6NK7: Electron Cryo-Microscopy of Chikungunya

Name: PDB 6NK7: Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor
Published: 2019-05-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor. Determined by electron microscopy at 4.99 Å resolution. Released 22 May 2019.

Method: Electron microscopy
Resolution: 4.99 Å
Organisms: Chikungunya virus, Mus musculus
Chains: 17
Atoms: 35,205
Mol. weight: 502.97 kDa
Ligands: NAG
Released: 22 May 2019

Explore 6NK7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NK7 contains 82 α-helices and 393 β-strands across 17 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: 7 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
β-strand	13-19	7	2
β-strand	24	1	3
β-strand	27-39	13	2
β-strand	43-48	6	4
β-strand	51-54	4	5
α-helix	55-57	3
β-strand	59-61	3	6
β-strand	77-81	5	6
β-strand	88	1	7
β-strand	91	1	7
β-strand	101-106	6	6
β-strand	107-110	4	5
α-helix	113-115	3
β-strand	119-123	5	4
β-strand	128-136	9	2
β-strand	141-147	7	2
β-strand	154-156	3	1
β-strand	159-163	5	1
β-strand	176-180	5	4
β-strand	183-185	3	4
α-helix	195-196	2
β-strand	203-204	2	8
β-strand	205	1	4
β-strand	214-215	2	8
β-strand	221	1	9
β-strand	233	1	9
α-helix	240-243	4
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	296-306	11	10
β-strand	314-322	9	10
β-strand	326-329	4	11
β-strand	330-332	3	12
β-strand	343-346	4	11
β-strand	349-356	8	10
β-strand	362-369	8	12
β-strand	373-379	7	12
α-helix	393-395	3
α-helix	406-414	9
α-helix	418-431	14

Chain B: 10 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	13
β-strand	15-19	5	14
β-strand	24	1	15
β-strand	27-38	12	14
β-strand	43-47	5	16
β-strand	51-54	4	17
β-strand	59	1	18
β-strand	64	1	19
α-helix	69-71	3
β-strand	77-81	5	18
β-strand	100	1	19
β-strand	102-106	5	18
β-strand	107-110	4	17
α-helix	112-115	4
β-strand	120-123	4	16
β-strand	130-137	8	14
β-strand	140-147	8	14
β-strand	154-156	3	20
β-strand	159-161	3	20
β-strand	162-163	2	13
β-strand	176-180	5	16
β-strand	183-185	3	16
α-helix	188-191	4
α-helix	195-196	2
β-strand	204	1	21
β-strand	205	1	16
β-strand	214	1	21
α-helix	221-224	4
α-helix	240-242	3
α-helix	251-254	4
β-strand	260-262	3	14
β-strand	267-269	3	14
β-strand	275-281	7	13
α-helix	284-286	3
β-strand	289	1	15
β-strand	296-305	10	22
β-strand	314-322	9	22
β-strand	326-329	4	23
β-strand	330-332	3	24
β-strand	343-346	4	23
β-strand	349-356	8	22
β-strand	362-369	8	24
β-strand	373-379	7	24
β-strand	387-388	2	25
α-helix	406-414	9
α-helix	418-435	18

Chain C: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	26
β-strand	11	1	27
β-strand	15-20	6	27
β-strand	24	1	28
β-strand	26-39	14	27
β-strand	43-48	6	29
β-strand	51-54	4	30
β-strand	59	1	31
β-strand	64	1	32
β-strand	77-82	6	31
β-strand	88	1	33
β-strand	91	1	33
β-strand	100	1	32
β-strand	101-106	6	31
β-strand	107-110	4	30
α-helix	112-115	4
β-strand	119-123	5	29
β-strand	128-137	10	27
β-strand	140-147	8	27
β-strand	153-156	4	34
β-strand	159-162	4	34
β-strand	163	1	26
β-strand	177-180	4	29
β-strand	183-186	4	29
α-helix	189-191	3
α-helix	195-196	2
β-strand	204	1	35
β-strand	205	1	29
β-strand	214	1	35
β-strand	221	1	36
α-helix	222-224	3
β-strand	233	1	36
α-helix	239-242	4
α-helix	256-258	3
β-strand	260-262	3	27
β-strand	267-269	3	27
β-strand	275-281	7	26
α-helix	284-286	3
β-strand	289	1	28
α-helix	294-295	2
β-strand	296-302	7	37
β-strand	314-322	9	37
β-strand	326-329	4	38
β-strand	331-332	2	39
β-strand	343-346	4	38
β-strand	349-356	8	37
β-strand	364-369	6	39
β-strand	372-377	6	39
β-strand	388	1	40
α-helix	406-413	8
α-helix	419-438	20

