8D87: Spike glycoprotein E1

Fitted crystal structure of the homotrimer of fusion glycoprotein E1 from SFV into subtomogram averaged CHIKV E1 glycoprotein density. Determined by electron microscopy at 27.2 Å resolution. Released 31 Aug 2022.

Method: Electron microscopy
Resolution: 27.2 Å
Organism: Chikungunya virus strain S27-African prototype
Chains: 3
Atoms: 9,317
Mol. weight: 131.85 kDa
Ligands: PO4, HO
Released: 31 Aug 2022

Explore 8D87 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8D87 contains 25 α-helices and 108 β-strands across 3 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: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	1
β-strand	15-19	5	2
β-strand	27-40	14	2
β-strand	46-48	3	3
β-strand	51-54	4	4
β-strand	59-60	2	5
β-strand	77-82	6	5
β-strand	101-106	6	5
β-strand	107-110	4	4
α-helix	114-116	3
β-strand	119-122	4	3
β-strand	126-137	12	2
β-strand	140-146	7	2
β-strand	153-156	4	6
β-strand	159-162	4	6
β-strand	177-179	3	3
β-strand	184-185	2	3
α-helix	192-194	3
β-strand	203-204	2	7
β-strand	205	1	3
β-strand	214-215	2	7
β-strand	220-221	2	8
α-helix	222-225	4
β-strand	233-234	2	8
α-helix	239-246	8
α-helix	251-253	3
β-strand	260-262	3	2
β-strand	267-269	3	2
β-strand	275-280	6	1
β-strand	289-290	2	2
α-helix	293-295	3
β-strand	296-306	11	9
β-strand	307	1	10
β-strand	314-322	9	9
β-strand	326-329	4	11
β-strand	330-332	3	12
β-strand	338-339	2	9
β-strand	343-346	4	11
β-strand	351-357	7	9
β-strand	364-369	6	12
β-strand	372-377	6	12
α-helix	380	1
β-strand	381	1	10
α-helix	382-385	4

Chain B: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	13
β-strand	15-19	5	14
α-helix	26	1
β-strand	27-40	14	14
β-strand	46-48	3	15
β-strand	51-54	4	16
β-strand	59-61	3	17
β-strand	77-81	5	17
β-strand	101-106	6	17
β-strand	107-110	4	16
α-helix	114-116	3
β-strand	119-122	4	15
β-strand	126-137	12	14
β-strand	140-147	8	14
β-strand	153-156	4	18
β-strand	159-162	4	18
β-strand	177-179	3	15
β-strand	184-185	2	15
α-helix	192-194	3
β-strand	203-204	2	19
β-strand	205	1	15
β-strand	214-215	2	19
β-strand	220-221	2	20
α-helix	222-225	4
β-strand	233-234	2	20
α-helix	239-246	8
α-helix	251-253	3
β-strand	260-262	3	14
β-strand	267-269	3	14
β-strand	275-280	6	13
β-strand	289-290	2	14
α-helix	293-295	3
β-strand	296-306	11	21
β-strand	307	1	22
β-strand	314-322	9	21
β-strand	326-329	4	23
β-strand	330-332	3	24
β-strand	338-339	2	21
β-strand	343-346	4	23
β-strand	351-357	7	21
β-strand	364-369	6	24
β-strand	372-377	6	24
α-helix	380	1
β-strand	381	1	22
α-helix	382-385	4

Chain C: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	25
β-strand	15-19	5	26
β-strand	27-40	14	26
β-strand	46-48	3	27
β-strand	51-54	4	28
β-strand	59-60	2	29
α-helix	66-68	3
β-strand	77-81	5	29
β-strand	102-106	5	29
β-strand	107-110	4	28
α-helix	114-116	3
β-strand	119-122	4	27
β-strand	126-137	12	26
β-strand	140-146	7	26
β-strand	153-156	4	30
β-strand	159-162	4	30
β-strand	177-179	3	27
β-strand	184-185	2	27
α-helix	192-194	3
β-strand	203-204	2	31
β-strand	205	1	27
β-strand	214-215	2	31
β-strand	220-221	2	32
α-helix	222-225	4
β-strand	233-234	2	32
α-helix	239-246	8
α-helix	251-253	3
β-strand	260-262	3	26
β-strand	267-269	3	26
β-strand	275-280	6	25
β-strand	289-290	2	26
β-strand	296-306	11	33
β-strand	307	1	34
β-strand	314-322	9	33
β-strand	326-329	4	35
β-strand	330-332	3	36
β-strand	338-339	2	33
β-strand	343-346	4	35
β-strand	351-357	7	33
β-strand	364-369	6	36
β-strand	372-377	6	36
α-helix	380	1
β-strand	381	1	34
α-helix	382-385	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein E1	A, B, C	protein	391	Chikungunya virus strain S27-African prototype	P03315 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8D87_1 Spike glycoprotein E1 (chains A, B, C)
YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYV
KCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHAS
AYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVY
KDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGF
KYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLT
CTVATCTHSSDFGGVLTLTYKTNKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTAS
ASPSFVVSLCSARATCSASCEPPKDHIVPYA

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
HO	Holmium atom	Ho	4

Water and common crystallization additives (BR) are not listed.

Primary citation

Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery. Mangala Prasad, V., Blijleven, J.S., Smit, J.M. et al. Nat Commun (2022) 13:4772-4772. DOI 10.1038/s41467-022-32431-9 · PubMed

Other PDB entries of the same protein (UniProt P03315 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2V33 1.55 Å, High resolution crystal structure of domain III of E1 fusion glycoprotein of Semliki…
1I9W 3.0 Å, Crystal structure of the fusion glycoprotein E1 from semliki forest virus
1VCP 3.0 Å, Semliki forest virus capsid protein (crystal form I)
2ALA 3.0 Å, Crystal structure of the Semliki Forest Virus envelope protein E1 in its monomeric…
8IHP 3.0 Å, Structure of Semliki Forest virus VLP in complex with the receptor VLDLR-LA3
8YVY 3.02 Å, Semliki Forest virus virion
1VCQ 3.1 Å, Semliki forest virus capsid protein (crystal form II)
1RER 3.2 Å, Crystal structure of the homotrimer of fusion glycoprotein E1 from Semliki Forest Virus.
8YW1 3.44 Å, Semliki Forest virus viron in complex with VLDLR
8YVZ 3.45 Å, Semliki Forest virus viron
8X0K 3.5 Å, Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)
8X0L 3.5 Å, Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold)

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