9KQR: Mature Semliki Forest Virus

Cryo-EM Structure of Mature Semliki Forest Virus. Determined by electron microscopy at 3.73 Å resolution. Released 22 Oct 2025.

Method: Electron microscopy
Resolution: 3.73 Å
Organism: Semliki Forest virus
Chains: 12
Atoms: 31,424
Mol. weight: 497.12 kDa
Released: 22 Oct 2025

Explore 9KQR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KQR contains 93 α-helices and 393 β-strands across 12 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: 11 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	62
β-strand	11	1	63
β-strand	15-19	5	63
β-strand	24	1	64
β-strand	27-38	12	63
α-helix	39-41	3
β-strand	44-48	5	65
β-strand	51-54	4	66
α-helix	56-58	3
β-strand	59-61	3	67
β-strand	77-80	4	67
β-strand	101-106	6	67
β-strand	107-110	4	66
β-strand	119-122	4	65
β-strand	129-136	8	63
β-strand	142-146	5	63
β-strand	153-155	3	62
β-strand	160-163	4	62
β-strand	178-179	2	65
β-strand	184-185	2	65
α-helix	189-191	3
β-strand	192	1	32
β-strand	204	1	68
β-strand	205	1	65
β-strand	214	1	68
β-strand	221	1	69
α-helix	223-225	3
β-strand	233	1	69
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	63
β-strand	267-269	3	63
β-strand	275-281	7	62
α-helix	284-286	3
β-strand	289	1	64
α-helix	294-295	2
β-strand	296-306	11	70
β-strand	307	1	71
β-strand	314-322	9	70
β-strand	326-329	4	72
β-strand	330-332	3	73
β-strand	337-339	3	74
β-strand	343-346	4	72
β-strand	352-355	4	70
β-strand	356-358	3	74
β-strand	364-369	6	73
β-strand	374-377	4	73
β-strand	381	1	71
α-helix	400-401	2
α-helix	405-436	32

Chain b: 10 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	9-11	3
β-strand	12	1	40
β-strand	34-36	3	41
β-strand	46	1	42
β-strand	49-57	9	41
β-strand	61-68	8	41
β-strand	70-71	2	43
β-strand	74-75	2	43
β-strand	78-79	2	41
α-helix	80-82	3
β-strand	86-87	2	44
β-strand	95-102	8	41
β-strand	103	1	42
β-strand	110-115	6	44
β-strand	123-128	6	44
β-strand	149-152	4	45
β-strand	155-156	2	46
β-strand	166-167	2	47
β-strand	170	1	48
β-strand	176	1	49
β-strand	181-183	3	50
β-strand	188-190	3	50
β-strand	198-200	3	49
β-strand	208-209	2	49
α-helix	222-224	3
β-strand	227-228	2	49
β-strand	235	1	40
β-strand	236	1	48
β-strand	254-255	2	47
α-helix	256	1
β-strand	260-261	2	46
β-strand	264-267	4	45
α-helix	268-273	6
β-strand	276-278	3	51
β-strand	281-283	3	51
β-strand	292-295	4	52
β-strand	296	1	53
β-strand	307-310	4	52
β-strand	317-319	3	51
β-strand	327	1	53
α-helix	333-334	2
β-strand	335	1	53
α-helix	351-358	8
α-helix	363-396	34
α-helix	407-409	3

Chain c: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	112-116	5
β-strand	123-125	3	54
β-strand	128-131	4	54
β-strand	134-136	3	55
β-strand	139-141	3	55
β-strand	143	1	56
β-strand	149	1	54
α-helix	153-156	4
β-strand	168	1	56
β-strand	184	1	57
β-strand	192-194	3	57
β-strand	199-201	3	57
β-strand	203	1	58
β-strand	206	1	58
β-strand	208-209	2	59
β-strand	224-225	2	57
β-strand	229-230	2	57
β-strand	233-234	2	60
β-strand	236-237	2	61
β-strand	238-239	2	59
β-strand	244-245	2	59
β-strand	248-249	2	60
β-strand	258-259	2	60
β-strand	265-266	2	61

