5VU2: E1 envelope glycoprotein

Electron cryo-microscopy of "immature" Chikungunya VLP. Determined by electron microscopy at 6.8 Å resolution. Released 6 Dec 2017.

Method: Electron microscopy
Resolution: 6.8 Å
Organisms: Chikungunya virus strain Senegal 37997, Chikungunya virus (strain 37997)
Chains: 24
Atoms: 32,676
Mol. weight: 911.44 kDa
Released: 6 Dec 2017

Explore 5VU2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VU2 contains 106 α-helices and 370 β-strands across 24 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.

Chains A, B, C and D: 8 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	8-10	3
β-strand	12	1	13
β-strand	17-19	3	14
β-strand	21	1	15
β-strand	28-30	3	14
β-strand	34-38	5	16
β-strand	46-56	11	16
β-strand	62-71	10	16
β-strand	74-79	6	16
β-strand	84-86	3	15
β-strand	90	1	15
β-strand	92-104	13	16
β-strand	108-116	9	15
β-strand	122-131	10	15
α-helix	133-135	3
β-strand	139	1	17
α-helix	144-145	2
β-strand	149-156	8	18
β-strand	166-170	5	19
β-strand	175-176	2	20
α-helix	178-180	3
β-strand	181-184	4	21
β-strand	187-190	4	21
β-strand	197-201	5	20
β-strand	208-211	4	20
β-strand	215-217	3	21
α-helix	222-224	3
β-strand	225-229	5	20
β-strand	235	1	13
β-strand	236-237	2	19
α-helix	243-245	3
β-strand	253-256	4	19
β-strand	261-268	8	18
α-helix	271-274	4
β-strand	275-279	5	22
β-strand	282-287	6	22
β-strand	293-299	7	17
β-strand	307-311	5	17
β-strand	315-320	6	22
β-strand	326-330	5	17
α-helix	334-335	2
β-strand	336-338	3	17

Chains E, F, G and H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	404-411	8
α-helix	418-438	21

Chains I, J, K and L: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	114-119	6	92
β-strand	122-128	7	92
β-strand	130	1	93
β-strand	133-134	2	94
β-strand	135	1	92
β-strand	137	1	95
β-strand	143-144	2	92
α-helix	147-150	4
β-strand	155-157	3	95
β-strand	162-164	3	95
β-strand	165-166	2	94
α-helix	169-174	6
β-strand	176	1	93
β-strand	178	1	96
β-strand	185-189	5	96
β-strand	192-197	6	96
β-strand	200-204	5	96
β-strand	216-218	3	96
β-strand	224-233	10	96
β-strand	237-245	9	96
β-strand	250-253	4	96
β-strand	259-260	2	96

Chain M: 7 helices, 37 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
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	140-147	8	2
β-strand	153-156	4	1
β-strand	159-163	5	1
β-strand	176-180	5	2
β-strand	183-186	4	2
α-helix	189-191	3
α-helix	195-196	2
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	239-246	8
α-helix	251-254	4
β-strand	260-262	3	2
β-strand	267-269	3	2
β-strand	275-281	7	1
α-helix	284-286	3
β-strand	289	1	3
β-strand	296-306	11	9
β-strand	307	1	10
β-strand	314-322	9	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	349-358	10	9
β-strand	362-369	8	12
β-strand	372-379	8	12
β-strand	381	1	10

Chains N and P: 8 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	35
β-strand	15-19	5	36
β-strand	24	1	37
β-strand	27-48	22	36
β-strand	51-54	4	38
β-strand	59-61	3	39
β-strand	77-82	6	39
β-strand	87-88	2	40
β-strand	91-92	2	40
β-strand	101-106	6	39
β-strand	107-110	4	38
α-helix	112-115	4
β-strand	119-137	19	36
β-strand	140-147	8	36
β-strand	153-156	4	35
β-strand	159-163	5	35
β-strand	176-180	5	36
β-strand	183-186	4	36
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-204	2	41
β-strand	205	1	36
β-strand	214-215	2	41
β-strand	220-221	2	42
α-helix	223-225	3
β-strand	233-234	2	42
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-262	3	36
β-strand	267-269	3	36
β-strand	275-281	7	35
α-helix	284-286	3
β-strand	289	1	37
α-helix	294-295	2
β-strand	296-306	11	43
β-strand	307	1	44
β-strand	314-322	9	43
β-strand	326-329	4	45
β-strand	330-332	3	46
β-strand	337-339	3	43
β-strand	343-346	4	45
β-strand	349-358	10	43
β-strand	362-369	8	46
β-strand	372-379	8	46
β-strand	381	1	44

