3J8Z: PDB entry 3J8Z

Cryo-EM reconstruction of quasi-HPV16 complex with H16.1A Fab. Determined by electron microscopy at 14.0 Å resolution. Released 6 May 2015.

Method: Electron microscopy
Resolution: 14.0 Å
Organisms: Human papillomavirus type 16, Mus musculus
Chains: 13
Atoms: 23,714
Mol. weight: 355.33 kDa
Released: 6 May 2015

Explore 3J8Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J8Z contains 135 α-helices and 286 β-strands across 13 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: 20 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	29-38	10	1
β-strand	42-46	5	1
β-strand	47	1	2
β-strand	52-53	2	3
β-strand	60-62	3	3
β-strand	64	1	2
β-strand	69	1	4
β-strand	71-76	6	5
β-strand	96-109	14	1
α-helix	112-113	2
β-strand	114	1	6
β-strand	118-123	6	7
β-strand	128	1	8
β-strand	145-149	5	7
β-strand	150	1	8
α-helix	151-152	2
β-strand	153-160	8	5
β-strand	165-171	7	9
α-helix	172-175	4
α-helix	184-187	4
β-strand	188-194	7	9
α-helix	199	1
β-strand	200-201	2	4
α-helix	202	1
β-strand	208	1	9
β-strand	209	1	10
α-helix	210-213	4
β-strand	214	1	11
α-helix	222-225	4
β-strand	228	1	10
β-strand	229-230	2	4
β-strand	231-232	2	9
α-helix	234-239	6
β-strand	248-255	8	5
β-strand	256-262	7	8
β-strand	266-267	2	11
α-helix	270-272	3
α-helix	273-275	3
α-helix	281-284	4
α-helix	286-288	3
β-strand	291-296	6	8
β-strand	300-301	2	12
β-strand	310-312	3	1
β-strand	323	1	1
α-helix	325-327	3
β-strand	328-335	8	5
β-strand	338	1	6
β-strand	342-347	6	13
α-helix	357-359	3
β-strand	360-365	6	13
β-strand	366-382	17	1
α-helix	385-395	11
α-helix	397-401	5
β-strand	447-450	4	5
β-strand	456	1	1
α-helix	459-461	3
α-helix	463-472	10

Chain B: 20 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	29-38	10	14
β-strand	42-46	5	14
β-strand	47	1	15
β-strand	52-53	2	16
β-strand	60-62	3	16
β-strand	64	1	15
β-strand	69	1	17
β-strand	71-76	6	12
β-strand	96-109	14	14
α-helix	112-113	2
β-strand	114	1	18
β-strand	118-123	6	19
β-strand	128	1	20
β-strand	145-149	5	19
β-strand	150	1	21
α-helix	151-152	2
β-strand	153-160	8	12
β-strand	165-171	7	22
α-helix	172-175	4
α-helix	184-187	4
β-strand	188-194	7	22
α-helix	199	1
β-strand	200-201	2	17
α-helix	202	1
β-strand	208	1	22
β-strand	209	1	23
α-helix	210-213	4
β-strand	214	1	13
α-helix	222-225	4
β-strand	228	1	23
β-strand	229-230	2	17
β-strand	231-232	2	22
α-helix	234-239	6
β-strand	248-255	8	12
β-strand	259-262	4	20
β-strand	266-267	2	13
α-helix	273-275	3
α-helix	281-284	4
α-helix	286-288	3
β-strand	291-294	4	20
α-helix	295	1
β-strand	296	1	21
β-strand	300-301	2	24
β-strand	310-312	3	14
β-strand	323	1	14
α-helix	325-327	3
β-strand	328-335	8	12
β-strand	338	1	18
β-strand	342-347	6	25
α-helix	357-359	3
β-strand	360-365	6	25
β-strand	366-382	17	14
α-helix	385-395	11
α-helix	397-401	5
β-strand	447-450	4	12
β-strand	456	1	14
α-helix	459-461	3
α-helix	463-472	10

Chain C: 21 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
α-helix	28	1
β-strand	29-38	10	26
β-strand	42-46	5	26
β-strand	47	1	27
β-strand	52-53	2	28
β-strand	60-62	3	28
β-strand	64	1	27
β-strand	69	1	29
β-strand	71-76	6	24
β-strand	96-109	14	26
α-helix	112-113	2
β-strand	114	1	30
β-strand	118-123	6	31
β-strand	128	1	32
β-strand	145-149	5	31
β-strand	150	1	33
α-helix	151-152	2
β-strand	153-160	8	24
β-strand	165-171	7	34
α-helix	172-175	4
α-helix	184-187	4
β-strand	188-194	7	34
α-helix	199	1
β-strand	200-201	2	29
α-helix	202	1
β-strand	208	1	34
β-strand	209	1	35
α-helix	210-213	4
β-strand	214	1	25
α-helix	222-225	4
β-strand	228	1	35
β-strand	229-230	2	29
β-strand	231-232	2	34
α-helix	234-239	6
β-strand	248-255	8	24
β-strand	259-262	4	32
β-strand	266-267	2	25
α-helix	270-272	3
α-helix	273-275	3
α-helix	281-284	4
α-helix	286-288	3
β-strand	291-294	4	32
β-strand	296	1	33
β-strand	300-301	2	36
β-strand	310-312	3	26
β-strand	323	1	26
α-helix	325-327	3
β-strand	328-335	8	24
β-strand	338	1	30
β-strand	342-347	6	37
α-helix	357-359	3
β-strand	360-365	6	37
β-strand	366-382	17	26
α-helix	385-395	11
α-helix	397-401	5
β-strand	447-450	4	24
β-strand	456	1	26
α-helix	459-461	3
α-helix	463-472	10

