9L99: Spike glycoprotein E1

Structure of Western equine encephalitis virus McMillan strain in complex with VLDLR LA1-2. Determined by electron microscopy at 3.6 Å resolution. Released 4 Jun 2025.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Western equine encephalitis virus, Homo sapiens
Chains: 5
Atoms: 12,710
Mol. weight: 181.14 kDa
Ligands: CA
Released: 4 Jun 2025

Explore 9L99 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L99 contains 36 α-helices and 156 β-strands across 5 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, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	8	1	2
β-strand	14-19	6	3
β-strand	24	1	4
β-strand	27-37	11	3
β-strand	41	1	5
β-strand	44-48	5	6
β-strand	51-54	4	7
α-helix	56-58	3
β-strand	59-61	3	8
β-strand	74	1	7
β-strand	78-80	3	8
β-strand	101-105	5	8
β-strand	107-110	4	7
α-helix	118	1
β-strand	119-123	5	6
β-strand	125	1	5
β-strand	130-137	8	3
β-strand	140-147	8	3
β-strand	176-180	5	6
β-strand	183-184	2	6
α-helix	189-191	3
β-strand	203-204	2	9
β-strand	205	1	6
β-strand	214-215	2	9
β-strand	220-221	2	10
β-strand	233-234	2	10
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
α-helix	259-262	4
β-strand	275	1	2
β-strand	278-281	4	1
α-helix	284-286	3
β-strand	289	1	4
β-strand	296-302	7	11
β-strand	307	1	12
β-strand	314-322	9	11
β-strand	326-329	4	13
β-strand	330-332	3	14
β-strand	337-339	3	11
β-strand	343-346	4	13
β-strand	353-358	6	11
β-strand	362	1	15
β-strand	365-369	5	14
β-strand	372-376	5	14
β-strand	379	1	15
β-strand	381	1	12
α-helix	382-383	2
β-strand	388	1	16
α-helix	404-410	7

Chain B: 7 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	9	1	17
β-strand	14-16	3	18
β-strand	25-27	3	18
β-strand	31-35	5	19
β-strand	42-51	10	19
β-strand	63-65	3	20
β-strand	77-79	3	20
β-strand	83-86	4	21
β-strand	90	1	21
β-strand	92-104	13	19
β-strand	110-115	6	21
β-strand	123-127	5	21
β-strand	148-155	8	22
β-strand	166-169	4	23
α-helix	170-173	4
β-strand	175	1	24
β-strand	180-182	3	25
β-strand	187-189	3	25
β-strand	197-202	6	24
β-strand	206-211	6	24
β-strand	215	1	25
α-helix	223-225	3
β-strand	226-230	5	24
β-strand	236	1	17
β-strand	237-238	2	23
β-strand	253-255	3	23
β-strand	261-268	8	22
α-helix	272-274	3
β-strand	275-279	5	26
β-strand	282-286	5	26
β-strand	293-299	7	27
β-strand	307-311	5	27
β-strand	317-319	3	26
β-strand	326-330	5	27
α-helix	334-335	2
β-strand	336-338	3	27
β-strand	339	1	16
α-helix	353-361	9
α-helix	366-369	4

Chain G: 10 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	28
β-strand	16-19	4	29
β-strand	24	1	30
β-strand	27-37	11	29
β-strand	41	1	31
β-strand	46-48	3	32
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	101-106	6	34
β-strand	107-110	4	33
β-strand	119-123	5	32
β-strand	125	1	31
β-strand	130-137	8	29
β-strand	140-147	8	29
β-strand	155	1	28
β-strand	160-163	4	28
β-strand	176-180	5	32
β-strand	183-185	3	32
α-helix	189-191	3
β-strand	203-204	2	35
β-strand	214-215	2	35
β-strand	220-221	2	36
α-helix	222-224	3
β-strand	233-234	2	36
α-helix	236-238	3
α-helix	239-245	7
α-helix	251-253	3
α-helix	256-258	3
β-strand	260	1	37
β-strand	269	1	37
β-strand	275-281	7	28
β-strand	289	1	30
α-helix	294-295	2
β-strand	296-303	8	38
β-strand	306-307	2	39
β-strand	308	1	38
β-strand	314-322	9	38
β-strand	326-329	4	40
β-strand	330-332	3	41
β-strand	337-339	3	38
β-strand	343-346	4	40
β-strand	351-358	8	38
β-strand	362	1	42
β-strand	367-369	3	41
β-strand	372-374	3	41
β-strand	379	1	42
β-strand	380-381	2	39
α-helix	382-383	2
β-strand	387-388	2	43
α-helix	404-410	7

