6BT3: V5 Fab Light-chain

Name: PDB 6BT3: High-Resolution Structure Analysis of Antibody V5 Conformational Epitope on Human Papillomavirus 16
Published: 2018-01-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

High-Resolution Structure Analysis of Antibody V5 Conformational Epitope on Human Papillomavirus 16. Determined by electron microscopy at 4.7 Å resolution. Released 17 Jan 2018.

Method: Electron microscopy
Resolution: 4.7 Å
Organisms: Mus musculus, Human papillomavirus type 16
Chains: 14
Atoms: 35,383
Mol. weight: 526.88 kDa
Released: 17 Jan 2018

Explore 6BT3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BT3 contains 136 α-helices and 401 β-strands across 14 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: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-11	2	2
β-strand	20-25	6	1
β-strand	31	1	3
β-strand	36	1	3
β-strand	39	1	4
β-strand	40-44	5	2
β-strand	51-55	5	2
β-strand	68-70	3	1
β-strand	78-81	4	1
α-helix	86-88	3
β-strand	91-93	3	2
β-strand	95	1	5
β-strand	96	1	4
β-strand	104	1	5
β-strand	108-110	3	2
β-strand	121-122	2	6
α-helix	125-127	3
α-helix	128-133	6
β-strand	135-145	11	6
β-strand	152-156	5	7
β-strand	159-160	2	7
β-strand	165-170	6	6
β-strand	179-188	10	6
α-helix	189-192	4
β-strand	198-202	5	7
β-strand	212-215	4	7
β-strand	216	1	8
β-strand	219	1	8

Chains B, D, F and H: 1 helix, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	9
β-strand	9-12	4	10
β-strand	17-18	2	11
β-strand	21-25	5	9
β-strand	34-37	4	12
β-strand	38-39	2	10
β-strand	47-52	6	12
β-strand	57-60	4	12
β-strand	68-69	2	11
β-strand	72-73	2	9
β-strand	78-80	3	9
β-strand	82-84	3	11
β-strand	92-94	3	10
β-strand	117-120	4	10
β-strand	126	1	13
β-strand	129-133	5	14
β-strand	147-148	2	15
β-strand	149-153	5	14
β-strand	155	1	16
β-strand	156	1	13
β-strand	162-164	3	17
α-helix	175	1
β-strand	176-180	5	16
β-strand	184-187	4	16
β-strand	190-191	2	15
β-strand	202-206	5	17
β-strand	208	1	18
β-strand	213	1	18
β-strand	216-219	4	17

Chains C and G: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-11	2	20
β-strand	19-25	7	19
β-strand	31	1	21
β-strand	36	1	21
β-strand	39	1	22
β-strand	42-44	3	20
β-strand	51-52	2	20
β-strand	68-72	5	19
β-strand	77-81	5	19
α-helix	86-88	3
β-strand	91-93	3	20
β-strand	96	1	22
β-strand	103	1	22
β-strand	108-110	3	20
β-strand	121-122	2	23
α-helix	125-127	3
α-helix	128-133	6
β-strand	135-145	11	23
β-strand	152-156	5	24
β-strand	159-161	3	24
β-strand	165-170	6	23
β-strand	179-188	10	23
α-helix	189-192	4
β-strand	198-202	5	24
β-strand	212-215	4	24
β-strand	216	1	25
β-strand	219	1	25

Chain E: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	36
β-strand	10-11	2	37
β-strand	20-25	6	36
β-strand	31	1	38
β-strand	36	1	38
β-strand	39	1	39
β-strand	40-44	5	37
β-strand	51-55	5	37
β-strand	68-70	3	36
β-strand	78-81	4	36
α-helix	86-88	3
β-strand	91-93	3	37
β-strand	95	1	40
β-strand	96	1	39
β-strand	104	1	40
β-strand	108-110	3	37
β-strand	121-122	2	41
α-helix	125-127	3
α-helix	128-133	6
β-strand	135-145	11	41
β-strand	152-156	5	42
β-strand	159-160	2	42
β-strand	165-170	6	41
β-strand	179-188	10	41
α-helix	189-192	4
β-strand	198-202	5	42
β-strand	212-215	4	42