Chains D and E: 21 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	29-38	10	38
β-strand	42-46	5	38
β-strand	47	1	39
β-strand	52-53	2	40
β-strand	60-62	3	40
β-strand	64	1	39
β-strand	69	1	41
β-strand	71-76	6	36
β-strand	96-109	14	38
α-helix	112-113	2
β-strand	114	1	42
β-strand	118-123	6	43
β-strand	128	1	44
β-strand	145-149	5	43
β-strand	150	1	45
α-helix	151-152	2
β-strand	153-160	8	36
β-strand	165-171	7	46
α-helix	172-175	4
α-helix	184-187	4
β-strand	188-194	7	46
α-helix	199	1
β-strand	200-201	2	41
α-helix	202	1
β-strand	208	1	46
β-strand	209	1	47
α-helix	210-213	4
β-strand	214	1	37
α-helix	222-225	4
β-strand	228	1	47
β-strand	229-230	2	41
β-strand	231-232	2	46
α-helix	234-239	6
β-strand	248-255	8	36
β-strand	259-262	4	44
β-strand	266-267	2	37
α-helix	270-272	3
α-helix	273-275	3
α-helix	281-284	4
α-helix	286-288	3
β-strand	291-294	4	44
α-helix	295	1
β-strand	296	1	45
β-strand	300-301	2	48
β-strand	310-312	3	38
β-strand	323	1	38
α-helix	325-327	3
β-strand	328-335	8	36
β-strand	338	1	42
β-strand	342-347	6	49
α-helix	357-359	3
β-strand	360-365	6	49
β-strand	366-382	17	38
α-helix	385-395	11
α-helix	397-401	5
β-strand	447-450	4	36
β-strand	456	1	38
α-helix	459-461	3
α-helix	463-472	10

Chains F, G, H and I: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	68
β-strand	18-23	6	69
α-helix	29-31	3
β-strand	33-39	7	68
β-strand	46-52	7	68
β-strand	56-59	4	68
α-helix	61-63	3
β-strand	67-72	6	69
α-helix	73-75	3
β-strand	77-82	6	69
α-helix	84-86	3
β-strand	88-95	8	68
α-helix	96	1
β-strand	100D-103	4	68
β-strand	107-111	5	68

Chains J, K, L and M: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	65
β-strand	10-14	5	66
β-strand	19-24	6	65
β-strand	30-30A	2	67
β-strand	30F-31	2	67
β-strand	33-38	6	66
β-strand	45-49	5	66
β-strand	53-54	2	66
α-helix	55	1
β-strand	62-67	6	65
β-strand	70-75	6	65
α-helix	80-82	3
β-strand	84-90	7	66
α-helix	96	1
β-strand	98	1	66
β-strand	102-107	6	66

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
L1	A, B, C, D, E	protein	455	Human papillomavirus type 16	P03101 (AlphaFold model)
H16.1A light chain	J, K, L, M	protein	115	Mus musculus
H16.1A heavy chain	F, G, H, I	protein	114	Mus musculus

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

>3J8Z_1 L1 (chains A, B, C, D, E)
AVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIHLPD
PNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTENASAYAANA
GVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPLELINTVIQDGD
MVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLRREQMFVRH
LFNRAGTVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPYWLQRAQGH
NNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYDLQFIFQLC
KITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKED
PLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQLGL

Sequence of entity 2 (J, K, L, M), FASTA

>3J8Z_2 H16.1A light chain (chains J, K, L, M)
DIVMTQSPSSLAMSAGQKVTMSCKSSQSLFDSRNQKNYLAWYQQKPGQSPTLLVYFASTR
ESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCQQHYSTPYTFGGGTKLEIKRA

Sequence of entity 3 (F, G, H, I), FASTA

>3J8Z_3 H16.1A heavy chain (chains F, G, H, I)
SGAELARPGASVKLSCKASGYTFTSYWMQWVKQRPGQGLEWIGAIYPGDGYTRYTQKFKG
MATLTADKSSSTAYMQLTSLASEDSAVYYCARTYAGYYVGYFDYWGQGTTLTVS

Primary citation

Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization. Guan, J., Bywaters, S.M., Brendle, S.A. et al. Virology (2015) 483:253-263. DOI 10.1016/j.virol.2015.04.016 · 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…
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

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