8DAN: Western equine encephalitis virus VLP

CryoEM structure of Western equine encephalitis virus VLP in complex with the avian MXRA8 receptor. Determined by electron microscopy at 4.74 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 4.74 Å
Organisms: Western equine encephalitis virus, Asarcornis scutulata
Chains: 12
Atoms: 35,000
Mol. weight: 498.56 kDa
Ligands: NAG
Released: 20 Dec 2023

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

Secondary structure: helices and β-sheets

8DAN contains 116 α-helices and 404 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 and D: 11 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	15-21	7	2
β-strand	24-48	25	2
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	59-61	3	4
β-strand	77-82	6	4
β-strand	101-106	6	4
β-strand	107-110	4	3
α-helix	114-117	4
β-strand	119-137	19	2
β-strand	140-147	8	2
β-strand	156	1	5
β-strand	159	1	5
β-strand	162-163	2	1
β-strand	176-180	5	2
β-strand	183-186	4	2
α-helix	189-191	3
β-strand	203-204	2	6
β-strand	205	1	2
β-strand	214-215	2	6
β-strand	220-221	2	7
β-strand	233-234	2	7
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	2
β-strand	267-269	3	2
β-strand	275-281	7	1
α-helix	284-286	3
β-strand	289	1	2
α-helix	294-295	2
β-strand	296-302	7	8
β-strand	307	1	9
β-strand	314-322	9	8
β-strand	326-329	4	10
β-strand	330-332	3	11
β-strand	337-339	3	8
β-strand	343-346	4	10
β-strand	351-358	8	8
β-strand	362-369	8	11
β-strand	372-379	8	11
β-strand	381	1	9
β-strand	387	1	12
α-helix	404-413	10
α-helix	417-437	21

Chains B and E: 8 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	13
β-strand	17-19	3	14
β-strand	28-30	3	14
β-strand	34-38	5	15
β-strand	46-50	5	15
β-strand	53-54	2	16
α-helix	57-58	2
β-strand	69	1	17
β-strand	70-71	2	16
β-strand	72-74	3	18
β-strand	77-79	3	18
β-strand	82	1	17
α-helix	83-85	3
β-strand	86-89	4	19
β-strand	93	1	19
β-strand	95-100	6	15
β-strand	103-107	5	15
β-strand	111-119	9	19
β-strand	124-133	10	19
β-strand	141	1	20
β-strand	151-158	8	21
β-strand	169-171	3	22
β-strand	172	1	23
β-strand	183-184	2	24
β-strand	191-192	2	24
α-helix	194-195	2
β-strand	199-204	6	25
β-strand	210-215	6	25
α-helix	226-228	3
β-strand	229-232	4	25
β-strand	239	1	13
β-strand	240	1	23
β-strand	256-258	3	22
α-helix	259-260	2
β-strand	264-271	8	21
β-strand	278-279	2	26
β-strand	282	1	27
β-strand	285	1	27
β-strand	286-290	5	26
β-strand	296-300	5	20
β-strand	302	1	28
β-strand	310-314	5	20
β-strand	318-322	5	26
β-strand	329-331	3	28
β-strand	332-333	2	20
β-strand	339-341	3	28
β-strand	343	1	12
α-helix	359-364	6
α-helix	372-398	27
α-helix	412-418	7

Chains C, F, I and L: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	34-41	8	29
α-helix	43	1
β-strand	44	1	30
β-strand	49-51	3	31
α-helix	56-58	3
α-helix	59-61	3
β-strand	70-77	8	32
β-strand	87-93	7	32
β-strand	99-100	2	32
α-helix	105-108	4
β-strand	109	1	33
α-helix	115-118	4
β-strand	120	1	34
β-strand	123-125	3	35
β-strand	134-142	9	32
β-strand	147-158	12	32
α-helix	161-163	3
β-strand	167-168	2	32
β-strand	173-178	6	32
β-strand	183-185	3	35
β-strand	188	1	34
β-strand	205-210	6	29
α-helix	211-212	2
β-strand	221-226	6	29
β-strand	232-234	3	29
α-helix	238-243	6
β-strand	245	1	31
α-helix	250-253	4
β-strand	258-260	3	31
α-helix	265-267	3
β-strand	271-277	7	29
β-strand	282-290	9	29
β-strand	293	1	30

