6NK6: Electron Cryo-Microscopy Of Chikungunya VLP

Electron Cryo-Microscopy Of Chikungunya VLP in complex with mouse Mxra8 receptor. Determined by electron microscopy at 4.06 Å resolution. Released 22 May 2019.

Method: Electron microscopy
Resolution: 4.06 Å
Organisms: Mus musculus, Chikungunya virus strain Senegal 37997
Chains: 16
Atoms: 39,805
Mol. weight: 568.59 kDa
Ligands: NAG
Released: 22 May 2019

Explore 6NK6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NK6 contains 132 α-helices and 469 β-strands across 16 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: 12 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	26
β-strand	15-19	5	27
β-strand	24	1	28
β-strand	27-48	22	27
β-strand	51-54	4	29
β-strand	59-61	3	30
β-strand	77-82	6	30
β-strand	87-88	2	31
β-strand	91-92	2	31
β-strand	101-106	6	30
β-strand	107-110	4	29
α-helix	112-115	4
β-strand	119-137	19	27
β-strand	140-147	8	27
β-strand	154-156	3	26
β-strand	159-163	5	26
β-strand	176-180	5	27
β-strand	183-186	4	27
α-helix	189-191	3
β-strand	203-204	2	32
β-strand	205	1	27
β-strand	214-215	2	32
β-strand	220-221	2	33
α-helix	223-225	3
β-strand	233-234	2	33
α-helix	236-238	3
α-helix	239-243	5
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	27
β-strand	267-269	3	27
β-strand	275-281	7	26
β-strand	289	1	28
α-helix	294-295	2
β-strand	296-306	11	34
β-strand	307	1	35
β-strand	314-322	9	34
β-strand	326-329	4	36
β-strand	330-332	3	37
β-strand	337-339	3	34
β-strand	343-346	4	36
β-strand	349-358	10	34
β-strand	362-369	8	37
β-strand	373-379	7	37
β-strand	381	1	35
α-helix	382-383	2
β-strand	387-388	2	38
α-helix	393-395	3
α-helix	406-413	8
α-helix	418-432	15

Chain B: 11 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	53
β-strand	15-19	5	54
β-strand	24	1	55
β-strand	27-40	14	54
α-helix	41-42	2
β-strand	44-48	5	56
β-strand	51-54	4	57
β-strand	59-61	3	58
β-strand	77-82	6	58
β-strand	87-88	2	59
β-strand	90	1	60
β-strand	91-92	2	59
β-strand	101-106	6	58
β-strand	107-110	4	57
α-helix	112-115	4
β-strand	119-123	5	56
β-strand	127-137	11	54
β-strand	140-147	8	54
β-strand	154-156	3	53
β-strand	159-163	5	53
β-strand	176-180	5	56
β-strand	183-186	4	56
α-helix	189-191	3
α-helix	195-196	2
β-strand	203-205	3	56
β-strand	214-215	2	56
β-strand	221	1	61
α-helix	223-225	3
β-strand	233	1	61
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	54
β-strand	267-269	3	54
β-strand	275-281	7	53
β-strand	289	1	55
α-helix	294-295	2
β-strand	296-306	11	62
β-strand	307	1	63
β-strand	314-322	9	62
β-strand	326-329	4	64
β-strand	332	1	65
β-strand	337-339	3	62
β-strand	343-346	4	64
β-strand	351-358	8	62
β-strand	362-369	8	65
β-strand	372-379	8	65
β-strand	381	1	63
α-helix	382-383	2
β-strand	387-388	2	66
α-helix	406-413	8
α-helix	418-432	15