Chain d: 11 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	96
β-strand	15-19	5	97
β-strand	24-25	2	98
β-strand	27-38	12	97
α-helix	39-41	3
β-strand	44-48	5	99
β-strand	51-54	4	100
α-helix	56-58	3
β-strand	59	1	101
β-strand	77-80	4	101
β-strand	103-106	4	101
β-strand	107-110	4	100
β-strand	119-122	4	99
β-strand	129-136	8	97
β-strand	142-146	5	97
β-strand	153-155	3	96
β-strand	160-163	4	96
β-strand	178-179	2	102
β-strand	184-185	2	102
α-helix	189-191	3
α-helix	195-196	2
β-strand	204	1	103
β-strand	205	1	99
β-strand	214	1	103
β-strand	221	1	104
α-helix	223-225	3
β-strand	233	1	104
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	97
β-strand	267-269	3	97
β-strand	275-281	7	96
β-strand	288-289	2	98
α-helix	290-292	3
α-helix	294-295	2
β-strand	296-306	11	105
β-strand	307	1	106
β-strand	314-322	9	105
β-strand	326-329	4	107
β-strand	330-332	3	108
β-strand	337-339	3	109
β-strand	343-346	4	107
β-strand	352-355	4	105
β-strand	356-358	3	109
β-strand	364-369	6	108
β-strand	374-377	4	108
β-strand	381	1	106
β-strand	388	1	89
α-helix	405-436	32

Chain e: 11 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	9-11	3
β-strand	12	1	75
β-strand	34-36	3	76
β-strand	46	1	77
β-strand	49-56	8	76
β-strand	62-68	7	76
β-strand	70-71	2	78
β-strand	74-75	2	78
β-strand	78-79	2	76
α-helix	80-82	3
β-strand	86	1	79
β-strand	96-101	6	76
β-strand	103	1	77
β-strand	110-115	6	79
β-strand	123-128	6	79
β-strand	139	1	80
β-strand	148-156	9	81
β-strand	166	1	82
β-strand	170	1	83
β-strand	176	1	84
β-strand	181-183	3	85
β-strand	188-190	3	85
β-strand	198-200	3	84
β-strand	208-210	3	84
α-helix	222-224	3
β-strand	227-228	2	84
β-strand	235	1	75
β-strand	236	1	83
α-helix	254	1
β-strand	255	1	82
α-helix	256	1
β-strand	260-268	9	81
α-helix	270-273	4
β-strand	274	1	86
β-strand	277-278	2	87
β-strand	281-283	3	87
β-strand	285	1	86
β-strand	292-294	3	80
β-strand	296-298	3	88
β-strand	308-310	3	80
β-strand	317-319	3	87
β-strand	325-327	3	88
α-helix	333-334	2
β-strand	335-336	2	88
β-strand	338	1	89
α-helix	351-358	8
α-helix	363-399	37
α-helix	407-409	3

Chain f: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	112-116	5
β-strand	123-125	3	90
β-strand	128-131	4	90
β-strand	134-136	3	91
β-strand	139-141	3	91
β-strand	143	1	92
β-strand	149	1	90
α-helix	153-156	4
β-strand	168	1	92
β-strand	192-194	3	93
β-strand	199-203	5	93
β-strand	206-209	4	93
β-strand	224	1	93
β-strand	230	1	93
β-strand	233-234	2	94
β-strand	236-237	2	95
β-strand	238-239	2	93
β-strand	244-245	2	93
β-strand	248-249	2	94
β-strand	259	1	94
α-helix	264	1
β-strand	265-266	2	95

Chain g: 8 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	130
β-strand	11	1	131
β-strand	15-19	5	131
β-strand	24	1	132
β-strand	27-38	12	131
β-strand	47-48	2	133
β-strand	51-54	4	134
α-helix	56-58	3
β-strand	59	1	120
β-strand	60-61	2	135
β-strand	77-80	4	136
β-strand	101-102	2	135
β-strand	103-106	4	136
β-strand	107-110	4	134
β-strand	119-120	2	133
β-strand	129-136	8	131
β-strand	142-146	5	131
β-strand	153-155	3	130
β-strand	160-163	4	130
β-strand	178-179	2	133
β-strand	184-185	2	133
α-helix	189-191	3
β-strand	204	1	137
β-strand	205	1	133
β-strand	214	1	137
β-strand	220-221	2	138
α-helix	223-225	3
β-strand	233-234	2	138
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	131
β-strand	267-269	3	131
β-strand	275-281	7	130
β-strand	289	1	132
α-helix	294-295	2
β-strand	296-306	11	139
β-strand	307	1	140
β-strand	314-322	9	139
β-strand	326-329	4	141
β-strand	330-332	3	142
β-strand	337-339	3	139
β-strand	343-346	4	141
β-strand	351-358	8	139
β-strand	364-369	6	142
β-strand	372-377	6	142
β-strand	381	1	140
β-strand	388	1	123
α-helix	405-436	32

