6W09: E1 glycoprotein

Human mAbs broadly protect against infection of arthritiogenic alphaviruses by recognizing conserved elements of the MXR8 receptor binding domain. Determined by electron microscopy at 5.3 Å resolution. Released 26 Aug 2020.

Method: Electron microscopy
Resolution: 5.3 Å
Organisms: Chikungunya virus, Homo sapiens
Chains: 20
Atoms: 19,520
Mol. weight: 538.09 kDa
Released: 26 Aug 2020

Explore 6W09 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W09 contains 74 α-helices and 517 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: 6 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	15-17	3	2
β-strand	20	1	3
β-strand	24	1	4
β-strand	26	1	3
β-strand	29-41	13	2
β-strand	44-48	5	5
β-strand	59-61	3	6
β-strand	77-82	6	6
β-strand	87-88	2	7
β-strand	91-92	2	7
β-strand	101-106	6	6
β-strand	119-123	5	5
β-strand	125-137	13	2
β-strand	140-146	7	2
β-strand	154-156	3	1
β-strand	159-163	5	1
β-strand	176-180	5	5
β-strand	183-186	4	5
α-helix	195-196	2
β-strand	203-205	3	5
β-strand	213-215	3	5
β-strand	220-221	2	8
β-strand	233-234	2	8
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	9
β-strand	267-269	3	9
β-strand	276-281	6	1
α-helix	284-286	3
β-strand	289	1	4
β-strand	297	1	10
β-strand	301-302	2	10
β-strand	307	1	11
β-strand	314-321	8	10
β-strand	326-329	4	12
β-strand	330-331	2	13
α-helix	337	1
β-strand	338-339	2	10
β-strand	343-346	4	12
β-strand	349-357	9	10
β-strand	362-369	8	13
β-strand	372-379	8	13
β-strand	381	1	11
α-helix	382-383	2
β-strand	387-388	2	14

Chain B: 5 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	15
β-strand	15-20	6	16
β-strand	26-48	23	16
β-strand	51-54	4	17
β-strand	59-61	3	18
β-strand	77-84	8	18
β-strand	100-106	7	18
β-strand	107-110	4	17
α-helix	112-116	5
β-strand	119-137	19	16
β-strand	140-147	8	16
β-strand	153-156	4	15
β-strand	159-163	5	15
β-strand	176-180	5	16
β-strand	183-185	3	16
β-strand	203-204	2	19
β-strand	205	1	16
β-strand	214-215	2	19
β-strand	220-221	2	20
α-helix	222-225	4
β-strand	233-234	2	20
α-helix	236-238	3
α-helix	239-245	7
β-strand	261-262	2	21
β-strand	267-268	2	21
β-strand	275-281	7	15
α-helix	284-286	3
β-strand	297-306	10	22
β-strand	307	1	23
β-strand	314-321	8	22
β-strand	326-329	4	24
β-strand	330-332	3	25
β-strand	338-339	2	26
β-strand	343-346	4	24
β-strand	349-355	7	22
β-strand	356-357	2	26
β-strand	362-369	8	25
β-strand	372-379	8	25
β-strand	381	1	23

Chain C: 6 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	27
β-strand	15-20	6	28
β-strand	26-40	15	28
β-strand	44-48	5	29
β-strand	51-54	4	30
β-strand	59-61	3	31
β-strand	77-84	8	31
β-strand	87-88	2	32
β-strand	91-92	2	32
β-strand	100-106	7	31
β-strand	107-110	4	30
β-strand	119-123	5	29
α-helix	124	1
α-helix	126	1
β-strand	127-137	11	28
β-strand	140-146	7	28
β-strand	154-156	3	27
β-strand	159-163	5	27
β-strand	176-180	5	29
β-strand	183-185	3	29
β-strand	203-205	3	33
β-strand	213-215	3	33
β-strand	220-221	2	34
α-helix	223-225	3
β-strand	233-234	2	34
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	35
β-strand	267-269	3	35
β-strand	275-281	7	27
β-strand	297-306	10	36
β-strand	307	1	37
β-strand	314-321	8	36
β-strand	326-328	3	38
β-strand	330-332	3	39
α-helix	337	1
β-strand	338-339	2	40
β-strand	344-346	3	38
β-strand	351-355	5	36
β-strand	356-357	2	40
β-strand	362-369	8	39
β-strand	372-379	8	39
β-strand	381	1	37
β-strand	388	1	41

