9EAU: RRV DKTA VLP

RRV DKTA VLP in complex with VLDLR-LBD-Fc. Determined by electron microscopy at 3.06 Å resolution. Released 23 Apr 2025.

Method: Electron microscopy
Resolution: 3.06 Å
Organisms: Ross river virus (STRAIN T48), Homo sapiens
Chains: 14
Atoms: 31,779
Mol. weight: 453.72 kDa
Ligands: CA
Released: 23 Apr 2025

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

Secondary structure: helices and β-sheets

9EAU contains 120 α-helices and 370 β-strands across 14 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	11	1	2
β-strand	14-19	6	2
β-strand	24	1	3
β-strand	27-48	22	2
β-strand	51-54	4	4
α-helix	56-58	3
β-strand	59-61	3	5
β-strand	77-82	6	5
β-strand	87-88	2	6
β-strand	91-92	2	6
β-strand	101-106	6	5
β-strand	107-110	4	4
β-strand	119-137	19	2
β-strand	140-147	8	2
β-strand	153-157	5	1
β-strand	159-163	5	1
β-strand	176-180	5	2
β-strand	183-186	4	2
α-helix	189-191	3
β-strand	203-204	2	7
β-strand	205	1	2
β-strand	214-215	2	7
β-strand	220-221	2	8
α-helix	223-225	3
β-strand	233-234	2	8
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	2
β-strand	267-269	3	2
β-strand	275-281	7	1
β-strand	289	1	3
β-strand	297-306	10	9
β-strand	307	1	10
β-strand	314-321	8	9
β-strand	326-329	4	11
β-strand	330-332	3	12
β-strand	337-339	3	9
β-strand	343-346	4	11
β-strand	351-358	8	9
β-strand	366-369	4	12
β-strand	372-375	4	12
β-strand	381	1	10
α-helix	382-383	2
β-strand	387-388	2	13
α-helix	399-401	3
α-helix	405-437	33

Chain B: 11 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
α-helix	7-11	5
β-strand	12	1	14
β-strand	19	1	15
β-strand	28	1	15
β-strand	34-38	5	16
β-strand	45-56	12	16
β-strand	62-70	9	16
β-strand	75-79	5	16
α-helix	80-82	3
β-strand	84-86	3	17
β-strand	90	1	17
α-helix	91	1
β-strand	92-104	13	16
β-strand	108-116	9	17
β-strand	122-131	10	17
α-helix	133-135	3
β-strand	139	1	18
β-strand	149-156	8	19
β-strand	166-170	5	20
α-helix	171-173	3
β-strand	175-176	2	21
β-strand	181-184	4	22
β-strand	187-190	4	22
β-strand	197-201	5	21
β-strand	208-210	3	21
β-strand	215-217	3	22
β-strand	225-229	5	21
β-strand	235	1	14
β-strand	236-237	2	20
β-strand	252-255	4	20
β-strand	260-267	8	19
α-helix	270-273	4
β-strand	274-278	5	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	13
α-helix	351-361	11
α-helix	363-401	39
α-helix	411-414	4

Chain C: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	112-120	9
β-strand	123-126	4	24
β-strand	129-133	5	24
β-strand	135-137	3	25
β-strand	140-142	3	25
β-strand	143-144	2	26
β-strand	150-151	2	24
β-strand	162-164	3	26
β-strand	169-171	3	26
β-strand	173	1	25
α-helix	174-175	2
α-helix	178-180	3
β-strand	183	1	25
α-helix	184	1
β-strand	185	1	27
β-strand	192-196	5	27
β-strand	199-204	6	27
β-strand	207-211	5	27
β-strand	220	1	24
β-strand	223-225	3	27
β-strand	231-241	11	27
β-strand	244-251	8	27
β-strand	252	1	28
β-strand	257	1	28
β-strand	260	1	27
β-strand	266	1	27

