8SQN: Western equine encephalitis virus VLP

CryoEM structure of Western equine encephalitis virus VLP in complex with the chimeric Du-D1-Mo-D2 MXRA8 receptor. Determined by electron microscopy at 3.89 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 3.89 Å
Organisms: Anas platyrhynchos, Western equine encephalitis virus
Chains: 9
Atoms: 28,497
Mol. weight: 405.97 kDa
Ligands: NAG
Released: 20 Dec 2023

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

Secondary structure: helices and β-sheets

8SQN contains 82 α-helices and 334 β-strands across 9 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: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	37-44	8	1
β-strand	49-51	3	2
β-strand	54	1	3
α-helix	56-58	3
β-strand	70-77	8	4
α-helix	84-86	3
β-strand	87-93	7	4
β-strand	100	1	4
β-strand	106	1	5
β-strand	109-110	2	5
α-helix	115-118	4
β-strand	120	1	6
β-strand	123-125	3	5
α-helix	130-132	3
β-strand	134-142	9	4
β-strand	147-158	12	4
α-helix	161-163	3
β-strand	165-168	4	4
β-strand	173-178	6	4
β-strand	183-185	3	5
β-strand	188	1	6
α-helix	192-194	3
β-strand	205-211	7	1
α-helix	215-216	2
β-strand	221-227	7	1
β-strand	232-234	3	1
α-helix	238-243	6
β-strand	244-246	3	2
α-helix	250-253	4
β-strand	255	1	3
β-strand	258-260	3	2
α-helix	265-267	3
β-strand	269-277	9	1
β-strand	282-293	12	1

Chain B: 9 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	7
β-strand	15-17	3	8
β-strand	21	1	9
β-strand	24	1	9
β-strand	29-48	20	8
β-strand	51-54	4	10
α-helix	56-58	3
β-strand	59-61	3	11
β-strand	77-82	6	11
β-strand	87-88	2	12
β-strand	91-92	2	12
β-strand	101-106	6	11
β-strand	107-110	4	10
α-helix	114-117	4
β-strand	119-137	19	8
β-strand	140-147	8	8
β-strand	156	1	13
β-strand	159	1	13
β-strand	162-163	2	7
β-strand	176-180	5	8
β-strand	183-186	4	8
α-helix	189-191	3
β-strand	203-205	3	8
β-strand	213-215	3	8
β-strand	219-221	3	14
β-strand	233-235	3	14
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	8
β-strand	267-269	3	8
β-strand	275-281	7	7
α-helix	284-286	3
β-strand	289	1	9
β-strand	296-302	7	15
β-strand	307	1	16
β-strand	314-322	9	15
β-strand	326-329	4	17
β-strand	330-332	3	18
β-strand	337-339	3	15
β-strand	343-346	4	17
β-strand	351-358	8	15
β-strand	362-369	8	18
β-strand	372-379	8	18
β-strand	381	1	16
β-strand	387-388	2	19
α-helix	404-413	10
α-helix	417-437	21

Chain D: 9 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	20
β-strand	17-19	3	21
β-strand	28-30	3	21
β-strand	34-38	5	22
β-strand	46-50	5	22
β-strand	53-56	4	23
α-helix	57	1
β-strand	65-68	4	23
β-strand	69	1	24
β-strand	70-71	2	23
β-strand	72-74	3	25
β-strand	77-79	3	25
β-strand	82	1	24
α-helix	83-85	3
β-strand	86-89	4	26
β-strand	93	1	26
β-strand	98-100	3	22
β-strand	103-106	4	22
β-strand	113-119	7	26
β-strand	124-130	7	26
β-strand	141	1	27
β-strand	151-158	8	28
β-strand	169-171	3	29
β-strand	172	1	30
β-strand	183-184	2	31
β-strand	191-192	2	31
α-helix	194-195	2
β-strand	199-204	6	32
β-strand	210-215	6	32
α-helix	226-228	3
β-strand	229-232	4	32
β-strand	239	1	20
β-strand	240	1	30
β-strand	256-258	3	29
β-strand	264-271	8	28
α-helix	274-277	4
β-strand	278-279	2	33
β-strand	286-291	6	33
β-strand	296-300	5	27
β-strand	302	1	27
β-strand	310-314	5	27
β-strand	317-322	6	33
β-strand	329-333	5	27
β-strand	336-341	6	27
β-strand	342-343	2	19
α-helix	358-364	7
α-helix	367-399	33
α-helix	408-409	2
α-helix	412-418	7