Chain C: 15 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	81
β-strand	15-19	5	82
β-strand	24	1	83
β-strand	27-39	13	82
β-strand	44-49	6	84
β-strand	51-54	4	85
β-strand	59-61	3	86
β-strand	77-82	6	86
β-strand	87-88	2	87
β-strand	91-92	2	87
β-strand	101-106	6	86
β-strand	107-110	4	85
α-helix	112-115	4
β-strand	118-123	6	84
β-strand	128-137	10	82
β-strand	140-146	7	82
β-strand	152	1	88
β-strand	153-156	4	81
β-strand	159-163	5	81
β-strand	176-180	5	84
β-strand	183-186	4	84
α-helix	189-191	3
β-strand	192	1	89
α-helix	195-196	2
β-strand	203-204	2	90
β-strand	205	1	84
β-strand	214-215	2	90
β-strand	221	1	91
α-helix	223-225	3
β-strand	233	1	91
α-helix	234-236	3
α-helix	239-243	5
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	82
β-strand	267-269	3	82
β-strand	275-281	7	81
β-strand	289	1	83
α-helix	294-295	2
β-strand	296-306	11	92
β-strand	307	1	93
β-strand	314-322	9	92
β-strand	326-329	4	94
β-strand	330-332	3	95
β-strand	337-339	3	92
β-strand	343-346	4	94
β-strand	351-358	8	92
β-strand	362-369	8	95
β-strand	372-379	8	95
α-helix	380	1
β-strand	381	1	93
α-helix	382-383	2
β-strand	387-388	2	96
α-helix	393-395	3
α-helix	406-413	8
α-helix	418-429	12
α-helix	432-434	3

Chain D: 12 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	112
β-strand	15-19	5	113
β-strand	24	1	114
β-strand	27-40	14	113
α-helix	41-42	2
β-strand	44-48	5	115
β-strand	51-54	4	116
β-strand	59-61	3	117
β-strand	77-82	6	117
β-strand	86	1	118
β-strand	87-88	2	119
β-strand	91-92	2	119
β-strand	101-106	6	117
β-strand	107-110	4	116
α-helix	112-115	4
β-strand	119-123	5	115
β-strand	127-137	11	113
β-strand	140-147	8	113
β-strand	152	1	89
β-strand	154-156	3	112
β-strand	159-163	5	112
β-strand	176-180	5	115
β-strand	183-186	4	115
α-helix	189-191	3
β-strand	192	1	88
α-helix	195-196	2
β-strand	203-204	2	120
β-strand	205	1	115
β-strand	214-215	2	120
β-strand	221	1	121
α-helix	223-225	3
β-strand	227	1	118
β-strand	233	1	121
α-helix	239-243	5
α-helix	251-254	4
α-helix	256-258	3
β-strand	260-262	3	113
β-strand	267-269	3	113
β-strand	275-281	7	112
β-strand	289	1	114
α-helix	294-295	2
β-strand	296-306	11	122
β-strand	307	1	123
β-strand	314-322	9	122
β-strand	326-329	4	124
β-strand	330-332	3	125
β-strand	337-339	3	122
β-strand	343-346	4	124
β-strand	351-358	8	122
β-strand	362-369	8	125
β-strand	372-379	8	125
β-strand	381	1	123
α-helix	382-383	2
β-strand	388	1	126
α-helix	406-413	8
α-helix	418-432	15

Chain E: 4 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	17-19	3	39
β-strand	28-30	3	39
β-strand	36-38	3	40
β-strand	45-49	5	40
β-strand	53-54	2	41
β-strand	66-71	6	41
β-strand	74-79	6	41
β-strand	84-86	3	42
β-strand	90	1	42
β-strand	93-97	5	40
β-strand	100-104	5	40
β-strand	111-116	6	42
β-strand	122-127	6	42
α-helix	133-135	3
β-strand	139	1	43
β-strand	148-156	9	44
β-strand	166-168	3	45
β-strand	169-170	2	46
β-strand	175-177	3	47
β-strand	181-183	3	48
β-strand	188-190	3	48
β-strand	197-200	4	47
β-strand	208-211	4	47
β-strand	215-217	3	48
β-strand	226-229	4	47
β-strand	236-237	2	46
β-strand	254-256	3	45
β-strand	261-269	9	44
α-helix	270-273	4
β-strand	275-279	5	49
β-strand	282-287	6	49
β-strand	293-299	7	43
β-strand	307-311	5	43
β-strand	315-320	6	49
β-strand	326-330	5	43
β-strand	336-338	3	43
β-strand	339-340	2	38
α-helix	355-359	5
α-helix	368-397	30

