-strand	88	1	103
β-strand	90-102	13	102
β-strand	106-113	8	103
β-strand	121-128	8	103
α-helix	131-133	3
β-strand	136	1	104
β-strand	146-153	8	105
β-strand	163-166	4	106
β-strand	167	1	107
β-strand	172-174	3	108
β-strand	178-180	3	109
β-strand	185-187	3	109
β-strand	195	1	110
β-strand	196-198	3	108
β-strand	208	1	110
β-strand	212	1	109
α-helix	220-222	3
β-strand	224-227	4	108
β-strand	233	1	100
β-strand	234	1	107
β-strand	242	1	93
β-strand	250-253	4	106
β-strand	258-265	8	105
α-helix	266-271	6
β-strand	272-274	3	111
β-strand	280-284	5	111
β-strand	290	1	104
β-strand	292-296	5	112
β-strand	304-305	2	112
β-strand	308	1	104
β-strand	312-316	5	111
β-strand	323-327	5	112
β-strand	330-335	6	112
α-helix	349-358	10
α-helix	363-394	32
α-helix	395-402	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Togavirin	A, D, G, J	protein	441	Eastern equine encephalitis virus	P08768
Togavirin	B, E, H, K	protein	420	Eastern equine encephalitis virus	Q4QXJ7
Togavirin	C, F, I, L	protein	261	Eastern equine encephalitis virus	Q4QXJ7

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

>6XO4_1 Togavirin (chains A, D, G, J)
YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVV
KCCGATQCTSKPHPDYQCQVFSGVYPFMYGGAYCFCDTENTQMSEAYVERSEECSIDHAK
AYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVV
YGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQVPSG
FERWKKDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDL
ECKITECTYAFDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTA
NIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWIKVLVGGTSA
FIVLGLIATAVVALVLFFHRH

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

>6XO4_2 Togavirin (chains B, E, H, K)
DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGV
DLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRH
TCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSI
HSAKVKITVPSGAQVKYYCKCPDVRKGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRL
PRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSD
ANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRY
PLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPTRA

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

>6XO4_3 Togavirin (chains C, F, I, L)
MFPYPTLNYPPMAPINPMAYRDPNPPRRRWRPFRPPLAAQIEDLRRSIASLTLKQRAPNP
PAGPPAKRKKPAPKPKPAQAKKKRPPPPAKKQKRKPKPGKRQRMCMKLESDKTFPIMLNG
QVNGYACVVGGRVFKPLHVEGRIDNEQLAAIKLKKASIYDLEYGDVPQCMKSDTLQYTSD
KPPGFYNWHHGAVQYENNRFTVPRGVGGKGDSGRPILDNKGRVVAIVLGGVNEGSRTALS
VVTWNQKGVTVKDTPEGSEPW

Primary citation

Human Antibodies Protect against Aerosolized Eastern Equine Encephalitis Virus Infection. Williamson, L.E., Gilliland Jr., T., Yadav, P.K. et al. Cell (2020) 183:1884-1900.e23. DOI 10.1016/j.cell.2020.11.011 · 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
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…
6XOB 8.5 Å, CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP with Fab EEEV-143.

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