Chain I: 18 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	29-38	10	70
β-strand	42-44	3	71
β-strand	47	1	72
β-strand	52-53	2	73
β-strand	60-62	3	73
β-strand	64	1	72
β-strand	69	1	74
β-strand	71-76	6	75
β-strand	96-101	6	70
β-strand	104-108	5	70
β-strand	118-123	6	76
β-strand	128	1	77
β-strand	145-149	5	76
α-helix	151-153	3
β-strand	154-160	7	75
β-strand	165-171	7	78
α-helix	172-174	3
α-helix	179-181	3
β-strand	188-194	7	78
α-helix	199	1
β-strand	200-201	2	74
α-helix	202	1
β-strand	208-209	2	74
α-helix	210-213	4
α-helix	222-225	4
β-strand	228-230	3	74
β-strand	231-232	2	78
α-helix	234-238	5
β-strand	248-253	6	75
β-strand	256-262	7	77
α-helix	273-275	3
α-helix	281-283	3
α-helix	286-288	3
β-strand	291-296	6	77
β-strand	311-312	2	70
β-strand	323	1	70
α-helix	325-327	3
β-strand	328-335	8	75
β-strand	342-347	6	79
α-helix	357-359	3
β-strand	360-365	6	79
β-strand	368-370	3	71
β-strand	371-382	12	70
α-helix	385-394	10
α-helix	397-401	5
β-strand	448-450	3	75
β-strand	456	1	70
α-helix	459-461	3
α-helix	463-472	10

Chain J: 20 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	80
β-strand	42-46	5	81
β-strand	47	1	82
β-strand	52-53	2	83
β-strand	60-62	3	83
β-strand	64	1	82
β-strand	69	1	84
β-strand	72-76	5	85
α-helix	80-82	3
β-strand	97-101	5	80
β-strand	105-108	4	80
α-helix	112-113	2
β-strand	118-120	3	86
β-strand	147-149	3	86
α-helix	150-152	3
β-strand	153-160	8	85
α-helix	163-164	2
β-strand	165-171	7	87
α-helix	173-175	3
α-helix	179-181	3
β-strand	188-194	7	87
β-strand	200	1	84
β-strand	209	1	88
α-helix	210-213	4
β-strand	214	1	89
α-helix	222-225	4
β-strand	228	1	88
β-strand	231-232	2	87
α-helix	234-238	5
β-strand	248-255	8	85
β-strand	256-261	6	90
β-strand	266	1	89
α-helix	270-272	3
α-helix	273-275	3
α-helix	281-284	4
α-helix	286-288	3
β-strand	292-296	5	90
β-strand	300-301	2	91
β-strand	323	1	80
α-helix	325-327	3
β-strand	328-335	8	85
β-strand	341-347	7	81
β-strand	360-370	11	81
β-strand	371-381	11	80
α-helix	385-394	10
α-helix	397-400	4
α-helix	426-428	3
α-helix	440-443	4
β-strand	448-450	3	85
β-strand	456	1	80
α-helix	459-461	3
α-helix	463-472	10

Chain K: 19 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	92
β-strand	42-46	5	93
β-strand	47	1	94
β-strand	52-53	2	95
β-strand	60-62	3	95
β-strand	64	1	94
β-strand	69	1	96
β-strand	73-76	4	91
α-helix	80-82	3
β-strand	97-101	5	92
β-strand	105-108	4	92
α-helix	112-113	2
β-strand	118-120	3	97
β-strand	147-149	3	97
α-helix	150-152	3
β-strand	153-160	8	91
α-helix	163-164	2
β-strand	165-170	6	98
α-helix	173-175	3
α-helix	179-181	3
β-strand	189-194	6	98
β-strand	200	1	96
β-strand	209	1	99
α-helix	210-213	4
β-strand	214	1	81
α-helix	222-225	4
β-strand	228	1	99
β-strand	231-232	2	98
α-helix	234-238	5
β-strand	248-255	8	91
β-strand	256-261	6	100
β-strand	266-267	2	81
α-helix	270-272	3
α-helix	273-275	3
α-helix	281-283	3
α-helix	286-288	3
β-strand	292-296	5	100
β-strand	300-301	2	101
β-strand	323	1	92
α-helix	325-327	3
β-strand	328-335	8	91
β-strand	341-347	7	93
β-strand	360-370	11	93
β-strand	371-381	11	92
α-helix	385-394	10
α-helix	397-400	4
α-helix	440-443	4
β-strand	448-450	3	91
β-strand	456	1	92
α-helix	459-461	3
α-helix	463-472	10