Chain D: 8 helices, 44 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	42
β-strand	15-19	5	43
β-strand	27-40	14	43
β-strand	44-48	5	44
β-strand	52-54	3	45
β-strand	59-61	3	46
β-strand	77-82	6	46
β-strand	87-88	2	47
β-strand	91-92	2	47
β-strand	101-106	6	46
β-strand	107-109	3	45
α-helix	112-114	3
β-strand	119-123	5	44
β-strand	127-137	11	43
β-strand	140-146	7	43
β-strand	147	1	48
β-strand	152	1	48
β-strand	154-156	3	42
β-strand	159-163	5	42
β-strand	176-180	5	44
β-strand	183-186	4	44
β-strand	204-205	2	44
β-strand	213-214	2	44
β-strand	220-221	2	49
α-helix	222-225	4
β-strand	233-234	2	49
α-helix	236-238	3
α-helix	239-245	7
α-helix	256-258	3
β-strand	260-262	3	50
β-strand	267-269	3	50
β-strand	275-281	7	42
α-helix	284-286	3
β-strand	296	1	51
β-strand	300-306	7	52
β-strand	307	1	53
β-strand	314-319	6	52
β-strand	322	1	51
β-strand	326-329	4	54
β-strand	330-332	3	55
β-strand	338-339	2	56
β-strand	343-346	4	54
β-strand	351-355	5	52
β-strand	356-357	2	56
β-strand	362-366	5	57
β-strand	367-369	3	55
β-strand	372	1	55
β-strand	375-379	5	57
α-helix	380	1
β-strand	381	1	53
α-helix	382	1
β-strand	387-388	2	58

Chain E: 6 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	8	1	59
β-strand	13-15	3	60
β-strand	24-26	3	60
β-strand	30	1	61
β-strand	34	1	62
β-strand	42-48	7	62
β-strand	49	1	63
β-strand	50	1	62
β-strand	63-67	5	63
β-strand	70-74	5	63
α-helix	76-78	3
β-strand	81-82	2	64
β-strand	86	1	64
α-helix	87	1
β-strand	88-100	13	62
β-strand	107-111	5	64
β-strand	119-123	5	64
α-helix	129-131	3
β-strand	144-149	6	65
β-strand	163-166	4	66
β-strand	170-173	4	67
α-helix	174-176	3
β-strand	184-186	3	68
β-strand	193-197	5	67
β-strand	206-207	2	67
β-strand	211-213	3	68
β-strand	221-226	6	67
β-strand	231	1	59
β-strand	232-233	2	66
β-strand	249-251	3	66
β-strand	260-265	6	65
α-helix	267-270	4
β-strand	271-275	5	69
β-strand	278-283	6	69
β-strand	289-295	7	70
β-strand	303-307	5	70
β-strand	311-316	6	69
β-strand	322-326	5	70
α-helix	330-331	2
β-strand	332-334	3	70
β-strand	335-336	2	14

Chain F: 5 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	8	1	71
β-strand	13-14	2	72
β-strand	17	1	73
β-strand	25-26	2	72
β-strand	34	1	74
β-strand	42-48	7	74
β-strand	49	1	75
β-strand	50	1	74
β-strand	62-67	6	75
β-strand	70-75	6	75
β-strand	80-82	3	73
β-strand	86	1	73
β-strand	89-99	11	74
α-helix	101-103	3
β-strand	104	1	76
β-strand	107-110	4	73
β-strand	111	1	77
β-strand	119	1	77
β-strand	122-123	2	73
β-strand	127	1	76
α-helix	129-131	3
β-strand	145-151	7	78
β-strand	163-166	4	79
β-strand	171-172	2	80
β-strand	181	1	81
β-strand	183	1	81
β-strand	193-196	4	80
β-strand	199	1	82
β-strand	206-207	2	80
β-strand	216	1	82
β-strand	222-225	4	80
β-strand	231	1	71
β-strand	232-233	2	79
β-strand	249-251	3	79
β-strand	258-264	7	78
α-helix	267-269	3
β-strand	271-275	5	83
β-strand	278-283	6	83
β-strand	289-295	7	84
β-strand	303-307	5	84
β-strand	311-316	6	83
β-strand	322-325	4	84
α-helix	330-331	2
β-strand	332-334	3	84

Chain G: 4 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	13-15	3	85
β-strand	24-26	3	85
β-strand	30-34	5	86
β-strand	42-48	7	86
β-strand	49	1	87
β-strand	50	1	86
β-strand	62-65	4	87
β-strand	72-75	4	87
α-helix	76-78	3
β-strand	80-82	3	88
β-strand	86	1	88
β-strand	88-100	13	86
β-strand	104-111	8	88
β-strand	119-127	9	88
β-strand	144-149	6	89
β-strand	162-163	2	90
β-strand	165-166	2	91
α-helix	167-170	4
β-strand	171-173	3	92
β-strand	179-180	2	93
β-strand	183-185	3	93
β-strand	192-194	3	92
β-strand	196	1	94
β-strand	206-207	2	92
β-strand	212-213	2	93
β-strand	222	1	94
β-strand	223-226	4	92
β-strand	232-233	2	91
β-strand	240	1	31
β-strand	248	1	91
β-strand	251-252	2	90
β-strand	260-265	6	89
α-helix	268-270	3
β-strand	271-275	5	95
β-strand	278-283	6	95
β-strand	289-295	7	96
β-strand	303-307	5	96
β-strand	311-316	6	95
β-strand	322-326	5	96
α-helix	330-331	2
β-strand	332-334	3	96
β-strand	335	1	41

