8X0M: Semliki Forest virus

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(5-fold). Determined by electron microscopy at 3.5 Å resolution. Released 27 Nov 2024.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Semliki Forest virus
Chains: 11
Atoms: 24,274
Mol. weight: 346.81 kDa
Ligands: CA, NAG
Released: 27 Nov 2024

Explore 8X0M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X0M contains 78 α-helices and 272 β-strands across 11 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: 4 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	107-119	13
β-strand	121-125	5	1
β-strand	128-133	6	1
β-strand	134-136	3	2
β-strand	139-142	4	2
β-strand	149-150	2	1
β-strand	161-163	3	2
β-strand	168-172	5	2
α-helix	173-174	2
α-helix	175-177	3
β-strand	191-194	4	3
β-strand	200-203	4	3
β-strand	206-210	5	3
β-strand	222-224	3	3
β-strand	230-240	11	3
β-strand	243-250	8	3
β-strand	257-259	3	3
α-helix	264	1
β-strand	265-266	2	3

Chain B: 10 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	337-339	3
α-helix	342-344	3
β-strand	345	1	4
β-strand	350-352	3	5
β-strand	361-363	3	5
β-strand	367-371	5	6
β-strand	379-383	5	6
β-strand	386-389	4	7
β-strand	395-404	10	7
β-strand	407-412	6	7
α-helix	413-415	3
β-strand	417-419	3	8
β-strand	425-430	6	6
β-strand	433-437	5	6
β-strand	441-449	9	8
β-strand	455-464	10	8
α-helix	466-468	3
β-strand	472	1	9
β-strand	482-489	8	10
β-strand	499-503	5	11
β-strand	508-509	2	12
β-strand	515-517	3	13
β-strand	520-523	4	13
β-strand	530-534	5	12
β-strand	542-544	3	12
β-strand	548-551	4	13
α-helix	555-557	3
β-strand	558-562	5	12
β-strand	568	1	4
β-strand	569-570	2	11
β-strand	577	1	14
β-strand	585-588	4	11
β-strand	593-600	8	10
α-helix	601-606	6
β-strand	607-609	3	15
β-strand	614-619	6	15
β-strand	625-631	7	9
β-strand	639-643	5	9
β-strand	647-652	6	15
β-strand	658-662	5	9
α-helix	666-667	2
β-strand	668-670	3	9
β-strand	671-672	2	16
α-helix	684-694	11
α-helix	696-734	39
α-helix	742-747	6

Chain C: 11 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	818-823	6	17
β-strand	830-834	5	18
β-strand	839	1	19
β-strand	842-863	22	18
β-strand	866-869	4	20
α-helix	871-873	3
β-strand	874-876	3	14
β-strand	892-897	6	14
β-strand	902	1	21
β-strand	907	1	21
β-strand	916-921	6	14
β-strand	922-925	4	20
β-strand	934-952	19	18
β-strand	955-962	8	18
β-strand	968-971	4	17
β-strand	974-978	5	17
β-strand	991-995	5	18
β-strand	998-1000	3	18
α-helix	1005-1006	2
β-strand	1018-1019	2	22
β-strand	1020	1	18
β-strand	1029-1030	2	22
β-strand	1035-1036	2	23
α-helix	1038-1040	3
β-strand	1048-1049	2	23
α-helix	1051-1053	3
α-helix	1054-1060	7
α-helix	1066-1068	3
α-helix	1071-1073	3
β-strand	1075-1077	3	18
β-strand	1082-1084	3	18
β-strand	1090-1096	7	17
α-helix	1099-1101	3
β-strand	1104	1	19
α-helix	1109-1110	2
β-strand	1112-1121	10	24
β-strand	1129-1136	8	24
β-strand	1141-1144	4	25
β-strand	1145-1147	3	26
β-strand	1152-1154	3	27
β-strand	1158-1161	4	25
β-strand	1166-1170	5	24
β-strand	1171-1173	3	27
β-strand	1179-1184	6	26
β-strand	1187-1192	6	26
β-strand	1202-1203	2	16
α-helix	1214-1216	3
α-helix	1220-1252	33

Chains D and H: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	87-89	3	84
β-strand	97-99	3	84
α-helix	100-102	3

Chain E: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	107-119	13
β-strand	121-125	5	28
β-strand	128-133	6	28
β-strand	134-136	3	29
β-strand	139-143	5	29
β-strand	149-150	2	28
β-strand	161-163	3	29
β-strand	168-172	5	29
α-helix	173-174	2
α-helix	175-177	3
β-strand	191-194	4	30
β-strand	200-203	4	30
β-strand	206-210	5	30
β-strand	222-224	3	30
β-strand	230-240	11	30
β-strand	243-250	8	30
β-strand	257-259	3	30
β-strand	265-266	2	30

