8DEE: Spike glycoprotein E1

Asymmetric Unit of Western Equine Encephalitis Virus. Determined by electron microscopy at 3.4 Å resolution. Released 5 Jul 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Western equine encephalitis virus
Chains: 12
Atoms: 30,716
Mol. weight: 491.43 kDa
Released: 5 Jul 2023

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

Secondary structure: helices and β-sheets

8DEE contains 89 α-helices and 370 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.

Chain A: 12 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	15-19	5	1
β-strand	24	1	2
β-strand	27-39	13	1
β-strand	42-48	7	3
β-strand	51-54	4	4
α-helix	56-58	3
β-strand	59-60	2	4
β-strand	74-81	8	4
β-strand	87	1	5
β-strand	90	1	6
β-strand	102-110	9	4
α-helix	112-115	4
β-strand	119-124	6	3
α-helix	126-127	2
β-strand	128-137	10	1
β-strand	140-148	9	1
β-strand	153-156	4	1
β-strand	159-163	5	1
β-strand	176-180	5	3
β-strand	183-185	3	3
α-helix	189-191	3
β-strand	203-204	2	7
β-strand	205	1	3
β-strand	214-215	2	7
β-strand	220-221	2	8
β-strand	228	1	5
β-strand	233-234	2	8
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-253	3
β-strand	260-262	3	1
β-strand	267-269	3	1
β-strand	275-281	7	1
β-strand	289	1	2
β-strand	298-306	9	9
β-strand	307	1	10
β-strand	314-321	8	9
β-strand	326	1	11
α-helix	328	1
β-strand	329	1	12
β-strand	330-332	3	13
β-strand	337-339	3	9
β-strand	343	1	12
β-strand	346	1	11
β-strand	349-358	10	9
β-strand	364-369	6	13
β-strand	372-377	6	13
α-helix	380	1
β-strand	381	1	10
α-helix	382-383	2
β-strand	387-388	2	14
α-helix	399-401	3
α-helix	404-437	34

Chain B: 11 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	17-19	3	15
β-strand	21	1	16
β-strand	28-30	3	15
β-strand	34-38	5	17
β-strand	45-52	8	17
β-strand	53	1	18
β-strand	54	1	17
β-strand	56	1	19
β-strand	62	1	19
β-strand	66-70	5	18
β-strand	78-82	5	18
α-helix	83-85	3
β-strand	86-89	4	16
β-strand	93	1	16
α-helix	94	1
β-strand	95-107	13	17
β-strand	111-120	10	16
β-strand	123-133	11	16
β-strand	141	1	20
β-strand	151-158	8	21
β-strand	168-170	3	22
β-strand	171-172	2	23
β-strand	174	1	24
β-strand	179	1	6
β-strand	183-186	4	25
β-strand	189-192	4	25
α-helix	194-195	2
β-strand	200-205	6	26
β-strand	209-214	6	26
β-strand	218-220	3	25
α-helix	226-228	3
β-strand	229-233	5	26
β-strand	240-241	2	23
α-helix	247	1
β-strand	248	1	24
α-helix	249	1
β-strand	257-259	3	22
β-strand	264-271	8	21
α-helix	274-277	4
β-strand	278-282	5	20
β-strand	285-302	18	20
β-strand	310-322	13	20
β-strand	329-333	5	20
α-helix	337-338	2
β-strand	339-341	3	20
β-strand	342-343	2	14
α-helix	355-365	11
α-helix	367-400	34
α-helix	413-419	7

Chain E: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	111-116	6	27
β-strand	119-127	9	27
β-strand	130-134	5	27
β-strand	140-141	2	27
α-helix	144-147	4
β-strand	152-154	3	27
β-strand	159-163	5	27
β-strand	173	1	27
β-strand	175	1	28
β-strand	182-186	5	28
β-strand	189-194	6	28
β-strand	197-201	5	28
α-helix	212	1
β-strand	213-215	3	28
α-helix	216	1
β-strand	221-230	10	28
β-strand	234-242	9	28
β-strand	248-251	4	28
β-strand	257-258	2	28

