8UFB: Eastern equine encephalitis virus (PE-6) VLP

Eastern equine encephalitis virus (PE-6) VLP in complex with full-length VLDLR (asymmetric unit). Determined by electron microscopy at 3.89 Å resolution. Released 17 Jan 2024.

Method: Electron microscopy
Resolution: 3.89 Å
Organisms: Eastern equine encephalitis virus, Homo sapiens
Chains: 20
Atoms: 34,656
Mol. weight: 1109.66 kDa
Ligands: CA, NAG
Released: 17 Jan 2024

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

Secondary structure: helices and β-sheets

8UFB contains 143 α-helices and 382 β-strands across 20 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: 15 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	15-19	5	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
α-helix	112-115	4
β-strand	119-137	19	2
β-strand	140-148	9	2
β-strand	155-157	3	1
β-strand	160-164	5	1
α-helix	165-167	3
β-strand	177-181	5	2
β-strand	184-186	3	2
α-helix	190-192	3
α-helix	196-197	2
α-helix	201-203	3
β-strand	204-206	3	2
β-strand	214-216	3	2
β-strand	221-222	2	7
α-helix	223-226	4
β-strand	234-235	2	7
α-helix	237-239	3
α-helix	240-247	8
α-helix	252-255	4
α-helix	257-259	3
β-strand	261-264	4	2
β-strand	267-270	4	2
β-strand	276-282	7	1
α-helix	285-287	3
β-strand	290	1	3
α-helix	291-293	3
β-strand	297-306	10	8
β-strand	308	1	9
β-strand	315-323	9	8
β-strand	328-330	3	10
β-strand	338-340	3	8
β-strand	344-346	3	10
β-strand	350-359	10	8
β-strand	365-368	4	11
β-strand	375-378	4	11
β-strand	382	1	9
α-helix	383-384	2
β-strand	388-389	2	12
α-helix	405-440	36

Chain B: 9 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5
α-helix	9-11	3
β-strand	12	1	13
β-strand	17-19	3	14
β-strand	27-29	3	14
β-strand	33-37	5	15
β-strand	44-56	13	15
β-strand	59-69	11	15
β-strand	72-77	6	15
β-strand	82-84	3	16
β-strand	88	1	16
β-strand	90-102	13	15
β-strand	106-115	10	16
β-strand	118-128	11	16
β-strand	136	1	17
β-strand	146-153	8	18
β-strand	163-167	5	19
β-strand	172-173	2	20
α-helix	175-177	3
β-strand	178-179	2	21
β-strand	186-187	2	21
β-strand	194-199	6	20
β-strand	205-209	5	20
β-strand	213-214	2	21
α-helix	220-222	3
β-strand	223-228	6	20
β-strand	233	1	13
β-strand	234-235	2	19
β-strand	248-253	6	19
β-strand	258-265	8	18
α-helix	268-271	4
β-strand	272-276	5	22
β-strand	279-284	6	22
β-strand	290-296	7	17
β-strand	304-308	5	17
β-strand	312-317	6	22
β-strand	323-327	5	17
α-helix	331-332	2
β-strand	333-335	3	17
β-strand	336-337	2	12
α-helix	349-359	11
α-helix	361-398	38
α-helix	407-412	6

Chain C: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	23
β-strand	12-19	8	23
β-strand	22-26	5	23
β-strand	32-33	2	23
α-helix	36-39	4
α-helix	42-43	2
β-strand	44-46	3	23
β-strand	51-55	5	23
α-helix	56-57	2
α-helix	58-60	3
β-strand	65	1	23
β-strand	67	1	24
β-strand	74-78	5	24
β-strand	81-86	6	24
β-strand	89-93	5	24
β-strand	105-107	3	24
β-strand	113-123	11	24
β-strand	126-134	9	24
β-strand	140-143	4	24
α-helix	148	1
β-strand	149-150	2	24

Chain D: 15 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	25
β-strand	15-19	5	26
β-strand	24	1	27
β-strand	27-49	23	26
β-strand	51-54	4	28
α-helix	56-58	3
β-strand	59-61	3	29
β-strand	77-82	6	29
β-strand	87-88	2	30
β-strand	90	1	31
β-strand	91-92	2	30
β-strand	101-106	6	29
β-strand	107-110	4	28
α-helix	112-115	4
β-strand	118-137	20	26
β-strand	140-148	9	26
β-strand	155-157	3	25
β-strand	160-164	5	25
α-helix	165-167	3
β-strand	177-181	5	26
β-strand	184-187	4	26
α-helix	190-192	3
α-helix	196-197	2
α-helix	201-203	3
β-strand	204-206	3	26
β-strand	214-216	3	26
β-strand	221-222	2	32
α-helix	223-226	4
β-strand	229	1	30
β-strand	234-235	2	32
α-helix	237-239	3
α-helix	240-247	8
α-helix	252-255	4
α-helix	257-259	3
β-strand	261-264	4	26
β-strand	267-270	4	26
β-strand	276-282	7	25
α-helix	285-287	3
β-strand	290	1	27
α-helix	291-293	3
β-strand	297-306	10	33
β-strand	308	1	34
β-strand	315-323	9	33
β-strand	327-330	4	35
β-strand	331-332	2	36
β-strand	339-340	2	33
β-strand	344-347	4	35
β-strand	350-358	9	33
β-strand	365-370	6	36
β-strand	373-378	6	36
β-strand	382	1	34
α-helix	383-384	2
β-strand	388-389	2	37
α-helix	405-440	36