Chain F: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	337-339	3
α-helix	341-344	4
β-strand	350-352	3	31
β-strand	361-363	3	31
β-strand	367-371	5	32
β-strand	379-389	11	32
β-strand	395-404	10	32
β-strand	407-412	6	32
α-helix	413-415	3
β-strand	417-419	3	33
β-strand	423	1	33
β-strand	425-437	13	32
β-strand	441-449	9	33
β-strand	455-464	10	33
β-strand	472	1	34
β-strand	482-489	8	35
β-strand	499-503	5	36
α-helix	504-507	4
β-strand	508-510	3	37
β-strand	514-517	4	38
β-strand	520-523	4	38
β-strand	530-534	5	37
β-strand	541-544	4	37
β-strand	548-551	4	38
α-helix	555-557	3
β-strand	558-562	5	37
β-strand	569-570	2	36
β-strand	577	1	39
β-strand	585-588	4	36
β-strand	593-600	8	35
α-helix	603-606	4
β-strand	607-609	3	40
β-strand	614-619	6	40
β-strand	625-631	7	34
β-strand	639-643	5	34
β-strand	647-652	6	40
β-strand	658-662	5	34
α-helix	666-667	2
β-strand	668-670	3	34
β-strand	671-672	2	41
α-helix	684-694	11
α-helix	696-734	39
α-helix	742-747	6

Chain G: 14 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	817-823	7	42
β-strand	830-834	5	43
β-strand	839	1	44
β-strand	842-855	14	43
β-strand	858-863	6	45
β-strand	866-869	4	46
α-helix	871-873	3
β-strand	874-876	3	39
α-helix	883-885	3
β-strand	892-897	6	39
β-strand	902	1	47
β-strand	907	1	47
β-strand	916-921	6	39
β-strand	922-925	4	46
β-strand	934-938	5	45
β-strand	942-952	11	43
β-strand	955-962	8	43
β-strand	969-971	3	42
β-strand	974-978	5	42
β-strand	991-995	5	45
β-strand	998-1000	3	45
α-helix	1005-1006	2
β-strand	1018-1019	2	48
β-strand	1020	1	45
β-strand	1029-1030	2	48
β-strand	1035-1036	2	49
α-helix	1038-1040	3
β-strand	1048-1049	2	49
α-helix	1051-1053	3
α-helix	1054-1061	8
α-helix	1066-1068	3
α-helix	1071-1073	3
α-helix	1074	1
β-strand	1075-1077	3	43
β-strand	1082-1084	3	43
β-strand	1090-1096	7	42
α-helix	1099-1101	3
β-strand	1104	1	44
α-helix	1109-1111	3
β-strand	1112-1121	10	50
β-strand	1122	1	51
β-strand	1129-1136	8	50
β-strand	1141-1144	4	52
β-strand	1145-1147	3	53
β-strand	1152-1154	3	54
β-strand	1158-1161	4	52
β-strand	1166-1170	5	50
β-strand	1171-1173	3	54
β-strand	1179-1184	6	53
β-strand	1187-1192	6	53
β-strand	1196	1	51
β-strand	1202-1203	2	41
α-helix	1206-1207	2
α-helix	1214-1216	3
α-helix	1220-1252	33

Chain I: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	107-119	13
β-strand	121-122	2	55
β-strand	123-124	2	56
β-strand	125	1	57
β-strand	128	1	57
β-strand	132-133	2	55
β-strand	134-136	3	58
β-strand	139-142	4	58
β-strand	149-150	2	56
α-helix	153-157	5
β-strand	161-163	3	58
β-strand	168-172	5	58
α-helix	173-174	2
α-helix	175-177	3
β-strand	191-195	5	59
β-strand	198-203	6	59
β-strand	206-210	5	59
β-strand	222-224	3	59
β-strand	230-240	11	59
β-strand	243-250	8	59
β-strand	257-259	3	59
β-strand	265-266	2	59

2 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
Capsid protein	A, E, I	protein	162	Semliki Forest virus	P03315 (AlphaFold model)
Spike glycoprotein E2	B, F, J	protein	418	Semliki Forest virus	P03315 (AlphaFold model)
Spike glycoprotein E1	C, G, K	protein	438	Semliki Forest virus	P03315 (AlphaFold model)
Very low-density lipoprotein receptor	D, H	protein	37	Semliki Forest virus	P98155 (AlphaFold model)

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

>8X0M_1 Capsid protein (chains A, E, I)
GKRERMCMKIENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSK
YDLECAQIPVHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFD
NKGRVVAIVLGGANEGSRTALSVVTWNKDMVTRVTPEGSEEW

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

>8X0M_2 Spike glycoprotein E2 (chains B, F, J)
SVSQHFNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSD
NHDYTKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRN
AVRACRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTL
LSQQSGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSP
FVPRADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLG
EDPQYHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYG
LYPAATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAP

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

>8X0M_3 Spike glycoprotein E1 (chains C, G, K)
YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYV
KCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHAS
AYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVY
KDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGF
KYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLT
CTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTAS
ASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAF
AIGAILVLVVVTCIGLRR

Sequence of entity 4 (D, H), FASTA

>8X0M_4 Very low-density lipoprotein receptor (chains D, H)
CRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENC

Ligands and cofactors

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

Primary citation

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(5-fold). Gao, F.G., Liu, S. To be published.

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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