6MX4: Chimeric Eastern Equine Encephalitis Virus

Name: PDB 6MX4: CryoEM structure of chimeric Eastern Equine Encephalitis Virus
Published: 2018-12-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

CryoEM structure of chimeric Eastern Equine Encephalitis Virus. Determined by electron microscopy at 4.4 Å resolution. Released 19 Dec 2018.

Method: Electron microscopy
Resolution: 4.4 Å
Organism: Eastern equine encephalitis virus
Chains: 12
Atoms: 31,491
Mol. weight: 498.78 kDa
Ligands: NAG
Released: 19 Dec 2018

Explore 6MX4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6MX4 contains 96 α-helices and 384 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: 12 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
β-strand	18-19	2	2
β-strand	24	1	3
β-strand	27-28	2	2
β-strand	31-32	2	4
β-strand	44-48	5	5
β-strand	51-52	2	6
α-helix	55-58	4
β-strand	59-61	3	7
β-strand	77-82	6	7
β-strand	87	1	8
β-strand	101-106	6	7
β-strand	109-110	2	6
α-helix	113-115	3
β-strand	119-123	5	5
β-strand	131	1	9
β-strand	134-135	2	4
β-strand	144	1	4
β-strand	147	1	9
β-strand	161-163	3	1
β-strand	177-181	5	5
β-strand	184-186	3	5
α-helix	196-197	2
β-strand	204-206	3	5
β-strand	214-216	3	5
β-strand	221-222	2	10
α-helix	224-225	2
β-strand	229	1	8
β-strand	234-235	2	10
α-helix	237-239	3
α-helix	252-255	4
β-strand	261-262	2	11
β-strand	269-270	2	11
β-strand	276-282	7	1
α-helix	285-287	3
α-helix	288-289	2
β-strand	290	1	3
α-helix	291-293	3
α-helix	295-296	2
β-strand	301-306	6	12
β-strand	307-308	2	13
β-strand	315-320	6	12
β-strand	327-330	4	14
β-strand	339-340	2	12
β-strand	344-347	4	14
β-strand	352	1	12
β-strand	355-358	4	12
β-strand	367	1	15
β-strand	376	1	15
β-strand	381-382	2	13
β-strand	389	1	16
α-helix	412-423	12
α-helix	432-436	5

Chains B and H: 10 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	12	1	17
β-strand	22	1	18
β-strand	25	1	18
β-strand	33-37	5	19
β-strand	44-53	10	19
β-strand	54	1	20
β-strand	64-69	6	20
β-strand	72-77	6	20
β-strand	82-84	3	21
β-strand	88	1	21
β-strand	90-102	13	19
β-strand	106-112	7	21
β-strand	121-128	8	21
α-helix	131-132	2
β-strand	136	1	22
β-strand	147-149	3	23
β-strand	152-153	2	24
β-strand	163-165	3	25
β-strand	173	1	26
β-strand	179-180	2	27
β-strand	185-186	2	27
β-strand	194	1	28
β-strand	199	1	29
α-helix	220-222	3
β-strand	223	1	29
β-strand	226	1	26
β-strand	228	1	28
β-strand	233	1	17
β-strand	251-253	3	25
β-strand	258-259	2	24
β-strand	262-264	3	23
α-helix	268-271	4
β-strand	272-276	5	30
β-strand	279-284	6	30
β-strand	290-294	5	22
β-strand	304-308	5	22
β-strand	312-314	3	30
β-strand	317	1	30
β-strand	323-325	3	22
α-helix	331-332	2
β-strand	333-335	3	22
β-strand	336	1	16
α-helix	351-353	3
α-helix	354-359	6
α-helix	363-383	21
α-helix	384-388	5
α-helix	389-391	3

Chain C: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	103-110	8
β-strand	113-118	6	31
β-strand	121-128	8	31
β-strand	133-134	2	31
β-strand	136	1	32
β-strand	142-143	2	31
α-helix	146-149	4
β-strand	156	1	32
β-strand	161	1	32
β-strand	186-188	3	33
β-strand	191-193	3	33
β-strand	201-203	3	34
β-strand	215-217	3	33
β-strand	223-227	5	33
β-strand	232	1	34
β-strand	234	1	35
β-strand	236-238	3	34
β-strand	241-244	4	33
β-strand	250-253	4	33