Chain L: 19 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	102
β-strand	42-46	5	103
β-strand	47	1	104
β-strand	52-53	2	105
β-strand	60-62	3	105
β-strand	64	1	104
β-strand	69	1	106
β-strand	73-76	4	101
α-helix	80-82	3
β-strand	97-101	5	102
β-strand	105-108	4	102
α-helix	112-113	2
β-strand	118-120	3	107
β-strand	147-149	3	107
α-helix	150-152	3
β-strand	153-160	8	101
α-helix	163-164	2
β-strand	165-170	6	108
α-helix	173-175	3
α-helix	179-181	3
β-strand	189-194	6	108
β-strand	200	1	106
β-strand	209	1	109
α-helix	210-213	4
β-strand	214	1	93
α-helix	222-226	5
β-strand	228	1	109
β-strand	231-232	2	108
α-helix	234-238	5
β-strand	248-255	8	101
β-strand	256-261	6	110
β-strand	266	1	93
α-helix	270-272	3
α-helix	273-275	3
α-helix	281-283	3
α-helix	286-288	3
β-strand	292-296	5	110
β-strand	300-301	2	111
β-strand	323	1	102
α-helix	325-327	3
β-strand	328-335	8	101
β-strand	341-347	7	103
β-strand	360-370	11	103
β-strand	371-381	11	102
α-helix	385-394	10
α-helix	397-400	4
α-helix	440-443	4
β-strand	448-450	3	101
β-strand	456	1	102
α-helix	459-461	3
α-helix	463-472	10

2 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
V5 Fab Light-chain	A, C, E, G	protein	220	Mus musculus
V5 Fab Heavy-chain	B, D, F, H	protein	223	Mus musculus
Major capsid protein L1	I, J, K, L, M, N	protein	503	Human papillomavirus type 16	P03101 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>6BT3_1 V5 Fab Light-chain (chains A, C, E, G)
DIVMTQSPSSLAMSVGQKVTMSCKSSQSLLDSRNQKNYLAWYQQKPGQSPKLLVYFASTR
ESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPLTFGAGTKLELKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWAIDGAERAGGVLNSFTGQDSKDSTYS
MSSTLTLTKDEYERHASYTCEATHKTSTAPIVKSFNRGAA

Sequence of entity 2 (B, D, F, H), FASTA

>6BT3_2 V5 Fab Heavy-chain (chains B, D, F, H)
EVKLEQSGAELARPGASVKLSCKASGYTFASYWMQWVKQRPGQGLEWIGAIYPGDGDTWY
TQKFKGKATLTADKSSSTAYMQLSSLASEDSAVYYCARPPYYYGTTYYFDYWGQGTTLTV
SGAKTTAPSVYPLAPAAGAAGAGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVL
ADLYTLSSSVTVTSSTWPAESITCNVAHPASSTKVDKKIEPRG

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

>6BT3_3 Major capsid protein L1 (chains I, J, K, L, M, N)
MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKI
LVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGH
PLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAV
NPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSE
PYGDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMV
TSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNF
KEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRF
VTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKF
TLGKRKATPTTSSTSTTAKRKKR

Primary citation

High-Resolution Structure Analysis of Antibody V5 and U4 Conformational Epitopes on Human Papillomavirus 16. Guan, J., Bywaters, S.M., Brendle, S.A. et al. Viruses (2017) 9. DOI 10.3390/v9120374 · PubMed

Other PDB entries of the same protein (UniProt P03101 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8XES 1.78 Å, The structure of HLA-A/L1-1
9NZU 1.9 Å, Atomic resolution cryoEM structure of HPV16 bound to heparin
8XFZ 2.32 Å, The structure of HLA-A/L1-2
7KZF 3.1 Å, High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and…
7CN2 3.43 Å, Subparticle refinement of human papillomavirus type 16 pesudovirus in complex with…
1DZL 3.5 Å, L1 protein of human papillomavirus 16
5KEP 4.3 Å, High resolution cryo-EM maps of Human Papillomavirus 16 reveal L2 location and…
5KEQ 4.3 Å, High resolution cryo-EM maps of Human papillomavirus 16 reveal L2 location and…
6BSP 4.7 Å, High-Resolution Structure Analysis of Antibody V5 and U4 Conformational Epitope on Human…
3J6R 9.1 Å, Electron cryo-microscopy of Human Papillomavirus Type 16 capsid
3JBA 12.0 Å, The U4 antibody epitope on human papillomavirus 16 identified by cryo-EM
3J8W 13.0 Å, Cryo-EM reconstruction of quasi-HPV16 complex with H263.A2 Fab

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