Chain O: 8 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	58
β-strand	15-19	5	59
β-strand	27-48	22	59
β-strand	51-54	4	60
β-strand	59-61	3	61
β-strand	77-82	6	61
β-strand	87-88	2	62
β-strand	91-92	2	62
β-strand	101-106	6	61
β-strand	107-110	4	60
α-helix	112-115	4
β-strand	119-137	19	59
β-strand	140-147	8	59
β-strand	153-156	4	58
β-strand	159-163	5	58
β-strand	176-180	5	59
β-strand	183-186	4	59
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-204	2	63
β-strand	205	1	59
β-strand	214-215	2	63
β-strand	220-221	2	64
α-helix	223-225	3
β-strand	233-234	2	64
α-helix	239-246	8
α-helix	251-254	4
β-strand	260-262	3	59
β-strand	267-269	3	59
β-strand	275-281	7	58
α-helix	284-286	3
α-helix	294-295	2
β-strand	296-306	11	65
β-strand	307	1	66
β-strand	314-322	9	65
β-strand	326-329	4	67
β-strand	330-332	3	68
β-strand	337-339	3	65
β-strand	343-346	4	67
β-strand	349-358	10	65
β-strand	362-369	8	68
β-strand	372-379	8	68
β-strand	381	1	66

Chain Q: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	354-357	4
α-helix	367-396	30
α-helix	398-400	3

Chain R: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	353-357	5
α-helix	358-360	3
α-helix	368-396	29
α-helix	398-400	3

3 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 envelope glycoprotein	A, B, C, D, M, N, O, P	protein	866	Chikungunya virus strain Senegal 37997	A0A0H4CWF2
E3 envelope glycoprotein	U, V, W, X	protein	60	Chikungunya virus strain Senegal 37997	Q5XXP3
capsid protein	I, J, K, L	protein	149	Chikungunya virus (strain 37997)	Q5XXP3
E1 envelope glycoprotein	E, F, G, H	protein	46	Chikungunya virus strain Senegal 37997	Q5XXP3
E2 envelope glycoprotein	Q, R, S, T	protein	81	Chikungunya virus strain Senegal 37997	Q5XXP3

Sequence of entity 1 (A, B, C, D, M, N, O, P), FASTA

>5VU2_1 E1 envelope glycoprotein (chains A, B, C, D, M, N, O, P)
STKDNFNVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDD
SHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRK
ISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTL
MSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSP
LVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNM
GEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYY
ELYPTMTVVVVSVATFILLSMVGMAAGMCMCARRRCITPYELTPGATVPFLLSLICCIRT
AKAATYQEAAIYLWNEQQPLFWLQALIPLAALIVLCNCLRLLPCCCKTLAFLAVMSVGAH
TVSAYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIP
SPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKT
EFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNK
IVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQA
PSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSL
TDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISF
STALASAEFRVQVCSTQVHCAAECHP

Sequence of entity 2 (U, V, W, X), FASTA

>5VU2_2 E3 envelope glycoprotein (chains U, V, W, X)
PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSPHRQRE

Sequence of entity 3 (I, J, K, L), FASTA

>5VU2_3 capsid protein (chains I, J, K, L)
CIFEVKHEGKVMGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVHMK
SDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGA
NEGARTALSVVTWNKDIVTKITPEGAEEW

Sequence of entity 4 (E, F, G, H), FASTA

>5VU2_4 E1 envelope glycoprotein (chains E, F, G, H)
HTTLGVQDISTTAMSWVQKITGGVGLIVAVAALILIVVLCVSFSRH

Sequence of entity 5 (Q, R, S, T), FASTA

>5VU2_5 E2 envelope glycoprotein (chains Q, R, S, T)
STNGTAHGHPHEIILYYYELYPTMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYEL
TPGATVPFLLSLLCCVRTTKA

Primary citation

Structural studies of Chikungunya virus maturation. Yap, M.L., Klose, T., Urakami, A. et al. Proc Natl Acad Sci U S A (2017) 114:13703-13707. DOI 10.1073/pnas.1713166114 · PubMed

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