8UA8: Semliki Forest virus VLP

Structure of Semliki Forest virus VLP in complex with VLDLR LA2. Determined by electron microscopy at 3.7 Å resolution. Released 14 Aug 2024.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Semliki Forest virus, Homo sapiens
Chains: 17
Atoms: 33,212
Mol. weight: 476.84 kDa
Ligands: CA, NAG
Released: 14 Aug 2024

Explore 8UA8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8UA8 contains 110 α-helices and 373 β-strands across 17 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: 10 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	15-19	5	2
β-strand	24-25	2	3
β-strand	27-39	13	2
β-strand	46-48	3	4
β-strand	51-54	4	5
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	128-137	10	2
β-strand	140-146	7	2
β-strand	152	1	7
β-strand	153-156	4	1
β-strand	159-163	5	1
β-strand	176-179	4	4
β-strand	184-186	3	4
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-204	2	8
β-strand	205	1	4
β-strand	214-215	2	8
β-strand	220-221	2	9
α-helix	223-225	3
β-strand	233-234	2	9
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
α-helix	284-286	3
β-strand	288-289	2	3
α-helix	290-292	3
β-strand	297-306	10	10
β-strand	307	1	11
β-strand	314-321	8	10
β-strand	326-329	4	12
β-strand	331-332	2	13
β-strand	337-339	3	10
β-strand	343-346	4	12
β-strand	352-358	7	10
β-strand	364-368	5	13
β-strand	373-377	5	13
β-strand	381	1	11
β-strand	387-388	2	14
α-helix	399-401	3
α-helix	405-437	33

Chain B: 7 helices, 33 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	36-38	3	17
β-strand	45-54	10	17
β-strand	66-71	6	17
β-strand	74-79	6	17
α-helix	80-82	3
β-strand	84-86	3	16
β-strand	90	1	16
β-strand	92-104	13	17
β-strand	111-116	6	16
β-strand	122-127	6	16
α-helix	133-135	3
β-strand	139	1	18
β-strand	149-156	8	19
β-strand	166-169	4	20
β-strand	175	1	21
β-strand	181-184	4	22
β-strand	187-190	4	22
β-strand	197-201	5	21
β-strand	208-211	4	21
β-strand	215-217	3	22
β-strand	225-229	5	21
β-strand	237	1	20
β-strand	252-255	4	20
β-strand	260-267	8	19
α-helix	270-273	4
β-strand	274-277	4	23
β-strand	281-286	6	23
β-strand	292-298	7	18
β-strand	306-310	5	18
β-strand	314-319	6	23
β-strand	325-329	5	18
α-helix	333-334	2
β-strand	335-337	3	18
β-strand	338-339	2	14
α-helix	350-361	12
α-helix	366-400	35
α-helix	409-414	6

Chain C: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	24
β-strand	14-15	2	24
α-helix	27-30	4
α-helix	32-41	10
α-helix	48-56	9

Chain D: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	117-119	3
β-strand	120-125	6	25
β-strand	128-136	9	25
β-strand	139-143	5	25
β-strand	149-150	2	25
α-helix	153-156	4
β-strand	161	1	25
β-strand	168-171	4	25
α-helix	172-174	3
α-helix	176-180	5
β-strand	182	1	25
β-strand	184	1	26
β-strand	191-194	4	27
β-strand	199-203	5	27
β-strand	206-210	5	27
β-strand	222-223	2	27
β-strand	230	1	26
β-strand	232-238	7	27
β-strand	243-251	9	27
β-strand	256-259	4	27
β-strand	265-266	2	27

Chain E: 14 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	28
β-strand	15-19	5	29
β-strand	24	1	30
β-strand	27-39	13	29
β-strand	46-48	3	31
β-strand	51-54	4	32
α-helix	57-58	2
β-strand	59-61	3	33
α-helix	67-69	3
β-strand	77-82	6	33
β-strand	87	1	34
β-strand	92	1	34
β-strand	101-106	6	33
β-strand	107-110	4	32
β-strand	119-123	5	31
β-strand	128-137	10	29
β-strand	140-147	8	29
β-strand	153-156	4	28
β-strand	159-163	5	28
β-strand	176-179	4	31
β-strand	184-186	3	31
α-helix	189-191	3
β-strand	192	1	7
α-helix	195-196	2
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	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	28
α-helix	284-286	3
β-strand	289	1	30
α-helix	290-292	3
β-strand	297-306	10	37
β-strand	307	1	38
β-strand	314-321	8	37
β-strand	326-329	4	39
β-strand	331-332	2	40
β-strand	337-339	3	37
β-strand	343-346	4	39
β-strand	352-358	7	37
β-strand	364-368	5	40
β-strand	373-377	5	40
α-helix	380	1
β-strand	381	1	38
α-helix	382-383	2
β-strand	387-388	2	41
α-helix	405-437	33

