8IHP: Semliki Forest virus VLP

Structure of Semliki Forest virus VLP in complex with the receptor VLDLR-LA3. Determined by electron microscopy at 3.0 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Semliki Forest virus, Homo sapiens
Chains: 15
Atoms: 32,337
Mol. weight: 464.69 kDa
Ligands: NAG, CA
Released: 12 Apr 2023

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

Secondary structure: helices and β-sheets

8IHP contains 85 α-helices and 385 β-strands across 15 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: 9 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	12	1	1
β-strand	17-19	3	2
β-strand	28-30	3	2
β-strand	37-38	2	3
β-strand	46-56	11	3
β-strand	62-68	7	3
β-strand	71	1	4
β-strand	74	1	4
β-strand	77-79	3	3
α-helix	80-82	3
β-strand	84-86	3	5
β-strand	92-104	13	3
β-strand	110-116	7	5
β-strand	122-128	7	5
β-strand	139	1	6
β-strand	149-156	8	7
β-strand	166-170	5	8
β-strand	175-176	2	9
α-helix	178-180	3
β-strand	181-183	3	10
β-strand	188-190	3	10
β-strand	197-201	5	9
β-strand	206-210	5	9
β-strand	215-217	3	10
α-helix	222-224	3
β-strand	225-229	5	9
β-strand	235	1	1
β-strand	236-237	2	8
β-strand	244	1	11
β-strand	252-255	4	8
β-strand	260-267	8	7
α-helix	270-272	3
β-strand	274-277	4	12
β-strand	281-286	6	12
β-strand	292-298	7	6
β-strand	306-310	5	6
β-strand	314-319	6	12
β-strand	325-329	5	6
α-helix	333-334	2
β-strand	335-337	3	6
β-strand	338-339	2	13
α-helix	351-361	11
α-helix	363-401	39
α-helix	409-415	7

Chain B: 10 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	14
β-strand	16-19	4	15
β-strand	24-25	2	16
β-strand	27-39	13	15
β-strand	42-48	7	17
β-strand	51-54	4	18
α-helix	56-58	3
β-strand	59-62	4	11
β-strand	77-81	5	11
β-strand	100-106	7	11
β-strand	107-110	4	18
β-strand	119-124	6	17
β-strand	128-137	10	15
β-strand	140-145	6	15
β-strand	154-156	3	14
β-strand	159-163	5	14
β-strand	176-179	4	17
β-strand	184-185	2	17
α-helix	189-191	3
β-strand	203-204	2	19
β-strand	205	1	17
β-strand	214-215	2	19
β-strand	220-221	2	20
α-helix	223-225	3
β-strand	233-234	2	20
α-helix	236-238	3
α-helix	239-246	8
α-helix	256-258	3
β-strand	260-261	2	21
β-strand	268-269	2	21
β-strand	275-281	7	14
α-helix	284-286	3
β-strand	288-289	2	16
α-helix	290-292	3
β-strand	297-306	10	22
β-strand	307	1	23
β-strand	314-321	8	22
β-strand	326-328	3	24
β-strand	331-332	2	25
β-strand	338-339	2	22
β-strand	344-346	3	24
β-strand	351-357	7	22
β-strand	364-368	5	25
β-strand	373-377	5	25
β-strand	381	1	23
β-strand	387-388	2	13
α-helix	399-401	3
α-helix	405-436	32

Chain C: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	107-115	9
β-strand	120-125	6	26
β-strand	128-136	9	26
β-strand	139-141	3	26
β-strand	142-143	2	27
β-strand	149-150	2	26
α-helix	153-156	4
β-strand	161	1	28
β-strand	168-169	2	27
β-strand	170	1	28
β-strand	172	1	26
α-helix	173-174	2
β-strand	182	1	26
β-strand	184	1	29
β-strand	191-194	4	30
β-strand	199-202	4	30
β-strand	207-210	4	30
β-strand	222-224	3	30
β-strand	230	1	29
β-strand	232-238	7	30
β-strand	243-251	9	30
β-strand	256-259	4	30
β-strand	265-266	2	30