Chain D: 7 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	41
β-strand	14-19	6	42
β-strand	27-48	22	42
β-strand	51-54	4	43
β-strand	59-61	3	44
β-strand	64	1	45
α-helix	67-69	3
β-strand	77-81	5	44
β-strand	87-88	2	46
β-strand	91-92	2	46
β-strand	100	1	45
β-strand	101-106	6	44
β-strand	107-110	4	43
α-helix	112-115	4
β-strand	119-136	18	42
β-strand	141-146	6	42
β-strand	153-156	4	41
β-strand	159-163	5	41
β-strand	176-180	5	42
β-strand	183-185	3	42
β-strand	203-204	2	47
β-strand	205	1	42
β-strand	214-215	2	47
α-helix	243-245	3
α-helix	256-258	3
β-strand	260-262	3	42
β-strand	267-269	3	42
β-strand	275-281	7	41
α-helix	290-292	3
β-strand	297-307	11	48
β-strand	314-321	8	48
β-strand	326-329	4	49
β-strand	330-332	3	50
β-strand	343-346	4	49
β-strand	349-356	8	48
β-strand	362	1	51
β-strand	365-369	5	50
β-strand	372-376	5	50
β-strand	379	1	51
β-strand	380-381	2	48
β-strand	387-388	2	52
α-helix	406-413	8
α-helix	419-435	17

Chain E: 2 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	53
β-strand	28	1	53
β-strand	34-38	5	54
β-strand	46-50	5	54
β-strand	53-54	2	55
β-strand	67-70	4	55
β-strand	75-77	3	55
β-strand	83-86	4	56
β-strand	90	1	56
β-strand	92-97	6	54
β-strand	100-104	5	54
β-strand	108	1	57
β-strand	111-116	6	56
β-strand	122-127	6	56
β-strand	131	1	57
β-strand	136	1	58
β-strand	139	1	58
β-strand	148-156	9	59
β-strand	166-167	2	60
β-strand	175-176	2	61
β-strand	181-183	3	62
β-strand	188-190	3	62
β-strand	197-200	4	61
β-strand	201	1	63
β-strand	208-211	4	61
β-strand	215-217	3	62
β-strand	225	1	63
β-strand	228-229	2	61
β-strand	255-256	2	60
β-strand	261-269	9	59
β-strand	275-279	5	64
β-strand	282-287	6	64
β-strand	293-298	6	65
β-strand	307-311	5	65
β-strand	315-320	6	64
β-strand	326-330	5	65
β-strand	336-338	3	65
α-helix	355-359	5
α-helix	369-394	26

Chain F: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	66
β-strand	19	1	67
β-strand	28	1	67
β-strand	34-38	5	68
β-strand	45-54	10	68
β-strand	57	1	69
β-strand	61	1	69
β-strand	66	1	70
β-strand	69-70	2	71
β-strand	75-76	2	71
β-strand	79	1	70
β-strand	84-86	3	72
β-strand	90	1	72
β-strand	92-104	13	68
β-strand	108	1	73
β-strand	111-116	6	72
β-strand	122-127	6	72
β-strand	131	1	73
α-helix	133-135	3
β-strand	148-156	9	74
β-strand	166	1	75
β-strand	175	1	76
α-helix	178-180	3
β-strand	181-184	4	77
β-strand	187-190	4	77
β-strand	197-200	4	76
β-strand	208-211	4	76
β-strand	215-217	3	77
β-strand	227-229	3	76
β-strand	237	1	66
β-strand	256	1	75
β-strand	261-269	9	74
α-helix	270-273	4
β-strand	275-279	5	78
β-strand	282-287	6	78
β-strand	293-299	7	79
β-strand	307-311	5	79
β-strand	315-320	6	78
β-strand	326-330	5	79
β-strand	333-338	6	79
β-strand	339-340	2	25
α-helix	355-361	7
α-helix	369-397	29
α-helix	398-400	3
α-helix	412-415	4

Chain G: 5 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	19	1	80
β-strand	28	1	80
β-strand	36-38	3	81
β-strand	46-49	4	81
β-strand	69-70	2	82
β-strand	75-76	2	82
β-strand	84-86	3	83
β-strand	90	1	83
α-helix	91	1
β-strand	92-97	6	81
β-strand	100-104	5	81
β-strand	111-114	4	83
β-strand	115-116	2	84
β-strand	122-123	2	84
β-strand	126-127	2	83
β-strand	150-156	7	85
β-strand	175-176	2	86
β-strand	181-183	3	87
β-strand	188-190	3	87
β-strand	197-200	4	86
β-strand	208-211	4	86
β-strand	215-217	3	87
β-strand	228-229	2	86
α-helix	243	1
β-strand	244	1	31
β-strand	261-267	7	85
α-helix	268-273	6
β-strand	275-279	5	88
β-strand	282-286	5	88
β-strand	293-299	7	89
β-strand	307-311	5	89
β-strand	316-320	5	88
β-strand	326-330	5	89
β-strand	337-338	2	89
β-strand	339	1	40
α-helix	356-361	6
α-helix	369-397	29