Chain F: 9 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12	1	42
β-strand	17-19	3	43
β-strand	21	1	44
β-strand	28-30	3	43
β-strand	34-38	5	45
β-strand	46-54	9	45
β-strand	66-71	6	45
β-strand	74-79	6	45
α-helix	80-82	3
β-strand	84-86	3	44
β-strand	90	1	44
β-strand	92-104	13	45
β-strand	110-116	7	44
β-strand	122-128	7	44
β-strand	139	1	46
β-strand	149-156	8	47
β-strand	166-170	5	48
β-strand	176	1	49
β-strand	181-184	4	50
β-strand	187-190	4	50
β-strand	197-200	4	49
β-strand	208-211	4	49
β-strand	215-217	3	50
α-helix	222-224	3
β-strand	227-229	3	49
β-strand	235	1	42
β-strand	236-237	2	48
β-strand	252-255	4	48
β-strand	260-267	8	47
α-helix	270-273	4
β-strand	274-277	4	51
β-strand	281-286	6	51
β-strand	292-298	7	46
β-strand	306-310	5	46
β-strand	314-319	6	51
β-strand	325-329	5	46
α-helix	333-334	2
β-strand	335-337	3	46
β-strand	338-339	2	41
α-helix	350-361	12
α-helix	366-396	31
α-helix	397-399	3
α-helix	409-414	6

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	27-30	4
α-helix	32-41	10
α-helix	48-55	8

Chain H: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	120-124	5	52
β-strand	129-134	6	52
β-strand	136	1	53
β-strand	139-143	5	52
β-strand	149-150	2	52
α-helix	153-156	4
β-strand	161	1	52
β-strand	168-172	5	52
α-helix	175-178	4
β-strand	182	1	53
α-helix	183	1
β-strand	184	1	54
β-strand	191-194	4	54
β-strand	199-203	5	54
β-strand	206-210	5	54
β-strand	222-224	3	54
β-strand	230-239	10	54
β-strand	243-251	9	54
β-strand	256-259	4	54

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
Glycoprotein E1	A, E, I, M	protein	438	Semliki Forest virus	P03315 (AlphaFold model)
Glycoprotein E2	B, F, J, N	protein	417	Semliki Forest virus	P03315 (AlphaFold model)
Assembly protein E3	C, G, K, O	protein	54	Semliki Forest virus	P03315 (AlphaFold model)
Capsid protein	D, H, L, P	protein	153	Semliki Forest virus	P03315 (AlphaFold model)
Very low-density lipoprotein receptor	R	protein	37	Homo sapiens	P98155 (AlphaFold model)

Sequence of entity 1 (A, E, I, M), FASTA

>8UA8_1 Glycoprotein E1 (chains A, E, I, M)
YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYV
KCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHAS
AYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVY
KDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGF
KYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLT
CTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTAS
ASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAF
AIGAILVLVVVTCIGLRR

Sequence of entity 2 (B, F, J, N), FASTA

>8UA8_2 Glycoprotein E2 (chains B, F, J, N)
FNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSDNHDYT
KIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRNAVRAC
RIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTLLSQQS
GNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSPFVPRA
DEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLGEDPQY
HEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYGLYPAA
TVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAPRAHA

Sequence of entity 3 (C, G, K, O), FASTA

>8UA8_3 Assembly protein E3 (chains C, G, K, O)
TAMCVLANATFPCFQPPCVPCCYENNAEATLRMLEDNVDRPGYYDLLQAALTCR

Sequence of entity 4 (D, H, L, P), FASTA

>8UA8_4 Capsid protein (chains D, H, L, P)
IENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKYDLECAQIP
VHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIV
LGGANEGSRTALSVVTWNKDMVTRVTPEGSEEW

Sequence of entity 5 (R), FASTA

>8UA8_5 Very low-density lipoprotein receptor (chains R)
CAESDFVCNNGQCVPSRWKCDGDPDCEDGSDESPEQC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structural basis for VLDLR recognition by eastern equine encephalitis virus. Yang, P., Li, W., Fan, X. et al. Nat Commun (2024) 15:6548-6548. DOI 10.1038/s41467-024-50887-9 · 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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