7CN2: PDB entry 7CN2

Subparticle refinement of human papillomavirus type 16 pesudovirus in complex with H16.001 Fab. Determined by electron microscopy at 3.43 Å resolution. Released 2 Sept 2020.

Method: Electron microscopy
Resolution: 3.43 Å
Organisms: Oryctolagus cuniculus, Human papillomavirus type 16
Chains: 18
Atoms: 32,841
Mol. weight: 486.38 kDa
Released: 2 Sept 2020

Explore 7CN2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7CN2 contains 121 α-helices and 370 β-strands across 18 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: 11 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	14-18	5
α-helix	24-26	3
β-strand	34-38	5	37
β-strand	42-46	5	38
β-strand	47	1	39
β-strand	53	1	40
β-strand	60	1	40
β-strand	64	1	39
β-strand	72-76	5	41
α-helix	77-79	3
β-strand	96-108	13	37
β-strand	118	1	42
β-strand	128	1	43
β-strand	149	1	42
β-strand	154-155	2	44
β-strand	156-160	5	41
β-strand	165-169	5	45
β-strand	190-194	5	45
β-strand	200-201	2	46
β-strand	208	1	45
α-helix	222-224	3
β-strand	229-230	2	46
β-strand	231-232	2	45
α-helix	236-239	4
β-strand	252-253	2	44
β-strand	257-260	4	47
β-strand	261	1	43
α-helix	270-272	3
β-strand	293-295	3	47
β-strand	312	1	37
β-strand	323-324	2	37
α-helix	325-327	3
β-strand	328-334	7	41
β-strand	342-347	6	48
β-strand	360-365	6	48
β-strand	366-370	5	38
β-strand	371-382	12	37
α-helix	387-394	8
α-helix	396-400	5
β-strand	418	1	49
β-strand	426	1	50
α-helix	440-443	4
β-strand	447-450	4	41
β-strand	456	1	37
α-helix	465-471	7

Chain B: 21 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	51
β-strand	42-46	5	52
β-strand	47	1	53
β-strand	52-53	2	54
β-strand	60-62	3	54
β-strand	64	1	53
β-strand	69	1	55
β-strand	71-76	6	56
α-helix	80-82	3
β-strand	83	1	57
β-strand	96-108	13	51
α-helix	112-113	2
β-strand	114	1	58
β-strand	117-123	7	59
β-strand	125-128	4	60
β-strand	145-150	6	59
α-helix	151-152	2
β-strand	153-160	8	56
β-strand	165-170	6	61
α-helix	179-180	2
α-helix	184-187	4
β-strand	188	1	50
β-strand	189-194	6	61
α-helix	199	1
β-strand	200	1	55
α-helix	201-202	2
β-strand	208	1	61
β-strand	209	1	62
α-helix	222-224	3
β-strand	228	1	62
β-strand	229	1	55
β-strand	231-232	2	61
α-helix	234-238	5
α-helix	241-243	3
β-strand	248-254	7	56
β-strand	255	1	63
β-strand	256-263	8	60
β-strand	266-267	2	64
α-helix	270-272	3
α-helix	273-275	3
α-helix	277-279	3
α-helix	281-283	3
β-strand	291-296	6	60
β-strand	300-301	2	65
β-strand	311-312	2	51
β-strand	324	1	51
β-strand	328-335	8	56
β-strand	338	1	58
α-helix	340	1
β-strand	341-342	2	52
β-strand	345-347	3	66
α-helix	357-359	3
β-strand	360-362	3	66
β-strand	365-370	6	52
β-strand	371-382	12	51
α-helix	385-394	10
α-helix	397-401	5
α-helix	414-416	3
β-strand	447-450	4	56
β-strand	456	1	51
α-helix	459-461	3
α-helix	463-472	10