Chain D: 9 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
α-helix	9-11	3
β-strand	12	1	31
β-strand	17-19	3	32
β-strand	28-30	3	32
β-strand	34-38	5	33
β-strand	46-54	9	33
β-strand	66-69	4	33
β-strand	76-79	4	33
α-helix	80-82	3
β-strand	84-86	3	34
β-strand	90	1	34
β-strand	92-104	13	33
β-strand	110-116	7	34
β-strand	122-128	7	34
β-strand	139	1	35
β-strand	149-156	8	36
β-strand	166-170	5	37
β-strand	175	1	38
α-helix	178-180	3
β-strand	182-183	2	39
β-strand	188-190	3	39
β-strand	197-201	5	38
β-strand	215-217	3	39
β-strand	225-229	5	38
β-strand	235	1	31
β-strand	236-237	2	37
β-strand	244	1	40
β-strand	252-255	4	37
β-strand	260-267	8	36
α-helix	270-273	4
β-strand	274-277	4	41
β-strand	281-286	6	41
β-strand	292-298	7	35
β-strand	306-310	5	35
β-strand	314-319	6	41
β-strand	325-329	5	35
β-strand	335-337	3	35
β-strand	338-339	2	42
α-helix	351-359	9
α-helix	363-396	34
α-helix	398-400	3
α-helix	409-414	6

Chain E: 11 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	43
β-strand	11	1	44
β-strand	15-19	5	44
β-strand	24	1	45
β-strand	27-33	7	44
β-strand	37-48	12	44
β-strand	51-54	4	46
α-helix	56-58	3
β-strand	59-62	4	40
β-strand	77-81	5	40
β-strand	100-106	7	40
β-strand	107-110	4	46
β-strand	119-137	19	44
β-strand	140-147	8	44
β-strand	154-156	3	43
β-strand	159-163	5	43
α-helix	164-166	3
β-strand	176-179	4	44
β-strand	184-185	2	44
α-helix	189-191	3
β-strand	203-204	2	47
β-strand	205	1	44
β-strand	214-215	2	47
β-strand	220-221	2	48
α-helix	223-225	3
β-strand	233-234	2	48
α-helix	236-238	3
α-helix	239-246	8
α-helix	256-258	3
β-strand	260-261	2	44
β-strand	268-269	2	44
β-strand	275-281	7	43
α-helix	284-286	3
β-strand	289	1	45
α-helix	294-295	2
β-strand	296-306	11	49
β-strand	307	1	50
β-strand	314-322	9	49
β-strand	326-329	4	51
β-strand	332	1	52
β-strand	338-339	2	49
β-strand	343-346	4	51
β-strand	351-357	7	49
β-strand	364-367	4	52
β-strand	374-377	4	52
β-strand	381	1	50
β-strand	387-388	2	42
α-helix	399-401	3
α-helix	405-435	31

Chain F: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	108-118	11
β-strand	120-125	6	53
β-strand	128-136	9	53
β-strand	139-143	5	53
β-strand	149-150	2	53
β-strand	161-163	3	53
β-strand	168-172	5	53
α-helix	175-180	6
β-strand	182	1	53
β-strand	183-184	2	54
β-strand	191-195	5	54
β-strand	198-203	6	54
β-strand	206-210	5	54
β-strand	222-224	3	54
β-strand	229-240	12	54
β-strand	243-251	9	54
β-strand	256-259	4	54
β-strand	265-266	2	54