Chain H: 6 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	44
β-strand	14-16	3	45
β-strand	25-27	3	45
β-strand	31-35	5	46
β-strand	42-51	10	46
β-strand	63	1	47
β-strand	64	1	46
β-strand	66-67	2	48
β-strand	75-76	2	48
β-strand	79	1	47
α-helix	80-82	3
β-strand	83-86	4	49
β-strand	90	1	49
β-strand	92-104	13	46
β-strand	110-115	6	49
β-strand	123-127	5	49
β-strand	148-155	8	50
β-strand	166-167	2	51
β-strand	168-169	2	52
α-helix	170-173	4
α-helix	177-179	3
β-strand	180-182	3	53
β-strand	187-189	3	53
β-strand	197-201	5	54
β-strand	207-211	5	54
β-strand	215-216	2	53
α-helix	223-225	3
β-strand	227-230	4	54
β-strand	236	1	44
β-strand	237-238	2	52
β-strand	254-255	2	51
β-strand	261-268	8	50
α-helix	271-274	4
β-strand	275-279	5	55
β-strand	282-286	5	55
β-strand	293-299	7	56
β-strand	307-311	5	56
β-strand	316-319	4	55
β-strand	326-330	5	56
α-helix	334-335	2
β-strand	336-338	3	56
β-strand	339-340	2	43

Chain N: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	37-39	3	57
β-strand	45-47	3	57
α-helix	48-50	3
β-strand	76-78	3	58
β-strand	84-86	3	58
α-helix	87-89	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike glycoprotein E1	A, G	protein	411	Western equine encephalitis virus	P13897
Spike glycoprotein E2	B, H	protein	369	Western equine encephalitis virus	P13897
Very low-density lipoprotein receptor	N	protein	80	Homo sapiens	P98155 (AlphaFold model)

Sequence of entity 1 (A, G), FASTA

>9L99_1 Spike glycoprotein E1 (chains A, G)
FEHATTVPNVPGIPYKALVERAGYAPLNLEITVVSSELTPSTNKEYVTCKFHTVIPSPQV
KCCGSLECKASSKADYTCRVFGGVYPFMWGGAQCFCDSENTQLSEAYVEFAPDCTIDHAV
ALKVHTAALKVGLRIVYGNTTAHLDTFVNGVTPGSSRDLKVIAGPISAAFSPFDHKVVIR
KGLVYNYDFPEYGAMKPGAFGDIQASSLDATDIVARTDIRLLKPSVKNIHVPYTQAVSGY
EMWKNNSGRPLQETAPFGCKIEVEPLRASNCAYGHIPISIDIPDAAFVRSSESPTILEVS
CTVADCIYSADFGGSLTLQYKADREGHCPVHSHSTTAVLKEATTHVTATGSITLHFSTSS
PQANFIVSLCGKKTTCNAECKPPADHIIGEPHKVDQEFQAAVSKTSWNWLL

Sequence of entity 2 (B, H), FASTA

>9L99_2 Spike glycoprotein E2 (chains B, H)
ITDDFTLTSPYLGFCPYCRHSAPCFSPIKIENVWDESDDGSIRIQVSAQFGYNQAGTADV
TKFRYMSYDHDHDIKEDSMEKIAISTSGPCRRLGHKGYFLLAQCPPGDSVTVSITSGASE
NSCTVEKKIRRKFVGREEYLFPPVQGKLVKCHVYDRLKETSAGYITMHRPGPHAYKSYLK
EASGEVYIKPPSGKNVTYECKCGDYSTGIVSTQTKMNGCTKARQCIAYKLDQTKWVFNSP
DLIRHTDHSVQGKLHIPFRLTPTVCPVPLAHTPTVTKWFKGITLHLTATRPTLLTTRKLG
LRADATAEWITGTTSRNFSVGREGLEYVWGNHEPVRVWAQESAPGDPHGWPHEIIIHYYH
RHPVYTVIV

Sequence of entity 3 (N), FASTA

>9L99_3 Very low-density lipoprotein receptor (chains N)
AKCEPSQFQCTNGRCITLLWKCDGDEDCVDGSDEKNCVKKTCAESDFVCNNGQCVPSRWK
CDGDPDCEDGSDESPEQCHM

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2

Primary citation

Structural basis for the recognition of two different types of receptors by Western equine encephalitis virus. Ma, B., Cao, Z., Ding, W. et al. Cell Rep (2025) 44:115724-115724. DOI 10.1016/j.celrep.2025.115724 · PubMed

Other PDB entries of the same protein (UniProt P13897), best resolution first:

9L3V 2.53 Å, structure of WEEV strain 71V1658 virus-like particle(3-fold region)
9DQY 2.8 Å, Structure of western equine encephalitis virus Imperial 181 VLP in complex with house…
9DQZ 2.9 Å, Structure of western equine encephalitis virus McMillan VLP in complex with human VLDLR
9L41 2.99 Å, Structure of WEEV strain 71V1658 virus-like particles (VLPs) in complex with human…
9UIO 3.03 Å, CryoEM structure of Western equine encephalitis virus California VLP in complex with…
9UIH 3.05 Å, CryoEM structure of Western equine encephalitis virus California VLP
9WSL 3.27 Å, CryoEM structure of Western equine encephalitis virus California VLP in complex with…
9DQV 3.3 Å, Structure of western equine encephalitis virus CBA87 VLP in complex with human PCDH10 EC1
9L1N 3.3 Å, Structure of Western equine encephalitis virus 71V1658 strain VLP in complex with human…
8DEE 3.4 Å, Asymmetric Unit of Western Equine Encephalitis Virus
9DQX 3.4 Å, Structure of western equine encephalitis virus CBA87 VLP
8SQN 3.89 Å, CryoEM structure of Western equine encephalitis virus VLP in complex with the chimeric…

Browse structure collections

About this viewer

MolViewer shows 9L99 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.