Chain E: 10 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	12	1	52
β-strand	22	1	53
β-strand	25	1	53
β-strand	33-37	5	54
β-strand	44-49	6	54
β-strand	54	1	55
β-strand	64-69	6	55
β-strand	72-77	6	55
β-strand	82-84	3	56
β-strand	88	1	56
β-strand	90-95	6	54
β-strand	98-102	5	54
β-strand	106-112	7	56
β-strand	121-128	8	56
α-helix	131-132	2
β-strand	136	1	57
β-strand	147-149	3	58
β-strand	152-153	2	59
β-strand	163-165	3	60
β-strand	173	1	61
β-strand	179-180	2	62
β-strand	185-186	2	62
β-strand	194	1	63
β-strand	199	1	64
α-helix	220-222	3
β-strand	223	1	64
β-strand	226	1	61
β-strand	228	1	63
β-strand	233	1	52
β-strand	251-253	3	60
β-strand	258-259	2	59
β-strand	262-264	3	58
α-helix	268-271	4
β-strand	272-276	5	65
β-strand	279-284	6	65
β-strand	290-294	5	57
β-strand	304-308	5	57
β-strand	312-314	3	65
β-strand	317	1	65
β-strand	323-325	3	57
α-helix	331-332	2
β-strand	333-335	3	57
β-strand	336	1	51
α-helix	351-353	3
α-helix	354-359	6
α-helix	363-383	21
α-helix	384-388	5
α-helix	389-391	3

Chain F: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	106-110	5
β-strand	113-118	6	66
β-strand	121-128	8	66
β-strand	133-134	2	66
β-strand	136	1	67
β-strand	142-143	2	66
α-helix	146-149	4
β-strand	156	1	67
β-strand	161	1	67
β-strand	186-188	3	68
β-strand	191-193	3	68
β-strand	201-202	2	69
β-strand	215-217	3	68
β-strand	223-227	5	68
β-strand	232-233	2	69
β-strand	236-238	3	69
β-strand	241-244	4	68
β-strand	250-253	4	68

Chain I: 2 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	103-110	8
β-strand	113-118	6	100
β-strand	121-128	8	100
β-strand	133-134	2	100
β-strand	136	1	101
β-strand	142-143	2	100
α-helix	146-149	4
β-strand	156	1	101
β-strand	161	1	101
β-strand	171	1	35
β-strand	177	1	102
β-strand	186-188	3	102
β-strand	191-193	3	102
β-strand	200-202	3	103
β-strand	215-217	3	102
β-strand	223-227	5	102
β-strand	232-233	2	103
β-strand	236-239	4	103
β-strand	241-244	4	102
β-strand	250-253	4	102

Chain J: 12 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	104
β-strand	18-19	2	105
β-strand	24	1	106
β-strand	27-28	2	105
β-strand	31-32	2	107
β-strand	44-48	5	108
β-strand	51-52	2	109
α-helix	55-58	4
β-strand	59-61	3	110
β-strand	77-82	6	110
β-strand	87	1	111
β-strand	101-106	6	110
β-strand	109-110	2	109
α-helix	113-115	3
β-strand	119-123	5	108
β-strand	131	1	112
β-strand	134-135	2	107
β-strand	144	1	107
β-strand	147	1	112
β-strand	161-163	3	104
β-strand	177-181	5	108
β-strand	184-186	3	108
α-helix	196-197	2
β-strand	204-206	3	108
β-strand	214-216	3	108
β-strand	221-222	2	113
α-helix	224-225	2
β-strand	229	1	111
β-strand	234-235	2	113
α-helix	237-239	3
α-helix	252-255	4
β-strand	261-262	2	114
β-strand	269-270	2	114
β-strand	276-282	7	104
α-helix	285-287	3
α-helix	288-289	2
β-strand	290	1	106
α-helix	291-293	3
α-helix	295-296	2
β-strand	301-306	6	115
β-strand	307-308	2	116
β-strand	315-320	6	115
β-strand	327-330	4	117
β-strand	339-340	2	115
β-strand	344-347	4	117
β-strand	352	1	115
β-strand	355-358	4	115
β-strand	367	1	118
β-strand	376	1	118
β-strand	381-382	2	116
α-helix	412-423	12
α-helix	432-436	5

