8YVZ: Semliki Forest virus viron

Semliki Forest virus viron. Determined by electron microscopy at 3.45 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 3.45 Å
Organisms: Semliki Forest virus 4, Homo sapiens
Chains: 20
Atoms: 34,740
Mol. weight: 496.83 kDa
Ligands: CA
Released: 11 Dec 2024

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

Secondary structure: helices and β-sheets

8YVZ contains 118 α-helices and 375 β-strands across 20 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	11	1	2
β-strand	15-19	5	2
β-strand	24	1	3
β-strand	27-42	16	2
β-strand	46-48	3	4
β-strand	51-54	4	5
α-helix	56-58	3
β-strand	59-61	3	6
β-strand	77-82	6	6
β-strand	101-106	6	6
β-strand	107-110	4	5
β-strand	119-123	5	4
β-strand	124-137	14	2
β-strand	140	1	2
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	4
β-strand	183-186	4	4
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	4
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	11
β-strand	343-346	4	13
β-strand	351-358	8	11
β-strand	364-369	6	14
β-strand	374-377	4	14
β-strand	381	1	12
β-strand	387-388	2	15
α-helix	399-401	3
α-helix	405-437	33

Chain B: 8 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12	1	16
β-strand	17-19	3	17
β-strand	21	1	18
β-strand	28-30	3	17
β-strand	38	1	19
β-strand	46	1	20
β-strand	47	1	19
β-strand	49-56	8	20
β-strand	62-70	9	20
β-strand	75-79	5	20
β-strand	84-86	3	18
β-strand	92-104	13	20
β-strand	108-116	9	18
β-strand	122-131	10	18
β-strand	139	1	21
β-strand	149-156	8	22
α-helix	171-174	4
β-strand	175-176	2	23
β-strand	181-183	3	24
β-strand	188-190	3	24
β-strand	197-200	4	23
β-strand	208-211	4	23
β-strand	228-229	2	23
β-strand	235	1	16
β-strand	260-267	8	22
α-helix	270-273	4
β-strand	274-277	4	25
β-strand	281-286	6	25
β-strand	292-298	7	21
β-strand	308-310	3	21
β-strand	314-319	6	25
β-strand	325-329	5	21
α-helix	333-334	2
β-strand	335-337	3	21
β-strand	338-339	2	15
α-helix	351-360	10
α-helix	365-396	32
α-helix	398-400	3
α-helix	408-413	6

Chain C: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	27-30	4
α-helix	32-40	9
α-helix	48-55	8

Chain D: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	108-119	12
β-strand	120-125	6	26
β-strand	128-136	9	26
β-strand	139-143	5	26
β-strand	149-150	2	26
α-helix	153-156	4
α-helix	160	1
β-strand	161-163	3	26
β-strand	168-172	5	26
α-helix	173-174	2
α-helix	175-177	3
β-strand	182	1	26
β-strand	184	1	27
β-strand	191-195	5	27
β-strand	198-203	6	27
β-strand	206-209	4	27
β-strand	222-224	3	27
β-strand	230-240	11	27
β-strand	243-251	9	27
β-strand	256-258	3	27
β-strand	265-266	2	27

Chains E, R, S and T: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	117	1	113
β-strand	129	1	113
α-helix	130-132	3
α-helix	144-146	3

Chain F: 11 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	28
β-strand	15-19	5	29
β-strand	24	1	30
β-strand	27-42	16	29
β-strand	46-48	3	31
β-strand	51-54	4	32
α-helix	56-58	3
β-strand	59-62	4	33
β-strand	77-82	6	33
β-strand	100-106	7	33
β-strand	107-110	4	32
β-strand	119-123	5	31
β-strand	124-136	13	29
β-strand	137	1	34
β-strand	140	1	34
β-strand	143-147	5	29
β-strand	153-156	4	28
β-strand	159-163	5	28
α-helix	164-166	3
β-strand	176-180	5	31
β-strand	183-185	3	31
α-helix	189-191	3
β-strand	203-204	2	35
β-strand	205	1	31
β-strand	214-215	2	35
β-strand	220-221	2	36
α-helix	223-225	3
β-strand	233-234	2	36
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	29
β-strand	267-269	3	29
β-strand	275-281	7	28
β-strand	289	1	30
α-helix	294-295	2
β-strand	296-305	10	37
β-strand	307	1	38
β-strand	314-322	9	37
β-strand	326-328	3	39
β-strand	331-332	2	40
β-strand	337-339	3	37
β-strand	344-346	3	39
β-strand	351-358	8	37
β-strand	364-368	5	40
β-strand	374-377	4	40
β-strand	381	1	38
α-helix	382-383	2
β-strand	387-388	2	41
α-helix	399-401	3
α-helix	405-437	33

