8YW1: Semliki Forest virus viron

Semliki Forest virus viron in complex with VLDLR. Determined by electron microscopy at 3.44 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 3.44 Å
Organisms: Semliki Forest virus 4, Homo sapiens
Chains: 33
Atoms: 67,744
Mol. weight: 967.94 kDa
Released: 11 Dec 2024

Explore 8YW1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YW1 contains 217 α-helices and 740 β-strands across 33 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 L: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	27-30	4
α-helix	32-39	8
α-helix	49-55	7

Chains A and E: 12 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	15-19	5	2
β-strand	24	1	3
β-strand	27-48	22	2
β-strand	51-54	4	4
α-helix	56-58	3
β-strand	59-61	3	5
β-strand	77-82	6	5
β-strand	101-106	6	5
β-strand	107-110	4	4
β-strand	119-136	18	2
β-strand	137	1	6
β-strand	140	1	6
β-strand	143-147	5	2
β-strand	152	1	7
β-strand	153-156	4	1
β-strand	159-163	5	1
α-helix	164-166	3
β-strand	176-180	5	2
β-strand	183-186	4	2
α-helix	189-191	3
β-strand	192	1	8
α-helix	195-196	2
β-strand	203-204	2	9
β-strand	205	1	2
β-strand	214-215	2	9
β-strand	220-221	2	10
α-helix	223-225	3
β-strand	233-234	2	10
α-helix	236-238	3
α-helix	239-245	7
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	3
α-helix	294-295	2
β-strand	296-306	11	11
β-strand	307	1	12
β-strand	314-322	9	11
β-strand	326-329	4	13
β-strand	330-332	3	14
β-strand	337-339	3	15
β-strand	343-346	4	13
β-strand	351-355	5	11
β-strand	356-358	3	15
β-strand	364-369	6	14
β-strand	374-377	4	14
β-strand	381	1	12
β-strand	387-388	2	16
α-helix	399-401	3
α-helix	405-437	33

Chains b and M: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	27
β-strand	16	1	27
α-helix	27-30	4
α-helix	32-41	10
α-helix	48-55	8

Chains B and R: 8 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12	1	17
β-strand	17-19	3	18
β-strand	21	1	19
β-strand	28-30	3	18
β-strand	38	1	20
β-strand	46	1	21
β-strand	47	1	20
β-strand	49-56	8	21
β-strand	62-70	9	21
β-strand	75-79	5	21
β-strand	84-86	3	19
β-strand	92-104	13	21
β-strand	108-116	9	19
β-strand	122-131	10	19
β-strand	139	1	22
β-strand	149-156	8	23
α-helix	171-173	3
β-strand	175-177	3	24
β-strand	181-183	3	25
β-strand	188-190	3	25
β-strand	197-200	4	24
β-strand	208-211	4	24
β-strand	227-229	3	24
β-strand	235	1	17
β-strand	260-267	8	23
α-helix	270-273	4
β-strand	274-277	4	26
β-strand	281-286	6	26
β-strand	292-298	7	22
β-strand	307-310	4	22
β-strand	314-319	6	26
β-strand	325-329	5	22
α-helix	333-334	2
β-strand	335-337	3	22
β-strand	338-339	2	16
α-helix	351-360	10
α-helix	365-396	32
α-helix	398-400	3
α-helix	408-413	6

Chains c and N: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	31
β-strand	16	1	31
α-helix	27-30	4
α-helix	32-40	9
α-helix	48-54	7

Chain C: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	112-114	3
β-strand	117-119	3	28
β-strand	127-129	3	28
α-helix	130-132	3
β-strand	158-160	3	29
β-strand	166-168	3	29
α-helix	169-171	3
α-helix	183-185	3
β-strand	197-199	3	30
β-strand	205-207	3	30
α-helix	208-210	3