Chain h: 11 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	9-11	3
β-strand	34-36	3	110
β-strand	46	1	111
β-strand	49-56	8	110
β-strand	62-71	10	110
β-strand	74-79	6	110
α-helix	80-82	3
β-strand	86-87	2	112
β-strand	97-100	4	110
β-strand	103	1	111
β-strand	110-116	7	112
β-strand	122-128	7	112
β-strand	139	1	113
β-strand	149-156	8	114
β-strand	166-167	2	115
β-strand	170	1	116
β-strand	176	1	117
α-helix	178-180	3
β-strand	181-183	3	118
β-strand	187	1	119
β-strand	188-190	3	118
β-strand	198-200	3	117
β-strand	208-210	3	117
β-strand	218	1	119
α-helix	222-224	3
β-strand	228	1	117
β-strand	236	1	116
β-strand	244	1	120
β-strand	254-255	2	115
α-helix	256	1
β-strand	260-267	8	114
α-helix	268-273	6
β-strand	274-278	5	121
β-strand	281-285	5	121
β-strand	292-295	4	113
β-strand	296-297	2	122
β-strand	307-310	4	113
β-strand	317-319	3	121
β-strand	326-327	2	122
α-helix	333-334	2
β-strand	335-336	2	122
β-strand	338	1	123
α-helix	351-358	8
α-helix	363-399	37
α-helix	411-414	4

4 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
Envelope glycoprotein E2	b, e, h, k	protein	422	Semliki Forest virus	P0DJZ6
Capsid protein	c, f, i, l	protein	267	Semliki Forest virus	P0DJZ6
Spike glycoprotein E1	a, d, g, j	protein	438	Semliki Forest virus	P03315 (AlphaFold model)

Sequence of entity 1 (b, e, h, k), FASTA

>9KQR_1 Envelope glycoprotein E2 (chains b, e, h, k)
SVSQHFNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSD
NHDYTKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRN
AVRACRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAETVEEIDMHMPPDTPDRTL
LSQQSGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSP
FVPRADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLG
EDPQYHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYG
LYPAATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAPRA
HA

Sequence of entity 2 (c, f, i, l), FASTA

>9KQR_2 Capsid protein (chains c, f, i, l)
MNYIPTQTFYGRRWRPRPAARPWPLQATPVAPVVPDFQAQQMQQLISAVNALTMRQNAIA
PARPPKPKKKKTTKPKPKTQPKKINGKTQQQKKKDKQADKKKKKPGKRERMCMKIENDCI
FEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKYDLECAQIPVHMRSD
ASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANE
GSRTALSVVTWNKDMVTRVTPEGSEEW

Sequence of entity 3 (a, d, g, j), FASTA

>9KQR_3 Spike glycoprotein E1 (chains a, d, g, j)
YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYV
KCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHAS
AYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVY
KDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGF
KYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLT
CTVATCTHSSDFGGVLTLTYKTNKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTAS
ASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAF
AIGAILVLVVVTCIGLRR

Primary citation

Structural study of Semliki Forest virus through Cryo-EM. Jia, X., Li, S., Yu, H. et al. Dian Zi Xian Wei Xue Bao (2025) 44:1. DOI 10.3969/j.issn.1000-6281.2025.01.03

Other PDB entries of the same protein (UniProt P0DJZ6), best resolution first:

9RBQ 2.7 Å, Semliki Forest virus trimer 1 in complex with ApoER2 LA5
9RBR 2.7 Å, Semliki Forest virus trimer 2 in complex with ApoER2 LA5

Browse structure collections

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