Chain E: 11 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	29
β-strand	11	1	30
β-strand	15-19	5	30
β-strand	24	1	31
β-strand	27-48	22	30
β-strand	51-54	4	32
α-helix	56-58	3
β-strand	59-61	3	33
β-strand	77-82	6	33
β-strand	87-88	2	34
β-strand	91-92	2	34
β-strand	101-106	6	33
β-strand	107-110	4	32
β-strand	119-137	19	30
β-strand	140-147	8	30
β-strand	152	1	35
β-strand	153-156	4	29
β-strand	159-163	5	29
β-strand	176-180	5	30
β-strand	183-186	4	30
α-helix	189-191	3
β-strand	203-205	3	30
β-strand	213-215	3	30
β-strand	220-221	2	36
α-helix	223-225	3
β-strand	233-234	2	36
α-helix	236-238	3
α-helix	239-246	8
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	30
β-strand	267-269	3	30
β-strand	275-281	7	29
α-helix	284-286	3
β-strand	289	1	31
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	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
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 F: 12 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
α-helix	7-11	5
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	45-56	12	44
β-strand	62-70	9	44
β-strand	75-79	5	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
α-helix	133-135	3
β-strand	139	1	46
β-strand	149-156	8	47
β-strand	166-170	5	48
α-helix	171-173	3
β-strand	175-176	2	49
β-strand	181-184	4	50
β-strand	187-190	4	50
β-strand	197-200	4	49
β-strand	208-210	3	49
β-strand	214	1	50
β-strand	226-229	4	49
β-strand	235	1	42
β-strand	236-237	2	48
α-helix	249-250	2
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	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	351-360	10
α-helix	363-401	39
α-helix	409-414	6

Chain G: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	113-120	8
β-strand	121-126	6	52
β-strand	129-137	9	52
β-strand	140-144	5	52
β-strand	150-151	2	52
α-helix	154-157	4
β-strand	162-164	3	52
β-strand	169-173	5	52
α-helix	174-175	2
α-helix	176-180	5
α-helix	182	1
β-strand	183	1	52
α-helix	184	1
β-strand	185	1	53
β-strand	192-195	4	53
β-strand	201-204	4	53
β-strand	207-209	3	53
α-helix	222	1
β-strand	223-225	3	53
β-strand	231-239	9	53
β-strand	241	1	54
β-strand	243	1	54
β-strand	246-252	7	53
β-strand	257-260	4	53
β-strand	265-267	3	53

Chain I: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	55
β-strand	14-19	6	56
β-strand	24	1	57
β-strand	27-48	22	56
β-strand	51-54	4	58
α-helix	56-58	3
β-strand	61	1	59
β-strand	77-82	6	59
β-strand	87-88	2	60
β-strand	91-92	2	60
β-strand	101-106	6	59
β-strand	107-110	4	58
β-strand	119-137	19	56
β-strand	140-147	8	56
β-strand	153-156	4	55
β-strand	159-163	5	55
β-strand	176-180	5	56
β-strand	183-186	4	56
α-helix	189-191	3
β-strand	203-205	3	56
β-strand	213-215	3	56
β-strand	220-221	2	61
α-helix	223-225	3
β-strand	233-234	2	61
α-helix	239-246	8
α-helix	251-253	3
α-helix	256-258	3
β-strand	260-262	3	56
β-strand	267-269	3	56
β-strand	275-281	7	55
α-helix	284-286	3
β-strand	289	1	57
β-strand	297-306	10	62
β-strand	307	1	63
β-strand	314-321	8	62
β-strand	326-329	4	64
β-strand	330-332	3	65
β-strand	337-339	3	62
β-strand	343-346	4	64
β-strand	351-358	8	62
β-strand	364-369	6	65
β-strand	372-377	6	65
β-strand	381	1	63
α-helix	382-383	2
β-strand	387-388	2	66
α-helix	399-401	3
α-helix	405-437	33