Chains d and O: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	108-118	11
β-strand	120-125	6	34
β-strand	128-136	9	34
β-strand	139-142	4	34
β-strand	149-150	2	34
α-helix	153-157	5
β-strand	161-163	3	34
β-strand	168-172	5	34
α-helix	173-174	2
α-helix	175-180	6
β-strand	182	1	34
β-strand	184	1	35
β-strand	191-195	5	35
β-strand	198-203	6	35
β-strand	206-209	4	35
β-strand	222-224	3	35
β-strand	230-240	11	35
β-strand	243-251	9	35
β-strand	256-259	4	35
β-strand	265-266	2	35

Chains D and T: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	108-119	12
β-strand	120-125	6	32
β-strand	128-136	9	32
β-strand	139-143	5	32
β-strand	149-150	2	32
α-helix	153-156	4
α-helix	160	1
β-strand	161-163	3	32
β-strand	168-172	5	32
α-helix	173-174	2
α-helix	175-177	3
β-strand	182	1	32
β-strand	184	1	33
β-strand	191-195	5	33
β-strand	198-203	6	33
β-strand	206-209	4	33
β-strand	222-224	3	33
β-strand	230-240	11	33
β-strand	243-251	9	33
β-strand	256-259	4	33
β-strand	265-266	2	33

9 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, E, F, G, H, U, V, W	protein	438	Semliki Forest virus 4	P03315 (AlphaFold model)
Spike glycoprotein E2	B, I, J, K, R, X, Y, Z	protein	418	Semliki Forest virus 4	P03315 (AlphaFold model)
Very low-density lipoprotein receptor	C	protein	121	Homo sapiens	P98155 (AlphaFold model)
capsid protein, partial	D, O, P, Q, T, d, e, f	protein	161	Semliki Forest virus 4	P03315 (AlphaFold model)
Spike glycoprotein E3	L, M, N, S, a, b, c, g	protein	52	Semliki Forest virus 4	P03315 (AlphaFold model)

Sequence of entity 1 (A, E, F, G, H, U, V, W), FASTA

>8YW1_1 Spike glycoprotein E1 (chains A, E, F, G, H, U, V, W)
YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYV
KCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHAS
AYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVY
KDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGF
KYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLT
CTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTAS
ASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAF
AIGAILVLVVVTCIGLRR

Sequence of entity 2 (B, I, J, K, R, X, Y, Z), FASTA

>8YW1_2 Spike glycoprotein E2 (chains B, I, J, K, R, X, Y, Z)
HFNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSDNHDY
TKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRNAVRA
CRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTLLSQQ
SGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSPFVPR
ADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLGEDPQ
YHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYGLYPA
ATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAPRAHA

Sequence of entity 3 (C), FASTA

>8YW1_3 Very low-density lipoprotein receptor (chains C)
RTCRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENCGNITCSPDEFTCSSGRCISRN
FVCNGQDDCSDGSDELDCAPPTCGAHEFQCSTSSCIPISWVCDDDADCSDQSDESLEQCG
R

Sequence of entity 4 (D, O, P, Q, T, d, e, f), FASTA

>8YW1_4 capsid protein, partial (chains D, O, P, Q, T, d, e, f)
KRERMCMKIENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKY
DLECAQIPVHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDN
KGRVVAIVLGGANEGSRTALSVVTWNKDMVTRVTPEGSEEW

Sequence of entity 5 (L, M, N, S, a, b, c, g), FASTA

>8YW1_5 Spike glycoprotein E3 (chains L, M, N, S, a, b, c, g)
MCVLANATFPCFQPPCVPCCYENNAEATLRMLEDNVDRPGYYDLLQAALTCR

Primary citation

Structural insights into Semiliki forest virus receptor binding modes indicate novel mechanism of virus endocytosis. Yang, D., Wang, N., Du, B. et al. PLoS Pathog (2024) 20:e1012770-e1012770. DOI 10.1371/journal.ppat.1012770 · 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.
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)
8X0M 3.5 Å, Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(5-fold)

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