Chain E: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	9-11	3
β-strand	12	1	38
β-strand	17-22	6	39
β-strand	25-29	5	39
β-strand	33-37	5	40
β-strand	44-49	6	40
β-strand	52-56	5	41
β-strand	59-69	11	41
β-strand	72-77	6	41
β-strand	82-84	3	42
β-strand	88	1	42
α-helix	89	1
β-strand	90-95	6	40
β-strand	98-102	5	40
β-strand	106-115	10	42
β-strand	118-128	11	42
β-strand	136	1	43
β-strand	146-153	8	44
β-strand	163-167	5	45
β-strand	172-173	2	46
β-strand	174	1	31
α-helix	175-177	3
β-strand	178-179	2	47
β-strand	186-187	2	47
β-strand	194-200	7	46
β-strand	204-209	6	46
β-strand	213-214	2	47
α-helix	220-222	3
β-strand	223-228	6	46
β-strand	233	1	38
β-strand	234-235	2	45
β-strand	248-253	6	45
β-strand	258-265	8	44
α-helix	268-271	4
β-strand	272-276	5	48
β-strand	279-284	6	48
β-strand	290-296	7	43
β-strand	304-308	5	43
β-strand	312-317	6	48
β-strand	323-327	5	43
α-helix	331-332	2
β-strand	333-335	3	43
β-strand	336-337	2	37
α-helix	349-359	11
α-helix	361-398	38
α-helix	407-412	6

Chain F: 4 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	49
β-strand	12-19	8	49
β-strand	22-26	5	49
β-strand	32-33	2	49
α-helix	36-39	4
α-helix	43	1
β-strand	44-46	3	49
β-strand	51-55	5	49
α-helix	58-61	4
α-helix	64	1
β-strand	65	1	49
β-strand	66-67	2	50
β-strand	74-78	5	50
β-strand	81-86	6	50
β-strand	89-93	5	50
β-strand	104-107	4	50
β-strand	112-122	11	50
β-strand	126-134	9	50
β-strand	140-143	4	50
β-strand	149-150	2	50

Chain G: 14 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	51
β-strand	15-19	5	52
β-strand	24	1	53
β-strand	27-38	12	52
β-strand	41-49	9	54
β-strand	51-54	4	55
α-helix	56-58	3
β-strand	59-61	3	56
β-strand	77-82	6	56
β-strand	87-88	2	57
β-strand	91-92	2	57
β-strand	101-106	6	56
β-strand	107-110	4	55
α-helix	112-115	4
β-strand	118-125	8	54
β-strand	129-137	9	52
β-strand	140-148	9	52
β-strand	155-157	3	51
β-strand	160-164	5	51
α-helix	165-167	3
β-strand	177-181	5	54
β-strand	184-186	3	54
α-helix	190-192	3
α-helix	201-203	3
β-strand	204-206	3	54
β-strand	214-216	3	54
β-strand	221-222	2	58
α-helix	223-226	4
β-strand	234-235	2	58
α-helix	237-239	3
α-helix	240-247	8
α-helix	252-255	4
α-helix	257-259	3
β-strand	261-264	4	52
β-strand	267-270	4	52
β-strand	276-282	7	51
α-helix	285-287	3
β-strand	290	1	53
α-helix	291-293	3
β-strand	297-306	10	59
β-strand	308	1	60
β-strand	315-323	9	59
β-strand	328-330	3	61
β-strand	331-332	2	62
β-strand	339-340	2	59
β-strand	344-346	3	61
β-strand	350-358	9	59
β-strand	365-370	6	62
β-strand	373-378	6	62
β-strand	382	1	60
α-helix	383-384	2
β-strand	388-389	2	63
α-helix	405-440	36

Chain H: 9 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	9-11	3
β-strand	12	1	64
β-strand	17-22	6	65
β-strand	25-29	5	65
β-strand	33-37	5	66
β-strand	44-56	13	66
β-strand	59-69	11	66
β-strand	72-77	6	66
β-strand	82-84	3	67
β-strand	88-89	2	67
β-strand	90-102	13	66
β-strand	106-115	10	67
β-strand	118-128	11	67
β-strand	136	1	68
β-strand	146-153	8	69
β-strand	163-167	5	70
β-strand	172-173	2	71
α-helix	175-177	3
β-strand	178-179	2	72
β-strand	186-187	2	72
β-strand	194-199	6	71
β-strand	205-209	5	71
β-strand	213-214	2	72
α-helix	220-222	3
β-strand	223-228	6	71
β-strand	233	1	64
β-strand	234-235	2	70
β-strand	248-253	6	70
β-strand	258-265	8	69
α-helix	268-271	4
β-strand	272-276	5	73
β-strand	279-284	6	73
β-strand	290-296	7	68
β-strand	304-308	5	68
β-strand	312-317	6	73
β-strand	323-326	4	68
α-helix	331-332	2
β-strand	333-335	3	68
β-strand	336-337	2	63
α-helix	349-359	11
α-helix	361-398	38
α-helix	407-412	6

