6BSP: U4 Heavy chain

High-Resolution Structure Analysis of Antibody V5 and U4 Conformational Epitope on Human Papillomavirus 16. Determined by electron microscopy at 4.7 Å resolution. Released 14 Feb 2018.

Method: Electron microscopy
Resolution: 4.7 Å
Organisms: Mus musculus, Human papillomavirus type 16
Chains: 8
Atoms: 23,690
Mol. weight: 338.53 kDa
Released: 14 Feb 2018

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

Secondary structure: helices and β-sheets

6BSP contains 122 α-helices and 220 β-strands across 8 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: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
β-strand	17-23	7	1
β-strand	34-37	4	2
β-strand	47-51	5	2
β-strand	57-58	2	2
β-strand	68-72	5	1
β-strand	77-82A	7	1
α-helix	84-86	3
β-strand	91-94	4	2

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	3
β-strand	24	1	3
β-strand	34-38	5	4
β-strand	45	1	4
β-strand	49	1	5
β-strand	53	1	5
β-strand	63-65	3	6
β-strand	70	1	3
β-strand	72-74	3	6
β-strand	85-89	5	4
α-helix	96	1
β-strand	102	1	4

Chain C: 21 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	7
β-strand	42-46	5	8
β-strand	47	1	9
β-strand	52-53	2	10
β-strand	60-62	3	10
β-strand	64	1	9
β-strand	69	1	11
β-strand	71-76	6	12
α-helix	80-82	3
β-strand	96-101	6	7
β-strand	105-108	4	7
α-helix	112-113	2
β-strand	118-123	6	13
β-strand	128	1	14
β-strand	145-149	5	13
α-helix	151-152	2
β-strand	153-160	8	12
α-helix	163-164	2
β-strand	165-171	7	15
α-helix	172-175	4
α-helix	179-181	3
β-strand	188-194	7	15
α-helix	199	1
β-strand	200-201	2	11
α-helix	202	1
β-strand	209	1	16
α-helix	210-213	4
α-helix	222-225	4
β-strand	228	1	16
β-strand	229-230	2	11
β-strand	231-232	2	15
α-helix	234-238	5
β-strand	248-254	7	12
β-strand	256-261	6	14
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	14
β-strand	323	1	7
α-helix	325-327	3
β-strand	328-335	8	12
α-helix	340-341	2
β-strand	342-347	6	17
α-helix	357-359	3
β-strand	360-365	6	17
β-strand	366-370	5	8
β-strand	371-382	12	7
α-helix	385-394	10
α-helix	397-401	5
β-strand	423	1	18
β-strand	448-450	3	12
β-strand	456	1	7
α-helix	463-472	10

Chain D: 19 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	29-30	2	19
β-strand	36-38	3	19
β-strand	44	1	20
β-strand	47	1	21
β-strand	53	1	22
β-strand	60	1	22
β-strand	64	1	21
β-strand	69	1	23
β-strand	72-74	3	24
β-strand	75-76	2	25
α-helix	80-82	3
β-strand	96-108	13	19
α-helix	111-113	3
β-strand	114	1	26
β-strand	118-120	3	27
β-strand	128	1	28
β-strand	147-149	3	27
β-strand	153-160	8	24
β-strand	165-171	7	29
α-helix	179-180	2
β-strand	188-194	7	29
β-strand	200	1	23
α-helix	210-213	4
α-helix	222-226	5
β-strand	229	1	23
β-strand	232	1	29
α-helix	234-239	6
β-strand	248-255	8	24
β-strand	256-261	6	28
α-helix	273-275	3
α-helix	281-284	4
α-helix	286-288	3
β-strand	292-296	5	28
β-strand	311	1	19
β-strand	325	1	30
β-strand	328	1	30
β-strand	330-335	6	24
β-strand	338	1	26
β-strand	342-347	6	31
β-strand	354	1	32
α-helix	357-359	3
β-strand	360-365	6	31
β-strand	368	1	20
β-strand	371-382	12	19
α-helix	385-386	2
α-helix	387-391	5
α-helix	392-394	3
α-helix	397-400	4
α-helix	426-428	3
α-helix	441-443	3
β-strand	449-450	2	25
α-helix	452-454	3
β-strand	456	1	19
α-helix	466-472	7

Chain E: 19 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	33
β-strand	42-46	5	34
β-strand	47	1	35
β-strand	52-53	2	36
β-strand	60-62	3	36
β-strand	64	1	35
β-strand	69	1	37
β-strand	72-76	5	38
α-helix	80-82	3
β-strand	97-101	5	33
β-strand	105-108	4	33
α-helix	112-113	2
β-strand	118-120	3	39
β-strand	147-149	3	39
α-helix	150-152	3
β-strand	153-160	8	38
α-helix	163-164	2
β-strand	165-170	6	40
α-helix	173-175	3
α-helix	179-181	3
β-strand	189-194	6	40
β-strand	200	1	37
β-strand	209	1	41
α-helix	210-213	4
β-strand	214	1	31
α-helix	222-226	5
β-strand	228	1	41
β-strand	231-232	2	40
α-helix	234-239	6
β-strand	248-254	7	38
β-strand	256-261	6	42
α-helix	273-275	3
α-helix	281-284	4
α-helix	286-288	3
β-strand	292-296	5	42
β-strand	300-301	2	43
β-strand	323	1	33
α-helix	325-327	3
β-strand	328-335	8	38
β-strand	342-347	6	44
α-helix	357-359	3
β-strand	360-365	6	44
β-strand	366-370	5	34
β-strand	371-381	11	33
α-helix	385-394	10
α-helix	397-401	5
α-helix	440-443	4
β-strand	448-450	3	38
β-strand	456	1	33
α-helix	459-461	3
α-helix	465-472	8

