6XOB: Togavirin

CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP with Fab EEEV-143. Determined by electron microscopy at 8.5 Å resolution. Released 23 Dec 2020.

Method: Electron microscopy
Resolution: 8.5 Å
Organisms: Eastern equine encephalitis virus, Homo sapiens
Chains: 20
Atoms: 37,540
Mol. weight: 682.49 kDa
Released: 23 Dec 2020

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

Secondary structure: helices and β-sheets

6XOB contains 84 α-helices and 548 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.

Chains A, D, G and J: 7 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	7-8	2	2
β-strand	14-15	2	3
β-strand	19-21	3	4
β-strand	24-27	4	4
β-strand	31-39	9	3
β-strand	43-46	4	5
β-strand	47	1	6
β-strand	51-54	4	7
α-helix	57-59	3
β-strand	107-110	4	7
α-helix	113-116	4
β-strand	121-123	3	5
β-strand	128-135	8	3
β-strand	143-148	6	3
β-strand	155-157	3	1
β-strand	160-163	4	1
β-strand	177-179	3	5
β-strand	186	1	5
β-strand	206	1	6
β-strand	221-222	2	8
β-strand	234-235	2	8
α-helix	240-246	7
α-helix	252-255	4
β-strand	261-262	2	3
β-strand	269-270	2	3
β-strand	276-277	2	2
β-strand	280-282	3	1
α-helix	285-287	3
α-helix	295-297	3
β-strand	302-307	6	9
β-strand	315-319	5	9
β-strand	327-330	4	10
β-strand	339-340	2	11
β-strand	344-347	4	10
β-strand	354-356	3	9
β-strand	357-358	2	11
β-strand	367-370	4	12
β-strand	373-376	4	12
α-helix	406-439	34

Chains B, E, H and K: 8 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	19	1	13
β-strand	27	1	13
β-strand	44-48	5	14
β-strand	64-67	4	15
β-strand	74-77	4	15
β-strand	81	1	16
β-strand	84	1	17
β-strand	88	1	17
β-strand	95	1	14
β-strand	98-102	5	14
β-strand	106-111	6	17
β-strand	113	1	16
β-strand	122-128	7	17
α-helix	130-132	3
β-strand	146-154	9	18
β-strand	164-165	2	19
β-strand	171-174	4	20
β-strand	178-180	3	21
β-strand	185-187	3	21
β-strand	195	1	22
β-strand	196	1	20
β-strand	208	1	22
α-helix	215-217	3
β-strand	225-228	4	20
β-strand	251-252	2	19
α-helix	253-254	2
β-strand	257-265	9	18
α-helix	267-270	4
β-strand	272-274	3	23
β-strand	280-284	5	23
β-strand	292-293	2	24
β-strand	296	1	25
β-strand	312-316	5	23
β-strand	323	1	25
β-strand	324-325	2	26
β-strand	326-327	2	24
β-strand	333-334	2	26
α-helix	349-358	10
α-helix	363-394	32
α-helix	395-402	8

Chains C, F, I and L: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	114	1	27
β-strand	116-117	2	28
β-strand	126	1	27
β-strand	128	1	29
β-strand	133	1	29
β-strand	134-135	2	30
β-strand	142-143	2	28
α-helix	148-150	3
β-strand	162-163	2	30
β-strand	187	1	31
β-strand	202-203	2	32
α-helix	208-211	4
β-strand	215-218	4	31
β-strand	222-229	8	31
β-strand	236-237	2	32
β-strand	240-244	5	31
β-strand	250-252	3	31
α-helix	258-259	2
β-strand	260	1	31

