9RBQ: Semliki Forest virus trimer 1

Name: PDB 9RBQ: Semliki Forest virus trimer 1 in complex with ApoER2 LA5
Published: 2026-01-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Semliki Forest virus trimer 1 in complex with ApoER2 LA5. Determined by electron microscopy at 2.7 Å resolution. Released 14 Jan 2026.

Method: Electron microscopy
Resolution: 2.7 Å
Organisms: Homo sapiens, Mus musculus, Semliki Forest virus
Chains: 13
Atoms: 25,585
Mol. weight: 434.96 kDa
Ligands: CA
Released: 14 Jan 2026

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

Secondary structure: helices and β-sheets

9RBQ contains 99 α-helices and 280 β-strands across 13 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: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	210-212	3	1
β-strand	221-223	3	1
α-helix	224-226	3
α-helix	242-245	4

Chain D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	2
β-strand	14-16	3	2
α-helix	24	1
α-helix	32-41	10
α-helix	48-55	8

Chain E: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	3
β-strand	14-17	4	3
α-helix	27-30	4
α-helix	32-41	10
α-helix	48-55	8

Chain F: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	4
β-strand	16-17	2	4
α-helix	27-30	4
α-helix	32-41	10
α-helix	49-55	7

Chain G: 13 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	5
β-strand	11	1	6
β-strand	15-19	5	6
β-strand	24-25	2	7
β-strand	27-48	22	6
β-strand	51-54	4	8
α-helix	56-58	3
β-strand	59-61	3	9
β-strand	77-84	8	9
β-strand	87	1	10
β-strand	92	1	10
β-strand	100-106	7	9
β-strand	107-110	4	8
β-strand	119-137	19	6
β-strand	140-147	8	6
β-strand	153-156	4	5
β-strand	159-163	5	5
α-helix	164-166	3
β-strand	176-180	5	6
β-strand	183-185	3	6
α-helix	189-191	3
β-strand	203-205	3	6
β-strand	213-215	3	6
β-strand	220-221	2	11
α-helix	223-225	3
β-strand	233-234	2	11
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	6
β-strand	267-269	3	6
β-strand	275-281	7	5
α-helix	284-286	3
β-strand	288-289	2	7
β-strand	297-306	10	12
β-strand	307	1	13
β-strand	314-321	8	12
β-strand	326-329	4	14
β-strand	330-332	3	15
β-strand	337-339	3	12
β-strand	343-346	4	14
β-strand	351-358	8	12
β-strand	364-369	6	15
β-strand	372-377	6	15
α-helix	380	1
β-strand	381	1	13
α-helix	382-383	2
β-strand	387-388	2	16
α-helix	399-401	3
α-helix	405-437	33

Chain H: 12 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	17
β-strand	11	1	18
β-strand	15-19	5	18
β-strand	24-25	2	19
β-strand	27-48	22	18
β-strand	51-54	4	20
α-helix	56-58	3
β-strand	59-61	3	21
β-strand	77-82	6	21
β-strand	87	1	22
β-strand	92	1	22
β-strand	101-106	6	21
β-strand	107-110	4	20
β-strand	119-137	19	18
β-strand	140-147	8	18
β-strand	154-156	3	17
β-strand	159-163	5	17
β-strand	176-180	5	18
β-strand	183-185	3	18
α-helix	189-191	3
β-strand	203-204	2	23
β-strand	205	1	18
β-strand	214-215	2	23
β-strand	220-221	2	24
α-helix	223-225	3
β-strand	233-234	2	24
α-helix	236-238	3
α-helix	239-246	8
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	18
β-strand	267-269	3	18
β-strand	275-281	7	17
β-strand	288-289	2	19
α-helix	294-295	2
β-strand	296-306	11	25
β-strand	307	1	26
β-strand	314-322	9	25
β-strand	326-329	4	27
β-strand	330-332	3	28
β-strand	337-339	3	25
β-strand	343-346	4	27
β-strand	352-358	7	25
β-strand	364-369	6	28
β-strand	372-377	6	28
α-helix	380	1
β-strand	381	1	26
α-helix	382-383	2
β-strand	387-388	2	29
α-helix	399-401	3
α-helix	405-437	33