Chain K: 10 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
β-strand	12	1	119
β-strand	22	1	120
β-strand	25	1	120
β-strand	33-37	5	121
β-strand	44-49	6	121
β-strand	54	1	122
β-strand	64-69	6	122
β-strand	72-77	6	122
β-strand	82-84	3	123
β-strand	88	1	123
β-strand	90-95	6	121
β-strand	98-102	5	121
β-strand	106-112	7	123
β-strand	121-128	8	123
α-helix	131-132	2
β-strand	136	1	124
β-strand	147-149	3	125
β-strand	152-153	2	126
β-strand	163-165	3	127
β-strand	173	1	128
β-strand	179-180	2	129
β-strand	185-186	2	129
β-strand	194	1	130
β-strand	199	1	131
α-helix	220-222	3
β-strand	223	1	131
β-strand	226	1	128
β-strand	228	1	130
β-strand	233	1	119
β-strand	251-253	3	127
β-strand	258-259	2	126
β-strand	262-264	3	125
α-helix	268-271	4
β-strand	272-276	5	132
β-strand	279-284	6	132
β-strand	290-294	5	124
β-strand	304-308	5	124
β-strand	312-314	3	132
β-strand	317	1	132
β-strand	323-325	3	124
α-helix	331-332	2
β-strand	333-335	3	124
α-helix	351-353	3
α-helix	354-359	6
α-helix	363-383	21
α-helix	384-388	5
α-helix	389-391	3

1 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
E1	A, D, G, J	protein	441	Eastern equine encephalitis virus	Q4QXJ7
E2	B, E, H, K	protein	420	Eastern equine encephalitis virus	Q4QXJ7
Capsid	C, F, I, L	protein	260	Eastern equine encephalitis virus	P27284

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

>6MX4_1 E1 (chains A, D, G, J)
YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVV
KCCGATQCTSKPHPDYQCQVFTGVYPFMWGGAYCFCDTENTQMSEAYVERSEECSIDHAK
AYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVV
YGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQAPSG
FERWKRDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDL
ECKITECTYASDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTA
NIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWLKVLVGGTSA
FIVLGLIATAVVALVLFFHRH

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

>6MX4_2 E2 (chains B, E, H, K)
DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGV
DLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRH
TCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSI
HSAKVKITVPSGAQVKYYCKCPDVREGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRL
PRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSD
ANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRY
PLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPTRA

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

>6MX4_3 Capsid (chains C, F, I, L)
MFPYPTLNYPPMAPINPMAYRDPNPPRQVAPFRPPLAAQIEDLRRSIANLTLKQRAPNPP
AGPPAKRKKPAPKPKPAQAKKKRPPPPAKKQKRKPKPGKRQRMCMKLESDKTFPIMLNGQ
VNGYACVVGGRVFKPLHVEGRIDNEQLAAIKLKKASIYDLEYGDVPQCMKSDTLQYTSDK
PPGFYNWHHGAVQYENNRFTVPRGVGGKGDSGRPILDNKGRVVAIVLGGVNEGSRTALSV
VTWNQKGVTVKDTPEGSEPW

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Cryo-EM Structures of Eastern Equine Encephalitis Virus Reveal Mechanisms of Virus Disassembly and Antibody Neutralization. Hasan, S.S., Sun, C., Kim, A.S. et al. Cell Rep (2018) 25:3136-3147.e5. DOI 10.1016/j.celrep.2018.11.067 · PubMed

Other PDB entries of the same protein (UniProt Q4QXJ7), best resolution first:

8XI4 3.4 Å, Structure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA1-2
8XI5 3.4 Å, Structure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA3-5
6XO4 4.2 Å, CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP
8YS4 4.8 Å, Overall structure of Eastern Equine Encephalitis virus VLP in complex with the receptor…
7V0P 5.2 Å, Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a potently neutralizing…
8YS2 5.2 Å, Overall structure of Eastern Equine Encephalitis virus VLP in complex with the receptor…
6ODF 5.8 Å, EEEV glycoproteins bound with heparan sulfate
7V0N 5.9 Å, Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a moderately/weakly…
7V0O 6.6 Å, Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a moderately/weakly…
6MW9 7.3 Å, CryoEM structure of chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-3 antibody
6MWV 7.3 Å, CryoEM structure of Chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-58…
6MWC 7.5 Å, CryoEM structure of chimeric Eastern Equine Encephalitis Virus with Fab of EEEV-5 antibody

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