Chains M, O, Q and S: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	129
α-helix	6-8	3
β-strand	10-11	2	130
β-strand	16	1	131
β-strand	22	1	132
β-strand	23	1	129
β-strand	37-38	2	133
β-strand	49-50	2	134
β-strand	59-60	2	134
β-strand	72-73	2	132
β-strand	78-79	2	132
β-strand	86	1	131
β-strand	94-95	2	133
β-strand	99	1	135
β-strand	104	1	135
β-strand	113-114	2	130
β-strand	127-128	2	136
β-strand	142-145	4	136
β-strand	156	1	137
β-strand	167-168	2	136
β-strand	173	1	138
α-helix	174-176	3
β-strand	180	1	138
β-strand	182-185	4	136
α-helix	191-194	4
β-strand	198-199	2	139
β-strand	201	1	137
β-strand	212-213	2	139

Chains N, P, R and T: 0 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	9-10	2	140
β-strand	16	1	141
β-strand	20	1	142
β-strand	23	1	143
β-strand	50-51	2	144
β-strand	55-56	2	144
β-strand	65	1	145
β-strand	72	1	143
β-strand	75	1	142
β-strand	76	1	145
β-strand	80	1	141
β-strand	86-87	2	140
β-strand	105-106	2	140
β-strand	121	1	146
β-strand	134	1	147
β-strand	136	1	146
β-strand	137	1	148
β-strand	142	1	149
β-strand	147	1	150
β-strand	153	1	151
β-strand	162	1	152
β-strand	167-169	3	149
β-strand	175-177	3	149
β-strand	179	1	148
β-strand	181	1	152
β-strand	182	1	147
β-strand	194	1	151
β-strand	195	1	153
β-strand	200	1	150
β-strand	208	1	153

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
EEEV-143 Fab heavy chain	M, O, Q, S	protein	214	Homo sapiens
EEEV-143 Fab light chain	N, P, R, T	protein	213	Homo sapiens

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

>6XOB_1 Togavirin (chains A, D, G, J)
YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVV
KCCGATQCTSKPHPDYQCQVFSGVYPFMYGGAYCFCDTENTQMSEAYVERSEECSIDHAK
AYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVV
YGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQVPSG
FERWKKDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDL
ECKITECTYAFDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTA
NIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWIKVLVGGTSA
FIVLGLIATAVVALVLFFHRH

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

>6XOB_2 Togavirin (chains B, E, H, K)
DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGV
DLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRH
TCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSI
HSAKVKITVPSGAQVKYYCKCPDVRKGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRL
PRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSD
ANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRY
PLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPTRA

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

>6XOB_3 Togavirin (chains C, F, I, L)
MFPYPTLNYPPMAPINPMAYRDPNPPRRRWRPFRPPLAAQIEDLRRSIASLTLKQRAPNP
PAGPPAKRKKPAPKPKPAQAKKKRPPPPAKKQKRKPKPGKRQRMCMKLESDKTFPIMLNG
QVNGYACVVGGRVFKPLHVEGRIDNEQLAAIKLKKASIYDLEYGDVPQCMKSDTLQYTSD
KPPGFYNWHHGAVQYENNRFTVPRGVGGKGDSGRPILDNKGRVVAIVLGGVNEGSRTALS
VVTWNQKGVTVKDTPEGSEPW

Sequence of entity 4 (M, O, Q, S), FASTA

>6XOB_4 EEEV-143 Fab heavy chain (chains M, O, Q, S)
QVQLVESGGGVVQPGRSLRLSCAASGFTFSNYGIHWVRQAPGKGLEWVAVISYDGRHKYI
ADPVKGRFTISRDNSKNMLYLQMNSLRTEDTAVYYCAKDTSGWYEFFDSWGQGIPVTVSS
ASPTSPKVFPLSLCSTQPDGNVVIACLVQGFFPQEPLSVTWSESGQGVTARNFPPSQDAS
GDLYTTSSQLTLPATQCLAGKSVTCHVKHYTNPS

Sequence of entity 5 (N, P, R, T), FASTA

>6XOB_5 EEEV-143 Fab light chain (chains N, P, R, T)
EIVMTQSPATLSVSPGERATLSCRASQSVATNVAWYQQKPGQAPRLLIYGASTRATGIPA
RFSGSGSGTEFTLTISSLQSEDFAVYYCQQCNDWLTFGQGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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…
6XO4 4.2 Å, CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP

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