Chain H: 7 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	4-7	4
β-strand	8	1	97
β-strand	13-14	2	98
β-strand	25-26	2	98
β-strand	32-34	3	99
β-strand	42-48	7	99
β-strand	49	1	100
β-strand	50	1	99
β-strand	52	1	101
β-strand	58	1	101
β-strand	62-67	6	100
β-strand	70-75	6	100
α-helix	76-78	3
β-strand	79-82	4	102
β-strand	86	1	102
β-strand	88-100	13	99
β-strand	107-111	5	102
β-strand	119-123	5	102
α-helix	129-132	4
β-strand	135	1	103
β-strand	145-152	8	104
β-strand	163	1	105
β-strand	165-166	2	106
α-helix	167-169	3
β-strand	171-172	2	107
α-helix	174-176	3
β-strand	179	1	108
β-strand	184-186	3	108
β-strand	192-195	4	107
β-strand	206-207	2	107
β-strand	211-213	3	108
β-strand	223-226	4	107
β-strand	231	1	97
β-strand	232-233	2	106
β-strand	251	1	105
β-strand	257-264	8	104
α-helix	267-269	3
β-strand	271-275	5	109
β-strand	278-283	6	109
β-strand	289-295	7	103
β-strand	303-307	5	103
β-strand	311-316	6	109
β-strand	322-326	5	103
α-helix	330-331	2
β-strand	332-334	3	103
β-strand	335-336	2	58

12 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	393	Chikungunya virus	Q88628
E2 glycoprotein	E, F, G, H	protein	338	Chikungunya virus	Q88628
Fab CHK-265 heavy chain	I, J, K, L	protein	218	Homo sapiens
Fab CHK-265 light chain	M, N, O, P	protein	211	Homo sapiens
E3	Q, R, S, T	protein	60	Chikungunya virus	Q88628

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

>6W09_1 E1 glycoprotein (chains A, B, C, D)
YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYV
KCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDTENTQLSEAHVEKSESCKTEFAS
AYRAHTASASAKLRVLYQGNNVTVSAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVY
KGDVYNMDYPPFGAGRPGQFGDIQSRTPESEDVYANTQLVLQRPSAGTVHVPYSQAPSGF
KYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMS
CEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTAL
ASAEFRVQVCSTQVHCAAECHPPKDHIVNYPAS

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

>6W09_2 E2 glycoprotein (chains E, F, G, H)
NFNVYKAIRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDW
TKLRYMDNHMPADAERARLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSGKISHS
CTHPFHHDPPVIGREKFHSRPQHRKELPCSTYAQSTAATAEEIEVHMPPDTPDRTLMSQQ
SGNVKITVNSQTVRYKCNCGDSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPR
NAELGDRKGKVHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEP
NYQEEWVTHKKEVIRTVPTEGLEVTWGNNEPYKYWPQL

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

>6W09_3 Fab CHK-265 heavy chain (chains I, J, K, L)
QIQLVQSGREVKNPGETVKISCKASGYTFTEYPMLWVKQAPGKGFRWMGLIYTNTGEPTY
AEEFKGRFVFSLEISASTAYLQINNLTNEDTATYFCVRDYFISLDYWGQGTTLTVSSAKT
TAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYT
LSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIESRR

Sequence of entity 4 (M, N, O, P), FASTA

>6W09_4 Fab CHK-265 light chain (chains M, N, O, P)
QAVVTQESALTTSPGETVTLTCRSNIGAVTSSNCANWVQEKPDHFFTGLIGDTNNRRSGV
PARFSGSLIGDKAALTITGAQTEDEAIYFCALWYNNLWVFGGGTKLTVLGQPKSSPSVTL
FPPSSEELETNKATLVCTITDFYPGVVTVDWKVDGTPVTQGMETTQPSKQSNNKYMASSY
LTLTARAWERHSSYSCQVTHEGHTVEKSLSR

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

>6W09_5 E3 (chains Q, R, S, T)
PVMCLLANTTFPCSQPPCTPCCYEKEPEKTLRMLEDNVMSPGYYQLLQASLTCSPRRQRR

Primary citation

Human mAbs Broadly Protect against Arthritogenic Alphaviruses by Recognizing Conserved Elements of the Mxra8 Receptor-Binding Site. Powell, L.A., Miller, A., Fox, J.M. et al. Cell Host Microbe (2020) 28:699-711.e7. DOI 10.1016/j.chom.2020.07.008 · 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
6NK7 4.99 Å, Electron Cryo-Microscopy of Chikungunya in Complex with Mouse Mxra8 Receptor

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