Chain F: 11 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	34
β-strand	15-21	7	35
β-strand	24-48	25	35
β-strand	51-54	4	36
α-helix	56-58	3
β-strand	59-61	3	37
β-strand	77-82	6	37
β-strand	87-88	2	38
β-strand	91-92	2	38
β-strand	101-106	6	37
β-strand	107-110	4	36
α-helix	114-117	4
β-strand	119-137	19	35
β-strand	140-147	8	35
β-strand	156	1	39
β-strand	159	1	39
β-strand	162-163	2	34
β-strand	176-180	5	35
β-strand	183-186	4	35
α-helix	189-191	3
β-strand	204	1	40
β-strand	205	1	35
β-strand	214	1	40
β-strand	219-221	3	41
β-strand	233-235	3	41
α-helix	236-238	3
α-helix	239-246	8
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	35
β-strand	267-269	3	35
β-strand	275-281	7	34
α-helix	284-286	3
β-strand	289	1	35
α-helix	294-295	2
β-strand	296-302	7	42
β-strand	307	1	43
β-strand	314-322	9	42
β-strand	326-329	4	44
β-strand	330-332	3	45
β-strand	337-339	3	42
β-strand	343-346	4	44
β-strand	351-358	8	42
β-strand	362-369	8	45
β-strand	372-379	8	45
β-strand	381	1	43
β-strand	387-388	2	46
α-helix	404-413	10
α-helix	417-437	21

Chain H: 8 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	47
β-strand	17-19	3	48
β-strand	28-30	3	48
β-strand	34-38	5	49
β-strand	46-50	5	49
β-strand	53-56	4	50
β-strand	65-71	7	50
β-strand	72-74	3	51
β-strand	77-79	3	51
α-helix	83-85	3
β-strand	86-89	4	52
β-strand	93	1	52
β-strand	98-100	3	49
β-strand	103-106	4	49
β-strand	113-119	7	52
β-strand	124-130	7	52
β-strand	141	1	53
β-strand	151-158	8	54
β-strand	169-172	4	55
β-strand	174	1	56
β-strand	183-184	2	57
β-strand	191-192	2	57
α-helix	194-195	2
β-strand	199-204	6	58
β-strand	210-215	6	58
α-helix	226-228	3
β-strand	229-232	4	58
β-strand	239	1	47
β-strand	240-241	2	55
β-strand	248	1	56
β-strand	256-258	3	55
β-strand	264-271	8	54
α-helix	274-276	3
β-strand	279	1	59
β-strand	282	1	60
β-strand	285	1	60
β-strand	286-291	6	59
β-strand	296-300	5	53
β-strand	302	1	61
β-strand	310-314	5	53
β-strand	317-322	6	59
β-strand	329-331	3	61
β-strand	332	1	53
α-helix	337-338	2
β-strand	339-341	3	61
β-strand	342-343	2	46
α-helix	358-364	7
α-helix	367-400	34
α-helix	412-418	7

Chain J: 8 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	62
β-strand	15-17	3	63
β-strand	24	1	64
β-strand	29-48	20	63
β-strand	51-54	4	65
α-helix	56-58	3
β-strand	59-61	3	66
β-strand	77-82	6	66
β-strand	87-88	2	67
β-strand	91-92	2	67
β-strand	101-106	6	66
β-strand	107-110	4	65
α-helix	114-117	4
β-strand	119-137	19	63
β-strand	140-147	8	63
β-strand	153-156	4	62
β-strand	159-163	5	62
β-strand	176-180	5	63
β-strand	183-185	3	63
α-helix	189-191	3
β-strand	204	1	68
β-strand	205	1	63
β-strand	214	1	68
β-strand	220-221	2	69
β-strand	233-234	2	69
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	63
β-strand	267-269	3	63
β-strand	275-281	7	62
β-strand	289	1	64
β-strand	296-302	7	70
β-strand	307	1	71
β-strand	314-322	9	70
β-strand	326-329	4	72
β-strand	330-332	3	73
β-strand	337-339	3	70
β-strand	343-346	4	72
β-strand	351-358	8	70
β-strand	362-369	8	73
β-strand	372-379	8	73
β-strand	381	1	71
β-strand	387-388	2	74
α-helix	404-413	10
α-helix	417-437	21