Chain I: 12 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	30
β-strand	11	1	31
β-strand	15-19	5	31
β-strand	24	1	32
β-strand	27-48	22	31
β-strand	51-54	4	33
α-helix	56-58	3
β-strand	59-61	3	34
β-strand	77-82	6	34
β-strand	87-88	2	35
β-strand	91-92	2	35
β-strand	101-106	6	34
β-strand	107-110	4	33
β-strand	119-137	19	31
β-strand	140-147	8	31
β-strand	153-156	4	30
β-strand	159-163	5	30
β-strand	176-180	5	31
β-strand	183-185	3	31
α-helix	189-191	3
β-strand	203-205	3	31
β-strand	213-215	3	31
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	251-254	4
α-helix	256-258	3
β-strand	260-262	3	31
β-strand	267-269	3	31
β-strand	275-281	7	30
α-helix	284-286	3
β-strand	289	1	32
β-strand	296-306	11	37
β-strand	307	1	38
β-strand	314-322	9	37
β-strand	326-329	4	39
β-strand	330-332	3	40
β-strand	337-339	3	37
β-strand	343-346	4	39
β-strand	351-358	8	37
β-strand	364-369	6	40
β-strand	372-377	6	40
α-helix	380	1
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 J: 12 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	6-11	6
β-strand	12	1	42
β-strand	17-19	3	43
β-strand	28-30	3	43
β-strand	34-38	5	44
β-strand	46-56	11	44
β-strand	62-71	10	44
β-strand	74-79	6	44
α-helix	80-82	3
β-strand	84-86	3	45
β-strand	90	1	45
α-helix	91	1
β-strand	92-104	13	44
β-strand	108-116	9	45
β-strand	122-131	10	45
β-strand	139	1	46
β-strand	149-156	8	47
β-strand	166-170	5	48
β-strand	175-176	2	49
α-helix	178-180	3
β-strand	181-184	4	50
β-strand	187-190	4	50
β-strand	197-201	5	49
β-strand	208-211	4	49
β-strand	215-218	4	50
α-helix	222-224	3
β-strand	225-229	5	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	274-278	5	51
β-strand	281-286	6	51
β-strand	292-298	7	46
β-strand	305-310	6	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	16
α-helix	351-361	11
α-helix	366-401	36
α-helix	406-408	3
α-helix	409-413	5

5 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
LDL receptor related protein 8,Ig gamma-2A chain C region, A allele	A	protein	301	Homo sapiens, Mus musculus	E9PKG2 (AlphaFold model), P01863 (AlphaFold model)
Protein E3	D, E, F	protein	66	Semliki Forest virus	P0DJZ6
Structural polyprotein	G, H, I	protein	438	Semliki Forest virus	A0A0F6PP03
Envelope glycoprotein E2	J, K, L	protein	422	Semliki Forest virus	P0DJZ6
Capsid protein	M, N, O	protein	267	Semliki Forest virus	P0DJZ6

Sequence of entity 1 (A), FASTA

>9RBQ_1 LDL receptor related protein 8,Ig gamma-2A chain C region, A allele (chains A)
GSADPACGPREFRCGGDGGGACIPERWVCDRQFDCEDRSDEAAELCGRPGPGATSAPAAG
SLEVLFQGPPRGPTIKPCPPCKCPAPNLLGGPSVFIFPPKIKDVLMISLSPIVTCVVVDV
SEDDPDVQISWFVNNVEVHTAQTQTHREDYNSTLRVVSALPIQHQDWMSGKEFKCKVNNK
DLPAPIERTISKPKGSVRAPQVYVLPPPEEEMTKKQVTLTCMVTDFMPEDIYVEWTNNGK
TELNYKNTEPVLDSDGSYFMYSKLRVEKKNWVERNSYSCSVVHEGLHNHHTTKSFSRTPG
K

Sequence of entity 2 (D, E, F), FASTA

>9RBQ_2 Protein E3 (chains D, E, F)
SAPLITAMCVLANATFPCFQPPCVPCCYENNAEATLRMLEDNVDRPGYYDLLQAALTCRN
GTRHRR

Sequence of entity 3 (G, H, I), FASTA

>9RBQ_3 Structural polyprotein (chains G, H, I)
YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYV
KCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHAS
AYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVY
KDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGF
KYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLT
CTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTAS
ASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAF
AIGAILVLVVVTCIGLRR

Sequence of entity 4 (J, K, L), FASTA

>9RBQ_4 Envelope glycoprotein E2 (chains J, K, L)
SVSQHFNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSD
NHDYTKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRN
AVRACRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTL
LSQQSGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSP
FVPRADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLG
EDPQYHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYG
LYPAATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAPRA
HA

Sequence of entity 5 (M, N, O), FASTA

>9RBQ_5 Capsid protein (chains M, N, O)
MNYIPTQTFYGRRWRPRPAARPWPLQATPVAPVVPDFQAQQMQQLISAVNALTMRQNAIA
PARPPKPKKKKTTKPKPKTQPKKINGKTQQQKKKDKQADKKKKKPGKRERMCMKIENDCI
FEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKYDLECAQIPVHMRSD
ASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANE
GSRTALSVVTWNKDMVTRVTPEGSEEW

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Primary citation

Molecular basis of ApoER2-mediated Semliki Forest virus entry. Du, B., Song, X., Zhao, B. et al. Nat Commun (2025) 17:845-845. DOI 10.1038/s41467-025-67550-6 · PubMed

Browse structure collections

About this viewer

MolViewer shows 9RBQ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.