Chain F: 8 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	67
β-strand	17-19	3	68
β-strand	21	1	69
β-strand	28-30	3	68
β-strand	34-38	5	70
β-strand	45-54	10	70
β-strand	66-70	5	70
β-strand	75-79	5	70
α-helix	80-82	3
β-strand	84-86	3	69
β-strand	90	1	69
α-helix	91	1
β-strand	92-104	13	70
β-strand	108-116	9	69
β-strand	122-131	10	69
α-helix	133-135	3
β-strand	139	1	71
β-strand	150-156	7	72
β-strand	167-168	2	73
β-strand	169-170	2	74
β-strand	175	1	75
β-strand	177	1	60
β-strand	181-184	4	76
β-strand	187-190	4	76
β-strand	197-200	4	75
β-strand	208-211	4	75
β-strand	215-217	3	76
α-helix	222-224	3
β-strand	227-229	3	75
β-strand	235	1	67
β-strand	236-237	2	74
β-strand	254-255	2	73
β-strand	261-267	7	72
α-helix	268-270	3
β-strand	275-279	5	77
β-strand	282-286	5	77
β-strand	293-299	7	71
β-strand	307-311	5	71
β-strand	316-320	5	77
β-strand	326-330	5	71
α-helix	334-335	2
β-strand	336-338	3	71
β-strand	339-340	2	66
α-helix	369-397	29
α-helix	409-415	7

Chain G: 4 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	17-19	3	97
β-strand	28-30	3	97
β-strand	37-38	2	98
β-strand	45-49	5	98
β-strand	66-71	6	99
β-strand	74-79	6	99
β-strand	84-86	3	100
β-strand	90	1	100
β-strand	96-97	2	98
β-strand	100-104	5	98
β-strand	108-116	9	100
β-strand	122-131	10	100
α-helix	133-135	3
β-strand	139	1	101
β-strand	150-156	7	102
β-strand	166-168	3	103
β-strand	169-170	2	104
β-strand	175	1	105
β-strand	188-189	2	106
β-strand	197-201	5	105
β-strand	208-211	4	105
β-strand	216-217	2	106
β-strand	225-229	5	105
β-strand	236-237	2	104
α-helix	243-244	2
β-strand	254-256	3	103
β-strand	261-267	7	102
β-strand	275-279	5	107
β-strand	282-286	5	107
β-strand	293-299	7	101
β-strand	307-311	5	101
β-strand	316-319	4	107
β-strand	326-330	5	101
β-strand	336-338	3	101
β-strand	339-340	2	96
α-helix	356-361	6
α-helix	369-397	29

Chain H: 8 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	127
β-strand	17-19	3	128
β-strand	28-30	3	128
β-strand	36-38	3	129
β-strand	45-49	5	129
β-strand	53-54	2	130
β-strand	66-71	6	130
β-strand	74-79	6	130
α-helix	80-82	3
β-strand	84-86	3	131
β-strand	90	1	131
β-strand	92-97	6	129
β-strand	100-104	5	129
β-strand	108-116	9	131
β-strand	122-131	10	131
α-helix	133-135	3
β-strand	136	1	132
β-strand	139	1	132
β-strand	148-156	9	133
β-strand	167	1	134
β-strand	169-170	2	135
β-strand	176	1	136
β-strand	183-185	3	137
β-strand	187-190	4	137
β-strand	197-198	2	136
β-strand	210-211	2	136
β-strand	215-217	3	137
β-strand	228-229	2	136
β-strand	235	1	127
β-strand	236-237	2	135
α-helix	250-252	3
β-strand	255	1	134
β-strand	261-269	9	133
α-helix	270-274	5
β-strand	275-279	5	138
β-strand	282-286	5	138
β-strand	293-299	7	132
β-strand	307-311	5	132
β-strand	316-320	5	138
β-strand	326-330	5	132
α-helix	334-335	2
β-strand	336-338	3	132
β-strand	339	1	126
α-helix	358-361	4
α-helix	369-397	29
α-helix	411-415	5