Chains G and J: 11 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	71
β-strand	15-21	7	72
β-strand	24-48	25	72
β-strand	51-54	4	73
α-helix	56-58	3
β-strand	59-61	3	74
β-strand	77-82	6	74
β-strand	101-106	6	74
β-strand	107-110	4	73
α-helix	114-117	4
β-strand	119-137	19	72
β-strand	140-147	8	72
β-strand	156	1	75
β-strand	159	1	75
β-strand	162-163	2	71
β-strand	176-180	5	72
β-strand	183-186	4	72
α-helix	189-191	3
β-strand	203-204	2	76
β-strand	205	1	72
β-strand	214-215	2	76
β-strand	220-221	2	77
β-strand	233-234	2	77
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	72
β-strand	267-269	3	72
β-strand	275-281	7	71
α-helix	284-286	3
β-strand	289	1	72
α-helix	294-295	2
β-strand	296-302	7	78
β-strand	307	1	79
β-strand	314-322	9	78
β-strand	326-329	4	80
β-strand	330-332	3	81
β-strand	337-339	3	78
β-strand	343-346	4	80
β-strand	351-358	8	78
β-strand	362-369	8	81
β-strand	372-379	8	81
β-strand	381	1	79
β-strand	387-388	2	82
α-helix	404-413	10
α-helix	417-437	21

Chains H and K: 8 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	83
β-strand	17-19	3	84
β-strand	28-30	3	84
β-strand	34-38	5	85
β-strand	46-50	5	85
β-strand	53-54	2	86
α-helix	57-58	2
β-strand	69	1	87
β-strand	70-71	2	86
β-strand	72-74	3	88
β-strand	77-79	3	88
β-strand	82	1	87
α-helix	83-85	3
β-strand	86-89	4	89
β-strand	93	1	89
β-strand	95-100	6	85
β-strand	103-107	5	85
β-strand	111-119	9	89
β-strand	124-133	10	89
β-strand	141	1	90
β-strand	151-158	8	91
β-strand	169-171	3	92
β-strand	172	1	93
β-strand	183-184	2	94
β-strand	191-192	2	94
α-helix	194-195	2
β-strand	199-204	6	95
β-strand	210-215	6	95
α-helix	226-228	3
β-strand	229-232	4	95
β-strand	239	1	83
β-strand	240	1	93
β-strand	256-258	3	92
α-helix	259-260	2
β-strand	264-271	8	91
β-strand	278-279	2	96
β-strand	282	1	97
β-strand	285	1	97
β-strand	286-290	5	96
β-strand	296-300	5	90
β-strand	302	1	98
β-strand	310-314	5	90
β-strand	318-322	5	96
β-strand	329-331	3	98
β-strand	332-333	2	90
β-strand	339-341	3	98
β-strand	342-343	2	82
α-helix	359-364	6
α-helix	372-398	27
α-helix	412-418	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E1 envelope glycoprotein	A, D, G, J	protein	438	Western equine encephalitis virus	Q1W679
E2 envelope glycoprotein	B, E, H, K	protein	415	Western equine encephalitis virus	Q1W679
Matrix remodeling-associated protein 8	C, F, I, L	protein	265	Asarcornis scutulata	A0A7K7KW08 (AlphaFold model)

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

>8DAN_1 E1 envelope glycoprotein (chains A, D, G, J)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVVPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTARLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMNPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRATNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKANREGHCPVHSHSTTAVLKEATTHVTATGSITLHFSTSS
PQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINTR

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

>8DAN_2 E2 envelope glycoprotein (chains B, E, H, K)
ITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADV
TKFRYMSYDHDHDIKEDSMEKLAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASE
NSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYLE
EASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKRDQTKWVFNSP
DLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLG
LRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYH
RHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLC

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

>8DAN_3 Matrix remodeling-associated protein 8 (chains C, F, I, L)
NSVVVSVLNISATLGSQAVLPCKSYRMVWTQDRLNDRQRVVHWDVYSTYYGDNKMERLCD
MYSAGDQRVYSSYNQGRIFMPQNAFTDGNFSLVIKDVAESDGGIYSCNLHHHYCHLYETV
KIQLDVTKKAKAAKEYWDGEKAVIVALEGSTVMLPCVNRNQIWTERHSEEEQQVVHWDRQ
PPGVPHDRADRLIDLYASGERRSYGPLFIRQKMNITDTAFALGDFSLRISELESADEGTY
SCHLHHHYCGLHERRIYQVFVTEPV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

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

Other PDB entries of the same protein (UniProt Q1W679), best resolution first:

9E96 4.05 Å, WEEV CBA87 VLP in complex with human PCDH10-EC1
8DAQ 4.35 Å, CryoEM structure of Western equine encephalitis virus VLP

Browse structure collections

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