8DAQ: Western equine encephalitis virus VLP

CryoEM structure of Western equine encephalitis virus VLP. Determined by electron microscopy at 4.35 Å resolution. Released 20 Dec 2023.

Method: Electron microscopy
Resolution: 4.35 Å
Organism: Western equine encephalitis virus
Chains: 8
Atoms: 26,336
Mol. weight: 375.21 kDa
Ligands: NAG
Released: 20 Dec 2023

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

Secondary structure: helices and β-sheets

8DAQ contains 72 α-helices and 332 β-strands across 8 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, C and G: 11 helices, 37 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	87-88	2	5
β-strand	91-92	2	5
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	141-147	7	2
α-helix	152-153	2
β-strand	154	1	6
α-helix	155	1
β-strand	161	1	6
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	7
β-strand	214-215	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
β-strand	289	1	2
β-strand	296-306	11	8
β-strand	307	1	9
β-strand	314-322	9	8
β-strand	327-329	3	10
β-strand	330-332	3	11
β-strand	337-339	3	8
β-strand	343-345	3	10
β-strand	351-358	8	8
β-strand	362	1	12
β-strand	365-369	5	11
β-strand	372-376	5	11
β-strand	379	1	12
β-strand	381	1	9
β-strand	387	1	13
α-helix	404-413	10
α-helix	417-437	21

Chains B, D and H: 7 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	14
β-strand	17-19	3	15
β-strand	21	1	16
β-strand	28-30	3	15
β-strand	37-38	2	17
β-strand	45-48	4	17
β-strand	53-54	2	18
β-strand	59	1	19
β-strand	61	1	19
β-strand	69	1	20
β-strand	70-71	2	18
β-strand	72-74	3	21
β-strand	77-79	3	21
β-strand	82	1	20
α-helix	83-85	3
β-strand	86-89	4	16
β-strand	93	1	16
β-strand	95-100	6	17
β-strand	103-107	5	17
β-strand	111-119	9	16
β-strand	124-133	10	16
β-strand	151-158	8	22
β-strand	166-171	6	23
β-strand	172	1	24
α-helix	180-182	3
β-strand	183-184	2	25
β-strand	191-192	2	25
β-strand	201-204	4	26
β-strand	210-213	4	26
β-strand	230-232	3	26
β-strand	239	1	14
β-strand	240	1	24
α-helix	247-249	3
β-strand	256-260	5	23
β-strand	264-271	8	22
α-helix	276-277	2
β-strand	278-279	2	27
β-strand	282	1	28
β-strand	285-287	3	28
β-strand	288-289	2	27
β-strand	290	1	29
β-strand	296-300	5	30
β-strand	302	1	31
β-strand	310-314	5	30
β-strand	318	1	29
β-strand	321-323	3	28
β-strand	329	1	31
β-strand	332	1	30
β-strand	341	1	31
β-strand	343	1	13
α-helix	359-364	6
α-helix	371-400	30
α-helix	413-418	6

Chain E: 11 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	63
β-strand	15-21	7	64
β-strand	24-48	25	64
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	64
β-strand	141-147	7	64
α-helix	152-153	2
β-strand	154	1	68
α-helix	155	1
β-strand	161	1	68
β-strand	162-163	2	63
β-strand	176-180	5	64
β-strand	183-186	4	64
α-helix	189-191	3
β-strand	203-204	2	69
β-strand	214-215	2	69
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	64
β-strand	267-269	3	64
β-strand	275-281	7	63
β-strand	289	1	64
β-strand	296-306	11	70
β-strand	307	1	71
β-strand	314-322	9	70
β-strand	327-329	3	72
β-strand	330-332	3	73
β-strand	337-339	3	70
β-strand	343-345	3	72
β-strand	351-358	8	70
β-strand	362	1	74
β-strand	365-369	5	73
β-strand	372-376	5	73
β-strand	379	1	74
β-strand	381	1	71
β-strand	387-388	2	75
α-helix	404-413	10
α-helix	417-437	21

Chain F: 7 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	76
β-strand	17-19	3	77
β-strand	21	1	78
β-strand	28-30	3	77
β-strand	37-38	2	79
β-strand	45-48	4	79
β-strand	53-54	2	80
β-strand	59	1	81
β-strand	61	1	81
β-strand	69	1	82
β-strand	70-71	2	80
β-strand	72-74	3	83
β-strand	77-79	3	83
β-strand	82	1	82
α-helix	83-85	3
β-strand	86-89	4	78
β-strand	93	1	78
β-strand	95-100	6	79
β-strand	103-107	5	79
β-strand	111-119	9	78
β-strand	124-133	10	78
β-strand	151-158	8	84
β-strand	166-171	6	85
β-strand	172	1	86
α-helix	180-182	3
β-strand	183-184	2	87
β-strand	191-192	2	87
β-strand	201-204	4	88
β-strand	210-213	4	88
β-strand	230-232	3	88
β-strand	239	1	76
β-strand	240	1	86
α-helix	247-249	3
β-strand	256-260	5	85
β-strand	264-271	8	84
α-helix	276-277	2
β-strand	278-279	2	89
β-strand	282	1	90
β-strand	285-287	3	90
β-strand	288-289	2	89
β-strand	290	1	91
β-strand	296-300	5	92
β-strand	302	1	93
β-strand	310-314	5	92
β-strand	318	1	91
β-strand	321-323	3	90
β-strand	329	1	93
β-strand	332	1	92
β-strand	341	1	93
β-strand	342-343	2	75
α-helix	359-364	6
α-helix	371-400	30
α-helix	413-418	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E1 envelope glycoprotein	A, C, E, G	protein	438	Western equine encephalitis virus	Q1W679
E2 envelope glycoprotein	B, D, F, H	protein	415	Western equine encephalitis virus	Q1W679

Sequence of entity 1 (A, C, E, G), FASTA

>8DAQ_1 E1 envelope glycoprotein (chains A, C, E, G)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVVPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTARLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMNPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRATNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKANREGHCPVHSHSTTAVLKEATTHVTATGSITLHFSTSS
PQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINTR

Sequence of entity 2 (B, D, F, H), FASTA

>8DAQ_2 E2 envelope glycoprotein (chains B, D, F, H)
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	8

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
8DAN 4.74 Å, CryoEM structure of Western equine encephalitis virus VLP in complex with the avian…

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