Chain G: 12 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	42
β-strand	15-19	5	43
β-strand	24	1	44
β-strand	27-48	22	43
β-strand	51-54	4	45
α-helix	56-58	3
β-strand	59-62	4	46
β-strand	77-82	6	46
β-strand	88	1	47
β-strand	91	1	47
β-strand	100-106	7	46
β-strand	107-110	4	45
β-strand	119-137	19	43
β-strand	140-147	8	43
β-strand	153-155	3	42
β-strand	160-163	4	42
α-helix	164-166	3
β-strand	176-180	5	43
β-strand	183-186	4	43
α-helix	189-191	3
β-strand	203-204	2	48
β-strand	205	1	43
β-strand	214-215	2	48
β-strand	220-221	2	49
α-helix	223-225	3
β-strand	233-234	2	49
α-helix	236-238	3
α-helix	239-246	8
α-helix	256-258	3
β-strand	260-262	3	43
β-strand	267-269	3	43
β-strand	275-281	7	42
α-helix	284-286	3
β-strand	289	1	44
α-helix	294-295	2
β-strand	297-306	10	50
β-strand	307	1	51
β-strand	314-321	8	50
β-strand	326-329	4	52
β-strand	330-332	3	53
β-strand	337-339	3	54
β-strand	343-346	4	52
β-strand	352-355	4	50
β-strand	356-358	3	54
β-strand	364-369	6	53
β-strand	374-377	4	53
β-strand	381	1	51
α-helix	382-383	2
β-strand	387-388	2	55
α-helix	399-401	3
α-helix	405-437	33

Chain H: 11 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	56
β-strand	11	1	57
β-strand	15-19	5	57
β-strand	24	1	58
β-strand	27-42	16	57
β-strand	46-48	3	59
β-strand	51-54	4	60
α-helix	56-58	3
β-strand	59-61	3	61
β-strand	77-82	6	61
β-strand	101-106	6	61
β-strand	107-110	4	60
β-strand	119-123	5	59
β-strand	124-137	14	57
β-strand	140-147	8	57
β-strand	152	1	8
β-strand	153-156	4	56
β-strand	159-163	5	56
α-helix	164-166	3
β-strand	176-180	5	59
β-strand	183-185	3	59
α-helix	189-191	3
β-strand	192	1	7
β-strand	203-204	2	62
β-strand	205	1	59
β-strand	214-215	2	62
β-strand	220-221	2	63
α-helix	223-225	3
β-strand	233-234	2	63
α-helix	236-238	3
α-helix	239-246	8
α-helix	256-258	3
β-strand	260-262	3	57
β-strand	267-269	3	57
β-strand	275-281	7	56
β-strand	289	1	58
α-helix	294-295	2
β-strand	296-305	10	64
β-strand	314-322	9	64
β-strand	326-328	3	65
β-strand	331-332	2	66
β-strand	337-339	3	64
β-strand	344-346	3	65
β-strand	351-358	8	64
β-strand	364-368	5	66
β-strand	374-377	4	66
α-helix	381-383	3
β-strand	387-388	2	67
α-helix	399-401	3
α-helix	405-437	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, F, G, H	protein	438	Semliki Forest virus 4	P03315 (AlphaFold model)
Spike glycoprotein E2	B, I, J, K	protein	418	Semliki Forest virus 4	P03315 (AlphaFold model)
Spike glycoprotein E3	C, L, M, N	protein	52	Semliki Forest virus 4	P03315 (AlphaFold model)
capsid protein, partial	D, O, P, Q	protein	161	Semliki Forest virus 4	P03315 (AlphaFold model)
Very low-density lipoprotein receptor	E, R, S, T	protein	44	Homo sapiens	P98155 (AlphaFold model)

Sequence of entity 1 (A, F, G, H), FASTA

>8YVZ_1 Spike glycoprotein E1 (chains A, F, G, H)
YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYV
KCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHAS
AYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVY
KDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGF
KYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLT
CTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTAS
ASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAF
AIGAILVLVVVTCIGLRR

Sequence of entity 2 (B, I, J, K), FASTA

>8YVZ_2 Spike glycoprotein E2 (chains B, I, J, K)
HFNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSDNHDY
TKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRNAVRA
CRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTLLSQQ
SGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSPFVPR
ADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLGEDPQ
YHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYGLYPA
ATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAPRAHA

Sequence of entity 3 (C, L, M, N), FASTA

>8YVZ_3 Spike glycoprotein E3 (chains C, L, M, N)
MCVLANATFPCFQPPCVPCCYENNAEATLRMLEDNVDRPGYYDLLQAALTCR

Sequence of entity 4 (D, O, P, Q), FASTA

>8YVZ_4 capsid protein, partial (chains D, O, P, Q)
KRERMCMKIENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKY
DLECAQIPVHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDN
KGRVVAIVLGGANEGSRTALSVVTWNKDMVTRVTPEGSEEW

Sequence of entity 5 (E, R, S, T), FASTA

>8YVZ_5 Very low-density lipoprotein receptor (chains E, R, S, T)
GSMRTCRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENCGN

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4

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.
8YW1 3.44 Å, Semliki Forest virus viron in complex with VLDLR
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)

Browse structure collections

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