Chain H: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
β-strand	19	1	90
β-strand	28	1	90
β-strand	34-38	5	91
β-strand	46-50	5	91
β-strand	69-70	2	92
β-strand	75-76	2	92
β-strand	86	1	93
β-strand	90	1	93
α-helix	91	1
β-strand	92-97	6	91
β-strand	100-104	5	91
β-strand	111-115	5	93
β-strand	123-127	5	93
β-strand	149-156	8	94
β-strand	175-176	2	95
β-strand	181-182	2	96
β-strand	188-190	3	96
β-strand	197-200	4	95
β-strand	208-211	4	95
β-strand	215-217	3	96
β-strand	228-229	2	95
α-helix	251-253	3
β-strand	261-268	8	94
β-strand	275-279	5	97
β-strand	282-287	6	97
β-strand	293-298	6	98
β-strand	307-311	5	98
β-strand	315-320	6	97
β-strand	326-330	5	98
β-strand	336-338	3	98
β-strand	339-340	2	52
α-helix	369-394	26

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 glycoprotein	A, B, C, D	protein	439	Chikungunya virus	Q88628
E2 glycoprotein	E, F, G, H	protein	419	Chikungunya virus	Q88628
Capsid protein	I, J, K, L	protein	151	Chikungunya virus	Q88628
E3 glycoprotein	U, V, W, X	protein	60	Chikungunya virus	D2KBQ2
Matrix remodeling-associated protein 8	N	protein	261	Mus musculus	Q9DBV4 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6NK7_1 E1 glycoprotein (chains A, B, C, D)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDTENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNVTVSAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESEDVYANTQLVLQRPSAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMS
CEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISVTAMSWVQKITGGVGLV
VAVAALILIVVLCVSFSRH

Sequence of entity 2 (E, F, G, H), FASTA

>6NK7_2 E2 glycoprotein (chains E, F, G, H)
NFNVYKAIRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDW
TKLRYMDNHMPADAERARLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDGRKISHS
CTHPFHHDPPVIGREKFHSRPQHGRELPCSTYAQSTAATAEEIEVHMPPDTPDRTLMSQQ
SGNVKITVNSQTVRYKCNCGDSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPR
NAELGDRKGKVHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEP
NYQEEWVTHKKEIRLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYYELYP
TMTVVVVSVASFVLLSMVGVAVGMCMCARRRCITPYELTPGATVPFLLSLICCIRTAKA

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

>6NK7_3 Capsid protein (chains I, J, K, L)
NDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVH
MKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLG
GANEGARTALSVVTWNKDIVTKITPEGAEEW

Sequence of entity 4 (U, V, W, X), FASTA

>6NK7_4 E3 glycoprotein (chains U, V, W, X)
PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSPHRQRR

Sequence of entity 5 (N), FASTA

>6NK7_5 Matrix remodeling-associated protein 8 (chains N)
SSSLVSESVVSLAAGTQAVLRCQSPRMVWTQDRLHDRQRVVHWDLSGGPGSQRRRLVDMY
SAGEQRVYEPRDRDRLLLSPSAFHDGNFSLLIRAVDRGDEGVYTCNLHHHYCHLDESLAV
RLEVTEDPLLSRAYWDGEKEVLVVAHGAPALMTCINRAHVWTDRHLEEAQQVVHWDRQLP
GVSHDRADRLLDLYASGERRAYGPPFLRDRVSVNTNAFARGDFSLRIDELERADEGIYSC
HLHHHYCGLHERRVFHLQVTE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

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 Q88628), best resolution first:

8FCG 3.09 Å, Cryo-EM structure of Chikungunya virus asymmetric unit
9J6D 3.11 Å, Structure of Chikungunya virus infectious particles, 2f block.
9BBN 3.3 Å, Cryo-EM structure of Chikungunya virus asymmetric unit with Fab C9
9BHH 3.5 Å, Cryo-EM structure of Chikungunya virus asymmetric unit with Fab IM-CKV063
6W09 5.3 Å, Human mAbs broadly protect against infection of arthritiogenic alphaviruses by…

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