3J7G: PDB entry 3J7G

Name: PDB 3J7G: Electron cryo-microscopy of human papillomavirus 16 and H16.V5 Fab fragments
Published: 2014-11-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Electron cryo-microscopy of human papillomavirus 16 and H16.V5 Fab fragments. Determined by electron microscopy at 13.6 Å resolution. Released 26 Nov 2014.

Method: Electron microscopy
Resolution: 13.6 Å
Organism: Human papillomavirus type 16
Chains: 5
Atoms: 16,610
Mol. weight: 254.37 kDa
Released: 26 Nov 2014

Explore 3J7G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J7G contains 103 α-helices and 194 β-strands across 5 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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
L1	A, B, C, D, E	protein	455	Human papillomavirus type 16	P03101 (AlphaFold model)

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

>3J7G_1 L1 (chains A, B, C, D, E)
AVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGLQYRVFRIHLPD
PNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDDTENASAYAANA
GVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPLELINTVIQDGD
MVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFFYLRREQMFVRH
LFNRAGTVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFNKPYWLQRAQGH
NNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGEEYDLQFIFQLC
KITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIACQKHTPPAPKED
PLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQLGL

Primary citation

A cryo-electron microscopy study identifies the complete H16.V5 epitope and reveals global conformational changes initiated by binding of the neutralizing antibody fragment. Lee, H., Brendle, S.A., Bywaters, S.M. et al. J Virol (2015) 89:1428-1438. DOI 10.1128/JVI.02898-14 · 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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