8 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
Matrix remodeling-associated protein 8	M, N, O, P	protein	269	Mus musculus	Q9DBV4 (AlphaFold model)
E1 glycoprotein	A, B, C, D	protein	439	Chikungunya virus strain Senegal 37997	Q5XXP3
E2 glycoprotein	E, F, G, H	protein	419	Chikungunya virus strain Senegal 37997	Q5XXP3
Capsid protein	I, J, K, L	protein	151	Chikungunya virus strain Senegal 37997	Q5XXP3

Sequence of entity 1 (M, N, O, P), FASTA

>6NK6_1 Matrix remodeling-associated protein 8 (chains M, N, O, P)
SSSLVSESVVSLAAGTQAVLRCQSPRMVWTQDRLHDRQRVVHWDLSGGPGSQRRRLVDMY
SAGEQRVYEPRDRDRLLLSPSAFHDGNFSLLIRAVDRGDEGVYTCNLHHHYCHLDESLAV
RLEVTEDPLLSRAYWDGEKEVLVVAHGAPALMTCINRAHVWTDRHLEEAQQVVHWDRQLP
GVSHDRADRLLDLYASGERRAYGPPFLRDRVSVNTNAFARGDFSLRIDELERADEGIYSC
HLHHHYCGLHERRVFHLQVTEPAFEPPSA

Sequence of entity 2 (A, B, C, D), FASTA

>6NK6_2 E1 glycoprotein (chains A, B, C, D)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELQSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNITVAAYANGDHAVTVKDAKFVVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNIPISIDIPDAAFTRVVDAPSVTDMS
CEVPACTHSSDFGGVAIIKYTASKKGKCAVHSMTNAVTIREADVEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAACHPPKDHIVNYPASHTTLGVQDISTTAMSWVQKITGGVGLI
VAVAALILIVVLCVSFSRH

Sequence of entity 3 (E, F, G, H), FASTA

>6NK6_3 E2 glycoprotein (chains E, F, G, H)
NFNVYKATRPYLAHCPDCGEGHSCHSPIALERIRNEATDGTLKIQVSLQIGIKTDDSHDW
TKLRYMDSHTPADAERAGLLVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHT
CTHPFHHEPPVIGRERFHSRPQHGKELPCSTYVQSTAATAEEIEVHMPPDTPDRTLMTQQ
SGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKIDQCHAAVTNHKNWQYNSPLVPR
NAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVTMLLYPDHPTLLSYRNMGQEP
NYHEEWVTHKKEVTLTVPTEGLEVTWGNNEPYKYWPQMSTNGTAHGHPHEIILYYYELYP
TMTVVIVSVASFVLLSMVGTAVGMCVCARRRCITPYELTPGATVPFLLSLLCCVRTTKA

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

>6NK6_4 Capsid protein (chains I, J, K, L)
NDCIFEVKHEGKVMGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVH
MKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLG
GANEGARTALSVVTWNKDIVTKITPEGAEEW

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Cryo-EM Structure of Chikungunya Virus in Complex with the Mxra8 Receptor. Basore, K., Kim, A.S., Nelson, C.A. et al. Cell (2019) 177:1725. DOI 10.1016/j.cell.2019.04.006 · PubMed

Other PDB entries of the same protein (UniProt Q9DBV4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6NK3 2.2 Å, Crystal structure of murine Mxra8 ectodomain
6JO7 2.4 Å, Crystal structure of mouse MXRA8
8SQN 3.89 Å, CryoEM structure of Western equine encephalitis virus VLP in complex with the chimeric…
8EWF 3.92 Å, CryoEM structure of Western equine encephalitis virus VLP in complex with the avian…
6NK7 4.99 Å, Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor

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