Chain L: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	75
β-strand	17-19	3	76
β-strand	28-30	3	76
β-strand	34-38	5	77
β-strand	46-50	5	77
β-strand	53-54	2	78
α-helix	57	1
β-strand	69-74	6	78
β-strand	77-82	6	78
α-helix	83-85	3
β-strand	86-89	4	79
β-strand	93	1	79
β-strand	95-100	6	77
β-strand	103-107	5	77
β-strand	113-119	7	79
β-strand	124-130	7	79
β-strand	141	1	80
β-strand	151-158	8	81
β-strand	169-171	3	82
β-strand	172	1	83
β-strand	183-184	2	84
β-strand	191-192	2	84
α-helix	194-195	2
β-strand	199-204	6	85
β-strand	210-215	6	85
β-strand	230-232	3	85
β-strand	239	1	75
β-strand	240	1	83
β-strand	256-258	3	82
α-helix	259-261	3
β-strand	264-271	8	81
α-helix	274-277	4
β-strand	278-279	2	86
β-strand	286-290	5	86
β-strand	296-300	5	80
β-strand	302	1	80
β-strand	310-314	5	80
β-strand	318-322	5	86
β-strand	329-333	5	80
β-strand	336-341	6	80
β-strand	342-343	2	74
α-helix	358-364	7
α-helix	367-400	34
α-helix	412-418	7

Chain N: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	87
β-strand	15-21	7	88
β-strand	24-48	25	88
β-strand	51-54	4	89
α-helix	56-58	3
β-strand	59-61	3	90
β-strand	77-82	6	90
β-strand	87	1	91
β-strand	92	1	91
β-strand	101-106	6	90
β-strand	107-110	4	89
α-helix	114-117	4
β-strand	119-137	19	88
β-strand	140-147	8	88
β-strand	154-155	2	92
β-strand	160-161	2	92
β-strand	162-163	2	87
β-strand	176-180	5	88
β-strand	183-186	4	88
α-helix	189-191	3
β-strand	203-205	3	88
β-strand	213-215	3	88
β-strand	220-221	2	93
β-strand	233-234	2	93
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	88
β-strand	267-269	3	88
β-strand	275-281	7	87
α-helix	284-286	3
β-strand	289	1	88
β-strand	296-302	7	94
β-strand	307	1	95
β-strand	314-322	9	94
β-strand	326-329	4	96
β-strand	330-332	3	97
β-strand	337-339	3	94
β-strand	343-346	4	96
β-strand	351-358	8	94
β-strand	362-369	8	97
β-strand	372-379	8	97
β-strand	381	1	95
β-strand	387-388	2	98
α-helix	404-413	10
α-helix	417-437	21

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
DuD1MoD2 chimeric MXRA8	A	protein	265	Anas platyrhynchos	A0A8B9TXK0 (AlphaFold model), Q9DBV4 (AlphaFold model)
E1 envelope glycoprotein	B, F, J, N	protein	438	Western equine encephalitis virus	P13897
E2 envelope glycoprotein	D, H, L, P	protein	415	Western equine encephalitis virus	P13897

Sequence of entity 1 (A), FASTA

>8SQN_1 DuD1MoD2 chimeric MXRA8 (chains A)
SSSLVSESVVSLAAGTQAVLRCQSPRMVWTQDRLNDRQRVVHWDVYSTYYGDNKMERLCD
MYSAGDQRVYSSYNQGRIFMPQNAFTDGNFSLVIKDVAESDGGIYSCNLHHHYCHLYETV
KIQLDVTKKAKAAKEYWDGEKAVIVALEGSTVMLPCVNRNQIWTERHLEEAQQVVHWDRQ
LPGVSHDRADRLLDLYASGERRAYGPPFLRDRVSVNTNAFARGDFSLRIDELERADEGIY
SCHLHHHYCGLHERRVFHLQVTEPA

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

>8SQN_2 E1 envelope glycoprotein (chains B, F, J, N)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVVPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTARLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMNPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRATNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKANREGHCPVHSHSTTAVLKEATTHVTATGSITLHFSTSS
PQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINTR

Sequence of entity 3 (D, H, L, P), FASTA

>8SQN_3 E2 envelope glycoprotein (chains D, H, L, P)
ITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADV
TKFRYMSYDHDHDIKEDSMEKLAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASE
NSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLE
EASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKRDQTKWVFNSP
DLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLG
LRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYH
RHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLC

Ligands and cofactors

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

Primary citation

Vertebrate-class-specific binding modes of the alphavirus receptor MXRA8. Zimmerman, O., Zimmerman, M.I., Raju, S. et al. Cell (2023) 186:4818-4833.e25. DOI 10.1016/j.cell.2023.09.007 · PubMed

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