Chain F: 8 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	29
β-strand	15-19	5	29
β-strand	24	1	30
β-strand	27-39	13	29
β-strand	42-48	7	31
β-strand	51-54	4	32
α-helix	56-58	3
β-strand	59-60	2	32
β-strand	74-81	8	32
β-strand	87	1	33
β-strand	102-110	9	32
α-helix	112-115	4
β-strand	119-124	6	31
β-strand	128-137	10	29
β-strand	140-148	9	29
β-strand	153-156	4	29
β-strand	159-163	5	29
β-strand	176-180	5	31
β-strand	183-185	3	31
α-helix	189-191	3
β-strand	203-204	2	34
β-strand	205	1	31
β-strand	214-215	2	34
β-strand	220-221	2	35
β-strand	228	1	33
β-strand	233-234	2	35
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	29
β-strand	267-269	3	29
β-strand	275-281	7	29
β-strand	289	1	30
β-strand	296-303	8	36
β-strand	307	1	37
β-strand	314-322	9	36
β-strand	326	1	38
β-strand	329	1	39
β-strand	330-332	3	40
β-strand	337-339	3	36
β-strand	343	1	39
β-strand	346	1	38
β-strand	349-358	10	36
β-strand	365-369	5	40
β-strand	372-376	5	40
β-strand	381	1	37
α-helix	382-383	2
β-strand	387-388	2	41
α-helix	404-438	35

Chain G: 10 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	17-19	3	42
β-strand	21	1	43
β-strand	28-30	3	42
β-strand	34-38	5	44
β-strand	45-56	12	44
β-strand	62-70	9	44
β-strand	78-82	5	44
α-helix	83-85	3
β-strand	86-89	4	43
β-strand	93	1	43
α-helix	94	1
β-strand	95-107	13	44
β-strand	111-120	10	43
β-strand	123-133	11	43
β-strand	141	1	45
β-strand	151-158	8	46
β-strand	168-172	5	47
β-strand	174	1	48
β-strand	183-186	4	49
β-strand	189-192	4	49
β-strand	200-205	6	50
β-strand	209-214	6	50
β-strand	218-219	2	49
α-helix	226-228	3
β-strand	229-233	5	50
β-strand	240-241	2	47
α-helix	247	1
β-strand	248	1	48
α-helix	249	1
β-strand	256-259	4	47
β-strand	264-271	8	46
α-helix	275-277	3
β-strand	278-282	5	45
β-strand	285-302	18	45
β-strand	310-322	13	45
β-strand	329-333	5	45
α-helix	337-338	2
β-strand	339-341	3	45
β-strand	342-343	2	41
α-helix	355-365	11
α-helix	367-404	38
α-helix	414-419	6

Chain I: 2 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	111-116	6	51
β-strand	119-127	9	51
β-strand	130-134	5	51
β-strand	140-141	2	51
α-helix	146-148	3
β-strand	152-154	3	51
β-strand	159-163	5	51
β-strand	173	1	51
β-strand	174	1	52
β-strand	182-186	5	53
β-strand	189-194	6	53
β-strand	197-201	5	53
α-helix	212	1
β-strand	213-215	3	53
β-strand	220	1	52
β-strand	221-230	10	53
β-strand	234-241	8	53
β-strand	249-251	3	53
β-strand	258	1	53

Chain J: 9 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	54
β-strand	15-19	5	55
β-strand	24	1	56
β-strand	27-39	13	55
β-strand	42-48	7	57
α-helix	50	1
β-strand	51-54	4	58
α-helix	56-58	3
β-strand	59-60	2	59
β-strand	77-81	5	59
β-strand	87	1	60
β-strand	102-106	5	59
β-strand	107-110	4	58
α-helix	112-115	4
β-strand	119-124	6	57
α-helix	126-127	2
β-strand	128-137	10	55
β-strand	140-148	9	55
β-strand	153-156	4	54
β-strand	159-163	5	54
β-strand	176-180	5	57
β-strand	183-185	3	57
α-helix	190-191	2
β-strand	203-204	2	61
β-strand	205	1	57
β-strand	214-215	2	61
β-strand	219-221	3	62
β-strand	228	1	60
β-strand	233-235	3	62
α-helix	239-245	7
α-helix	251-253	3
β-strand	260-262	3	55
β-strand	267-269	3	55
β-strand	275-281	7	54
β-strand	289	1	56
β-strand	298-306	9	63
β-strand	307	1	64
β-strand	314-321	8	63
β-strand	326	1	65
β-strand	329	1	66
β-strand	330-332	3	67
β-strand	337-339	3	63
β-strand	343	1	66
β-strand	346	1	65
β-strand	349-358	10	63
β-strand	362-369	8	67
β-strand	372-379	8	67
β-strand	381	1	64
α-helix	382-383	2
β-strand	387-388	2	68
α-helix	404-437	34