Chain C: 13 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	57
β-strand	29-38	10	67
β-strand	42-43	2	68
β-strand	46	1	69
β-strand	47	1	70
β-strand	52-53	2	71
β-strand	60-62	3	71
β-strand	64	1	70
β-strand	69	1	72
β-strand	71-76	6	65
α-helix	80-82	3
β-strand	96-108	13	67
β-strand	118-123	6	73
β-strand	128	1	74
α-helix	135-138	4
β-strand	145-149	5	73
α-helix	151-152	2
β-strand	153-160	8	65
β-strand	165-171	7	75
α-helix	173-175	3
α-helix	185-187	3
β-strand	188-194	7	75
α-helix	199	1
β-strand	200-201	2	72
α-helix	202	1
β-strand	208	1	75
β-strand	209	1	76
α-helix	210-213	4
β-strand	214	1	66
α-helix	222-224	3
β-strand	228	1	76
β-strand	229-230	2	72
β-strand	231-232	2	75
α-helix	234-238	5
β-strand	249-255	7	65
β-strand	256-260	5	77
β-strand	261	1	74
β-strand	266	1	66
α-helix	281-283	3
β-strand	293-296	4	77
β-strand	300-301	2	78
β-strand	310-312	3	67
β-strand	323	1	67
β-strand	328-335	8	65
β-strand	345-347	3	79
β-strand	360-362	3	79
β-strand	366	1	69
β-strand	369-370	2	68
β-strand	371-382	12	67
α-helix	385-394	10
β-strand	447-450	4	65
β-strand	455-456	2	67
α-helix	463-472	10

Chain D: 16 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	28-38	11	80
β-strand	42-46	5	81
β-strand	47	1	82
β-strand	52	1	83
β-strand	62	1	83
β-strand	64	1	82
β-strand	69	1	84
β-strand	72-76	5	78
β-strand	96-108	13	80
β-strand	114	1	85
β-strand	118-123	6	86
β-strand	127-128	2	87
α-helix	135-138	4
β-strand	145-149	5	86
α-helix	151-152	2
β-strand	153-160	8	78
α-helix	163-164	2
β-strand	165-168	4	88
β-strand	169	1	89
α-helix	173-175	3
α-helix	185-187	3
β-strand	191-194	4	88
α-helix	199	1
β-strand	200	1	84
α-helix	201-202	2
β-strand	208	1	89
α-helix	210-213	4
α-helix	222-224	3
β-strand	229	1	84
β-strand	231-232	2	88
α-helix	234-238	5
β-strand	248-255	8	78
β-strand	256-262	7	87
β-strand	266-267	2	79
α-helix	270-272	3
α-helix	281-283	3
β-strand	291-296	6	87
β-strand	300	1	90
β-strand	311-312	2	80
β-strand	330-335	6	78
β-strand	338	1	85
β-strand	342-347	6	91
α-helix	357-359	3
β-strand	360-365	6	91
β-strand	366-370	5	81
β-strand	371-382	12	80
α-helix	385-394	10
α-helix	396-401	6
β-strand	447-450	4	78
β-strand	456	1	80
α-helix	463-472	10

Chain E: 17 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
α-helix	21-23	3
α-helix	24-26	3
β-strand	28-38	11	92
β-strand	42	1	93
β-strand	45-46	2	94
β-strand	47	1	95
β-strand	53	1	96
β-strand	60	1	96
β-strand	64	1	95
β-strand	69	1	97
β-strand	71-76	6	98
α-helix	80-82	3
β-strand	83	1	99
β-strand	96-107	12	92
α-helix	112-113	2
β-strand	114	1	100
β-strand	118-123	6	101
β-strand	128	1	102
α-helix	135-138	4
β-strand	145-149	5	101
β-strand	153-160	8	98
α-helix	163-164	2
β-strand	165-170	6	103
α-helix	179-181	3
α-helix	184-187	4
β-strand	189-194	6	103
β-strand	200-201	2	97
β-strand	208	1	103
α-helix	222-224	3
β-strand	229-230	2	97
β-strand	231	1	103
α-helix	234-238	5
β-strand	249-254	6	98
β-strand	255	1	90
β-strand	256-262	7	102
β-strand	266-267	2	91
α-helix	270-272	3
α-helix	281-283	3
β-strand	291-296	6	102
β-strand	300	1	104
β-strand	311-312	2	92
β-strand	323	1	92
β-strand	328-334	7	98
β-strand	338	1	100
β-strand	342-347	6	105
β-strand	360-365	6	105
β-strand	366-367	2	94
β-strand	370	1	93
β-strand	372-382	11	92
α-helix	385-394	10
α-helix	397-401	5
β-strand	448-450	3	98
β-strand	455-456	2	92
α-helix	463-472	10
α-helix	476-478	3