9 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
E1 protein	A, D, G, J	protein	441	Eastern equine encephalitis virus	P08768
E2 protein	B, E, H, K	protein	414	Eastern equine encephalitis virus	P08768
Capsid protein	C, F, I, L	protein	151	Eastern equine encephalitis virus	W8S146
Isoform Short of Very low-density lipoprotein receptor	R, S, T, U, V, W, X, Y	protein	748	Homo sapiens	P98155 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>8UFB_1 E1 protein (chains A, D, G, J)
YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVV
KCCGATQCTSKPHPDYQCQVFSGVYPFMYGGAYCFCDTENTQMSEAYVERSEECSIDHAK
AYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVV
YGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQVPSG
FERWKKDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDL
ECKITECTYAFDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTA
NIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYAAQHTESFTSAISATAWSWIKVLVGGTSA
FIVLGLIATAVVALVLFFHRH

Sequence of entity 2 (B, E, H, K), FASTA

>8UFB_2 E2 protein (chains B, E, H, K)
DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGV
DLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRH
TCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSI
HSAKVKITVPSGAQVKYYCKCPDVRKGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRL
PRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSD
ANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRY
PLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCC

Sequence of entity 3 (C, F, I, L), FASTA

>8UFB_3 Capsid protein (chains C, F, I, L)
DKTFPIMLNGQVNGYACVVGGRVFKPLHVEGRIDNEQLAAIKLKKASIYDLEYGDVPQCM
KSDTLQYTSDKPPGFYNWHHGAVQYENNRFTVPRGVGGKGDSGRPILDNKGRVVAIVLGG
VNEGSRTALSVVTWNQKGVTVKDTPEGSEPW

Sequence of entity 4 (R, S, T, U, V, W, X, Y), FASTA

>8UFB_4 Isoform Short of Very low-density lipoprotein receptor (chains R, S, T, U, V, W, X, Y)
GRKAKCEPSQFQCTNGRCITLLWKCDGDEDCVDGSDEKNCVKKTCAESDFVCNNGQCVPS
RWKCDGDPDCEDGSDESPEQCHMRTCRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEE
NCGNITCSPDEFTCSSGRCISRNFVCNGQDDCSDGSDELDCAPPTCGAHEFQCSTSSCIP
ISWVCDDDADCSDQSDESLEQCGRQPVIHTKCPASEIQCGSGECIHKKWRCDGDPDCKDG
SDEVNCPSRTCRPDQFECEDGSCIHGSRQCNGIRDCVDGSDEVNCKNVNQCLGPGKFKCR
SGECIDISKVCNQEQDCRDWSDEPLKECHINECLVNNGGCSHICKDLVIGYECDCAAGFE
LIDRKTCGDIDECQNPGICSQICINLKGGYKCECSRGYQMDLATGVCKAVGKEPSLIFTN
RRDIRKIGLERKEYIQLVEQLRNTVALDADIAAQKLFWADLSQKAIFSASIDDKVGRHVK
MIDNVYNPAAIAVDWVYKTIYWTDAASKTISVATLDGTKRKFLFNSDLREPASIAVDPLS
GFVYWSDWGEPAKIEKAGMNGFDRRPLVTADIQWPNGITLDLIKSRLYWLDSKLHMLSSV
DLNGQDRRIVLKSLEFLAHPLALTIFEDRVYWIDGENEAVYGANKFTGSELATLVNNLND
AQDIIVYHELVQPSGKNWCEEDMENGGCEYLCLPAPQINDHSPKYTCSCPSGYNVEENGR
DCQRINVTTAVSEVSVPPKGTSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	12
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

Structural and functional basis of VLDLR usage by Eastern equine encephalitis virus. Adams, L.J., Raju, S., Ma, H. et al. Cell (2024) 187:360-374.e19. DOI 10.1016/j.cell.2023.11.031 · PubMed

Other PDB entries of the same protein (UniProt P08768), best resolution first:

8UFA 2.86 Å, Eastern equine encephalitis virus (PE-6) VLP (asymmetric unit)
8UA9 3.0 Å, Structure of eastern equine encephalitis virus VLP unliganded quasi-threefold spike…
8UFC 3.09 Å, Eastern equine encephalitis virus (PE-6) VLP in complex with VLDLR LA(1-2) (asymmetric…
8DWO 3.5 Å, Cryo-EM Structure of Eastern Equine Encephalitis Virus in complex with SKE26 Fab
8UA4 3.58 Å, Structure of eastern equine encephalitis virus VLP in complex with VLDLR LA1
6XO4 4.2 Å, CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP
6XOB 8.5 Å, CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP with Fab EEEV-143.

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