Chain K: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	17-19	3	69
β-strand	21	1	70
β-strand	28-30	3	69
β-strand	34-38	5	71
β-strand	45-52	8	71
β-strand	53	1	72
β-strand	54	1	71
β-strand	56	1	73
β-strand	62	1	73
β-strand	66-70	5	72
β-strand	78-82	5	72
α-helix	83-85	3
β-strand	86-89	4	70
β-strand	93-94	2	70
β-strand	95-107	13	71
β-strand	111-120	10	70
β-strand	123-133	11	70
β-strand	141	1	74
β-strand	151-158	8	75
β-strand	168-172	5	76
β-strand	174	1	77
β-strand	183-186	4	78
β-strand	189-192	4	78
β-strand	200-205	6	79
β-strand	209-214	6	79
β-strand	218-220	3	78
β-strand	229-233	5	79
β-strand	240-241	2	76
α-helix	247	1
β-strand	248	1	77
α-helix	249	1
β-strand	256-259	4	76
β-strand	264-271	8	75
α-helix	274-277	4
β-strand	278-282	5	74
β-strand	285-302	18	74
β-strand	310-322	13	74
β-strand	329-333	5	74
α-helix	337-338	2
β-strand	339-341	3	74
β-strand	342-343	2	68
α-helix	355-365	11
α-helix	367-404	38
α-helix	413-419	7

4 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
Spike glycoprotein E1	A, F, J, N	protein	439	Western equine encephalitis virus	P13897
Spike glycoprotein E2	B, G, K, O	protein	418	Western equine encephalitis virus	P13897
Capsid protein	E, I, M, R	protein	259	Western equine encephalitis virus	P13897

Sequence of entity 1 (A, F, J, N), FASTA

>8DEE_1 Spike glycoprotein E1 (chains A, F, J, N)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCRFHTVIPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTAVGSITLHFSTSS
PQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLLALFGGASSL
IVVGLIVLVCSSMLINTRR

Sequence of entity 2 (B, G, K, O), FASTA

>8DEE_2 Spike glycoprotein E2 (chains B, G, K, O)
SITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTAD
VTKFRYMSFDHDHDIKEDSMDKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGAS
ENSCTVEKKIRRKFVGREEYLFPPVHGKLVKCHVYDHLKETSAGYITMHRPGPHAYKSYL
EEASGEVYIKPPSGKNVTYECKCGDYSTGIVSTRTKMNGCTKAKQCIAYKSDQTKWVFNS
PDLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKL
GLRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYY
HRHPVYTVIVLCGVALAILVGTASSAACIAKARRDCLTPYALAPNATVPTALAVLCCI

Sequence of entity 3 (E, I, M, R), FASTA

>8DEE_3 Capsid protein (chains E, I, M, R)
MFPYPQLNFPPVYPTNPMAYRDPNPPRCRWRPFRPPLAAQIEDLRRSIANLTFKQRSPNP
PPGPPPKKKKSAPKPKPTQPKKKKQQAKKTKRKPKPGKRQRMCMKLESDKTFPIMLNGQV
NGYACVVGGRLMKPLHVEGKIDNEQLAAVKLKKASMYDLEYGDVPQNMKSDTLQYTSDKP
PGFYNWHHGAVQYENGRFTVPRGVGGKGDSGRPILDNRGRVVAIVLGGANEGTRTALSVV
TWNQKGVTIKDTPEGSEPW

Primary citation

Vaccine elicitation and structural basis for antibody protection against alphaviruses. Sutton, M.S., Pletnev, S., Callahan, V. et al. Cell (2023) 186:2672-2689.e25. DOI 10.1016/j.cell.2023.05.019 · PubMed

Other PDB entries of the same protein (UniProt P13897), best resolution first:

9L3V 2.53 Å, structure of WEEV strain 71V1658 virus-like particle(3-fold region)
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9DQZ 2.9 Å, Structure of western equine encephalitis virus McMillan VLP in complex with human VLDLR
9L41 2.99 Å, Structure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human…
9UIO 3.03 Å, CryoEM structure of Western equine encephalitis virus California VLP in complex with…
9UIH 3.05 Å, CryoEM structure of Western equine encephalitis virus California VLP
9WSL 3.27 Å, CryoEM structure of Western equine encephalitis virus California VLP in complex with…
9DQV 3.3 Å, Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1
9L1N 3.3 Å, Structure of Western equine encephalitis virus 71V1658 strain VLP in complex with human…
9DQX 3.4 Å, Structure of western equine encephalitis virus CBA87 VLP
9L99 3.6 Å, Structure of Western equine encephalitis virus McMillan strain in complex with VLDLR LA1-2
8SQN 3.89 Å, CryoEM structure of Western equine encephalitis virus VLP in complex with the chimeric…

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