Chain F: 19 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	99
α-helix	16-18	3
α-helix	24-27	4
β-strand	29-38	10	106
β-strand	42-43	2	49
β-strand	46	1	107
β-strand	47	1	108
β-strand	52-53	2	109
β-strand	60-62	3	109
β-strand	64	1	108
β-strand	71-76	6	110
α-helix	77-79	3
α-helix	80-82	3
β-strand	96-108	13	106
β-strand	114	1	111
β-strand	118-124	7	112
β-strand	128	1	113
α-helix	135-138	4
β-strand	144-149	6	112
β-strand	153-160	8	110
β-strand	165	1	114
β-strand	166-167	2	115
β-strand	168-171	4	116
α-helix	173-175	3
α-helix	184-187	4
β-strand	188-191	4	116
β-strand	194	1	114
α-helix	199-200	2
β-strand	201	1	117
α-helix	202	1
β-strand	208	1	116
β-strand	230	1	117
β-strand	231-232	2	115
α-helix	234-239	6
β-strand	248-254	7	110
β-strand	255	1	104
β-strand	256-262	7	113
β-strand	266-267	2	105
α-helix	270-272	3
α-helix	273-275	3
α-helix	281-283	3
α-helix	286-288	3
β-strand	291-296	6	113
β-strand	300	1	63
β-strand	311-312	2	106
β-strand	323	1	106
β-strand	328-335	8	110
β-strand	338	1	111
β-strand	342-347	6	64
β-strand	360-365	6	64
β-strand	366	1	107
β-strand	369-370	2	49
β-strand	371-382	12	106
α-helix	387-394	8
α-helix	396-400	5
β-strand	420-421	2	38
α-helix	434-435	2
β-strand	447-450	4	110
β-strand	456	1	106
α-helix	465-471	7
α-helix	476-478	3

Chains g, i, j, k, L and m: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
α-helix	9-12	4
β-strand	18-24	7	2
β-strand	25	1	1
β-strand	33-38	6	3
β-strand	45-49	5	3
β-strand	53-54	2	3
β-strand	62	1	2
β-strand	65	1	2
β-strand	70-76	7	2
β-strand	85-90	6	3
α-helix	107-109	3

Chains G, I, J, K and M: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	4
α-helix	6-8	3
β-strand	10-11	2	5
β-strand	17-23	7	4
β-strand	32-38	7	6
β-strand	45-50	6	6
β-strand	57-59	3	6
β-strand	67-71	5	4
β-strand	76-80	5	4
α-helix	85-87	3
β-strand	89-96	8	6
β-strand	109	1	6
β-strand	111	1	4
β-strand	114-116	3	6
β-strand	117-118	2	5

1 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
The light chain variable region of H16.001 Fab fragment	L, g, i, j, k, m	protein	110	Oryctolagus cuniculus
The heavy chain variable region of H16.001 Fab fragment	G, H, I, J, K, M	protein	120	Oryctolagus cuniculus
Major capsid protein L1	A, B, C, D, E, F	protein	505	Human papillomavirus type 16	P03101 (AlphaFold model)

Sequence of entity 1 (L, g, i, j, k, m), FASTA

>7CN2_1 The light chain variable region of H16.001 Fab fragment (chains L, g, i, j, k, m)
DPMLTQTAASVEVAVGGTVTIKCQASQSIGGYLSWYQQKPGQRPKLLIYRASTLASGVPS
RFKGSGSGTEYTLTFSGVECADAAAYYCQQGYTSSDINNAFGGGTEVVVK

Sequence of entity 2 (G, H, I, J, K, M), FASTA

>7CN2_2 The heavy chain variable region of H16.001 Fab fragment (chains G, H, I, J, K, M)
QSVKESEGRLVTPGTPLTLTCTASGFTMSRYHMTWVRQAPGKGLEWIGIIYARNSDTYYA
NWAKGRFTISKTSTTVDLKITSPTIEDTATYFCARVDSDSSGAFDRLDLWGQGTLVTVSS

Sequence of entity 3 (A, B, C, D, E, F), FASTA

>7CN2_3 Major capsid protein L1 (chains A, B, C, D, E, F)
MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKI
LVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGH
PLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAV
NPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSE
PYGDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMV
TSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNF
KEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRF
VTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKF
TLGKRKATPTTSSTSTTAKRKKRKL

Primary citation

Structural characterization of a neutralizing mAb H16.001, a potent candidate for a common potency assay for various HPV16 VLPs. Huang, W., He, M., Ning, T. et al. NPJ Vaccines (2020) 5:89-89. DOI 10.1038/s41541-020-00236-w · 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…
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…
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

Browse structure collections

About this viewer

MolViewer shows 7CN2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.