Chain G: 7 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	55
β-strand	17-19	3	56
β-strand	28-30	3	56
β-strand	36-38	3	57
β-strand	46-56	11	57
β-strand	62-71	10	57
β-strand	74-79	6	57
α-helix	80-82	3
β-strand	84-86	3	58
β-strand	90	1	58
β-strand	92-104	13	57
β-strand	110-116	7	58
β-strand	122-128	7	58
β-strand	139	1	59
β-strand	149-156	8	60
β-strand	166-170	5	61
β-strand	175-177	3	62
β-strand	181-182	2	63
β-strand	188-190	3	63
β-strand	197	1	62
β-strand	200-201	2	64
β-strand	206	1	64
β-strand	215-217	3	63
α-helix	222-224	3
β-strand	225-226	2	64
β-strand	227-229	3	62
β-strand	235	1	55
β-strand	236-237	2	61
β-strand	252-255	4	61
β-strand	260-267	8	60
α-helix	268-272	5
β-strand	274-277	4	65
β-strand	281-286	6	65
β-strand	292-298	7	59
β-strand	306-310	5	59
β-strand	314-319	6	65
β-strand	325-329	5	59
α-helix	333-334	2
β-strand	335-337	3	59
β-strand	338-339	2	66
α-helix	351-359	9
α-helix	363-400	38
α-helix	412-415	4

Chain H: 8 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	67
β-strand	11	1	68
β-strand	15-19	5	68
β-strand	24-25	2	69
β-strand	27-48	22	68
β-strand	51-54	4	70
β-strand	59-62	4	71
β-strand	77-81	5	71
β-strand	83	1	71
β-strand	100-106	7	71
β-strand	107-110	4	70
β-strand	119-137	19	68
β-strand	140-147	8	68
β-strand	154-156	3	67
β-strand	159-163	5	67
β-strand	176-179	4	68
β-strand	184-185	2	68
α-helix	189-191	3
β-strand	203-204	2	72
β-strand	205	1	68
β-strand	214-215	2	72
β-strand	220-221	2	73
α-helix	223-225	3
β-strand	233-234	2	73
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	74
β-strand	267-269	3	74
β-strand	275-281	7	67
α-helix	284-286	3
β-strand	288-289	2	69
α-helix	294-296	3
β-strand	297-306	10	75
β-strand	307	1	76
β-strand	314-321	8	75
β-strand	326	1	77
β-strand	329	1	78
β-strand	331-332	2	79
β-strand	337-339	3	75
β-strand	343	1	78
β-strand	346	1	77
β-strand	351-358	8	75
β-strand	364-368	5	79
β-strand	373-377	5	79
β-strand	381	1	76
β-strand	387-388	2	66
α-helix	405-434	30

7 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 E2	A, D, G, J	protein	422	Semliki Forest virus	P03315 (AlphaFold model)
Spike glycoprotein E1	B, E, H, K	protein	438	Semliki Forest virus	P03315 (AlphaFold model)
Capsid protein	C, F, I, L	protein	162	Semliki Forest virus	P03315 (AlphaFold model)
Very low-density lipoprotein receptor	M, N, O	protein	39	Homo sapiens	P98155 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>8IHP_1 Spike glycoprotein E2 (chains A, D, G, J)
SVSQHFNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSD
NHDYTKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRN
AVRACRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTL
LSQQSGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSP
FVPRADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLG
EDPQYHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYG
LYPAATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAPRA
HA

Sequence of entity 2 (B, E, H, K), FASTA

>8IHP_2 Spike glycoprotein E1 (chains B, E, H, K)
YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYV
KCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHAS
AYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVY
KDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGF
KYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLT
CTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTAS
ASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAF
AIGAILVLVVVTCIGLRR

Sequence of entity 3 (C, F, I, L), FASTA

>8IHP_3 Capsid protein (chains C, F, I, L)
GKRERMCMKIENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSK
YDLECAQIPVHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFD
NKGRVVAIVLGGANEGSRTALSVVTWNKDMVTRVTPEGSEEW

Sequence of entity 4 (M, N, O), FASTA

>8IHP_4 Very low-density lipoprotein receptor (chains M, N, O)
RTCRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12
CA	Calcium ion	Ca	3

Primary citation

Structure of Semliki Forest virus in complex with its receptor VLDLR. Cao, D., Ma, B., Cao, Z. et al. Cell (2023) 186:2208-2218.e15. DOI 10.1016/j.cell.2023.03.032 · 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…
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)
8X0M 3.5 Å, Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(5-fold)

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