Chain F: 20 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	45
β-strand	42-46	5	46
β-strand	47	1	47
β-strand	52-53	2	48
β-strand	60-62	3	48
β-strand	64	1	47
β-strand	69	1	49
β-strand	72-76	5	43
α-helix	80-82	3
β-strand	96-101	6	45
β-strand	105-108	4	45
α-helix	112-113	2
β-strand	118-120	3	50
β-strand	147-149	3	50
α-helix	150-152	3
β-strand	153-160	8	43
α-helix	163-164	2
β-strand	165-170	6	51
α-helix	173-175	3
α-helix	179-181	3
β-strand	189-194	6	51
β-strand	200	1	49
β-strand	209	1	52
α-helix	210-213	4
β-strand	214	1	44
α-helix	222-226	5
β-strand	228	1	52
β-strand	231-232	2	51
α-helix	234-238	5
β-strand	248-255	8	43
β-strand	256-261	6	53
β-strand	266	1	44
α-helix	270-272	3
α-helix	273-275	3
β-strand	278	1	32
α-helix	281-284	4
α-helix	286-288	3
β-strand	292-296	5	53
β-strand	300-301	2	54
β-strand	323	1	45
α-helix	325-327	3
β-strand	328-335	8	43
β-strand	342-347	6	55
α-helix	357-359	3
β-strand	360-365	6	55
β-strand	366-370	5	46
β-strand	371-382	12	45
α-helix	385-394	10
α-helix	397-401	5
α-helix	440-443	4
β-strand	448-450	3	43
β-strand	456	1	45
α-helix	459-461	3
α-helix	463-472	10

Chain G: 21 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	56
β-strand	42-46	5	57
β-strand	47	1	58
β-strand	52-53	2	59
β-strand	60-62	3	59
β-strand	64	1	58
β-strand	69	1	60
β-strand	71-76	6	54
α-helix	80-82	3
β-strand	97-101	5	56
β-strand	105-108	4	56
α-helix	112-113	2
β-strand	118-120	3	61
β-strand	147-149	3	61
α-helix	150-152	3
β-strand	153-160	8	54
α-helix	163-164	2
β-strand	165-170	6	62
α-helix	173-175	3
α-helix	179-181	3
β-strand	189-194	6	62
β-strand	200	1	60
β-strand	209	1	63
α-helix	210-213	4
β-strand	214	1	55
α-helix	222-226	5
β-strand	228	1	63
β-strand	231-232	2	62
α-helix	234-238	5
β-strand	248-255	8	54
β-strand	256-261	6	64
β-strand	266	1	55
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	64
β-strand	300-301	2	65
β-strand	323	1	56
α-helix	325-327	3
β-strand	328-335	8	54
β-strand	342-347	6	66
α-helix	357-359	3
β-strand	360-365	6	66
β-strand	366-370	5	57
β-strand	371-381	11	56
α-helix	385-394	10
α-helix	397-401	5
α-helix	413-415	3
α-helix	440-443	4
β-strand	448-450	3	54
β-strand	456	1	56
α-helix	459-461	3
α-helix	465-472	8

Chain H: 20 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	67
β-strand	42-46	5	18
β-strand	47	1	68
β-strand	52-53	2	69
β-strand	60-62	3	69
β-strand	64	1	68
β-strand	69	1	70
β-strand	71-76	6	65
α-helix	80-82	3
β-strand	97-101	5	67
β-strand	105-108	4	67
α-helix	112-113	2
β-strand	118-120	3	71
β-strand	147-149	3	71
α-helix	150-152	3
β-strand	153-160	8	65
α-helix	163-164	2
β-strand	165-170	6	72
α-helix	173-175	3
α-helix	179-181	3
β-strand	189-194	6	72
β-strand	200	1	70
β-strand	209	1	73
α-helix	210-213	4
β-strand	214	1	66
α-helix	222-226	5
β-strand	228	1	73
β-strand	229	1	70
β-strand	231-232	2	72
α-helix	234-238	5
β-strand	248-255	8	65
β-strand	256-261	6	74
β-strand	266-267	2	66
α-helix	273-275	3
α-helix	281-284	4
α-helix	286-288	3
β-strand	292-296	5	74
β-strand	300-301	2	24
β-strand	323	1	67
α-helix	325-327	3
β-strand	328-335	8	65
β-strand	342-347	6	75
α-helix	357-359	3
β-strand	360-365	6	75
β-strand	366-370	5	18
β-strand	371-381	11	67
α-helix	385-394	10
α-helix	397-401	5
α-helix	429	1
α-helix	440-443	4
β-strand	448-450	3	65
β-strand	456	1	67
α-helix	459-461	3
α-helix	465-472	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
U4 Heavy chain	A	protein	109	Mus musculus
U4 Light chain	B	protein	110	Mus musculus
Major capsid protein L1	C, D, E, F, G, H	protein	469	Human papillomavirus type 16	P03101 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6BSP_1 U4 Heavy chain (chains A)
SGGGLVKPGGSLKLSCEASGFTFSSYAMSWVRQTPEKRLEWVASISSGGNTHYPDSVKGR
FTISRDNARNILYLQMSSLRSEDTAMYYCARGLYYGYDEGSDFDYWGQG

Sequence of entity 2 (B), FASTA

>6BSP_2 U4 Light chain (chains B)
DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSNTQKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYYSYPLTFGAGTKL

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

>6BSP_3 Major capsid protein L1 (chains C, D, E, F, G, H)
YLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYR
VFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTEN
ASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAVNPGDCPPLELI
NTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLR
REQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPY
WLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYD
LQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKH
TPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKF

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…
6BT3 4.7 Å, High-Resolution Structure Analysis of Antibody V5 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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