Chain J: 14 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
α-helix	6-11	6
β-strand	12	1	67
β-strand	17-19	3	68
β-strand	28-30	3	68
β-strand	34-38	5	69
β-strand	46-56	11	69
β-strand	62-71	10	69
β-strand	74-79	6	69
α-helix	80-82	3
β-strand	84-86	3	70
β-strand	90	1	70
α-helix	91	1
β-strand	92-104	13	69
α-helix	105-106	2
β-strand	108-116	9	70
β-strand	122-131	10	70
α-helix	133-135	3
β-strand	139	1	71
β-strand	149-156	8	72
β-strand	166-170	5	73
α-helix	171-173	3
β-strand	175-176	2	74
α-helix	178-180	3
β-strand	181-184	4	75
β-strand	187-190	4	75
β-strand	196	1	76
β-strand	197-199	3	74
β-strand	211	1	76
β-strand	214	1	75
β-strand	227-229	3	74
β-strand	235	1	67
β-strand	236-237	2	73
α-helix	249-250	2
β-strand	252-255	4	73
β-strand	260-267	8	72
α-helix	270-273	4
β-strand	276-278	3	77
β-strand	281-286	6	77
β-strand	292-298	7	71
β-strand	306-310	5	71
β-strand	314-319	6	77
β-strand	325-329	5	71
α-helix	333-334	2
β-strand	335-337	3	71
β-strand	338-339	2	66
α-helix	351-360	10
α-helix	363-401	39
α-helix	409-414	6

6 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 E1	A, E, I, M	protein	438	Ross river virus (STRAIN T48)	C9DZM3
Spike glycoprotein E2	B, F, J, N	protein	419	Ross river virus (STRAIN T48)	Q076B2
Capsid protein	C, G, K, O	protein	158	Ross river virus (STRAIN T48)	P08491
Very low-density lipoprotein receptor	Y, Z	protein	39	Homo sapiens	P98155 (AlphaFold model)

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

>9EAU_1 Spike glycoprotein E1 (chains A, E, I, M)
YEHTATIPNVVGFPYKAHIERNGFSPMTLQLEVVETSLEPTLNLEYITCEYKTVVPSPFI
KCCGTSECSSKEQPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCKHDHAS
AYKAHTASLKATIRISYGTINQTTEAFVNGEHAVNVGGSKFIFGPISTAWSPFDNKIVVY
KDDVYNQDFPPYGSGQPGRFGDIQSRTVESKDLYANTALKLSRPSPGVVHVPYTQTPSGF
KYWLKEKGSSLNTKAPFGCKIKTNPVRAMDCAVGSIPVSMDIPDSAFTRVVDAPAVTDLS
CQVVVCTHSSDFGGVATLSYKTDKPGDCAVHSHSNVATLQEATVKVKTAGKVTVHFSTAS
ASPAFKVSVCDAKTTCTAACEPPKDHIVPYGASHNNQVFPDMSGTAMTWVQRLASGLGGL
ALIAVVVLVLVTCITMRR

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

>9EAU_2 Spike glycoprotein E2 (chains B, F, J, N)
SVTEHFNVYKATRPYLAYCADCGDGYFCYSPVAIEKIRDEASDGMLKIQVSAQIGLDKAG
THAHTKIRYMAGHDVQESKRDSLRVYTSAACSIHGTMGHFIVAHCPPGDYLKVSFEDADS
HVKACKVQYKHDPLPVGREKFVVRPHFGVELPCTSYQLTTAPTDEEIDMHTPPDIPDRTL
LSQTAGNVKITAGGRTIRYNCTCGRDNVGTTSTDKTINTCKIDQCHAAVTSHDKWQFTSP
FVPRADQTARRGKVHVPFPLTNVTCRVPLARAPDVTYGKKEVTLRLHPDHPTLFSYRSLG
AEPHPYEEWVDKFSERIIPVTEEGIEYQWGNNPPVRLWAQLTTEGKPHGWPHEIIQYYYG
LYPAATIAAVSGASLMALLTLAATCCMLATARRKCLTPYALTPGAVVPLTLGLLCCAPR

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

>9EAU_3 Capsid protein (chains C, G, K, O)
RMCMKIENDCIFEVKLDGKVTGYACLVGDKVMKPAHVKGTIDNPDLAKLTYKKSSKYDLE
CAQIPVHMKSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGR
VVAIVLGGANEGARTALSVVTWTKDMVTRVTPEGTEEW

Sequence of entity 4 (Y, Z), FASTA

>9EAU_4 Very low-density lipoprotein receptor (chains Y, Z)
RTCRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENC

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Primary citation

Structural basis for plasticity in receptor engagement by an encephalitic alphavirus. Raju, S., Palakurty, S., Sariol, A. et al. Cell (2025) 188:2943. DOI 10.1016/j.cell.2025.02.036 · PubMed

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