5KEP: Major capsid protein L1

High resolution cryo-EM maps of Human Papillomavirus 16 reveal L2 location and heparin-induced conformational changes. Determined by electron microscopy at 4.3 Å resolution. Released 25 Jan 2017.

Method: Electron microscopy
Resolution: 4.3 Å
Organism: Human papillomavirus type 16
Chains: 6
Atoms: 22,267
Mol. weight: 323.65 kDa
Released: 25 Jan 2017

Explore 5KEP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KEP contains 114 α-helices and 197 β-strands across 6 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: 18 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	21-23	3
β-strand	29-37	9	1
β-strand	42	1	2
β-strand	47	1	3
β-strand	52-53	2	4
β-strand	60-62	3	4
β-strand	64	1	3
β-strand	69	1	5
β-strand	71-76	6	6
β-strand	83	1	7
β-strand	96-101	6	1
β-strand	104-106	3	1
α-helix	112-113	2
β-strand	119-123	5	8
β-strand	128	1	9
β-strand	145-148	4	8
β-strand	153-160	8	6
β-strand	165-170	6	10
α-helix	173-175	3
α-helix	179-180	2
β-strand	189-194	6	10
α-helix	199	1
β-strand	200	1	5
α-helix	201-202	2
β-strand	209	1	11
α-helix	210-213	4
α-helix	222-226	5
β-strand	228	1	11
β-strand	231-232	2	10
α-helix	234-238	5
β-strand	248-254	7	6
β-strand	256-262	7	9
α-helix	270-272	3
α-helix	273-275	3
α-helix	286-288	3
β-strand	291-296	6	9
β-strand	311-312	2	1
β-strand	323	1	1
α-helix	325-327	3
β-strand	328-335	8	6
β-strand	341-347	7	12
α-helix	357-359	3
β-strand	360-366	7	12
β-strand	370	1	2
β-strand	373-382	10	1
α-helix	385-394	10
α-helix	398-401	4
β-strand	447-450	4	6
β-strand	456	1	1
α-helix	459-461	3
α-helix	463-471	9

Chain B: 19 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	29-37	9	13
β-strand	44-46	3	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	18
α-helix	80-82	3
β-strand	96-101	6	13
β-strand	105-108	4	13
α-helix	112-113	2
β-strand	118-123	6	19
β-strand	145-149	5	19
α-helix	150-152	3
β-strand	153-160	8	18
α-helix	163-164	2
β-strand	165-171	7	20
α-helix	173-175	3
α-helix	179-181	3
β-strand	188-194	7	20
β-strand	200	1	17
β-strand	209	1	21
α-helix	210-213	4
β-strand	214	1	22
α-helix	222-225	4
β-strand	228	1	21
β-strand	231-232	2	20
α-helix	234-238	5
β-strand	248-255	8	18
β-strand	256-262	7	23
β-strand	266-267	2	22
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	23
β-strand	300-301	2	24
β-strand	323	1	13
α-helix	325-327	3
β-strand	328-335	8	18
β-strand	341-347	7	14
α-helix	357-359	3
β-strand	360-368	9	14
β-strand	371-382	12	13
α-helix	385-394	10
α-helix	397-401	5
α-helix	440-443	4
β-strand	448-450	3	18
β-strand	456	1	13
α-helix	463-472	10

Chain C: 19 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	25
β-strand	42	1	26
β-strand	45-46	2	27
β-strand	47	1	28
β-strand	52-53	2	29
β-strand	60-62	3	29
β-strand	64	1	28
β-strand	69	1	30
β-strand	71-76	6	24
α-helix	80-82	3
β-strand	96-101	6	25
β-strand	105-108	4	25
α-helix	112-113	2
β-strand	118-123	6	31
β-strand	145-149	5	31
α-helix	150-152	3
β-strand	153-160	8	24
α-helix	163-164	2
β-strand	165-170	6	32
α-helix	173-175	3
α-helix	179-181	3
β-strand	189-194	6	32
β-strand	200	1	30
β-strand	209	1	33
α-helix	210-213	4
β-strand	214	1	14
α-helix	222-225	4
β-strand	228	1	33
β-strand	231-232	2	32
α-helix	234-238	5
β-strand	248-255	8	24
β-strand	256-262	7	34
β-strand	266-267	2	14
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	34
β-strand	300-301	2	35
β-strand	323	1	25
α-helix	325-327	3
β-strand	328-335	8	24
β-strand	342-347	6	36
α-helix	357-359	3
β-strand	360-365	6	36
β-strand	366-367	2	27
β-strand	370	1	26
β-strand	371-382	12	25
α-helix	385-394	10
α-helix	396-400	5
α-helix	440-443	4
β-strand	448-450	3	24
β-strand	456	1	25
α-helix	465-472	8

Chain D: 17 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	37
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	35
α-helix	84-85	2
β-strand	96-101	6	37
β-strand	105-108	4	37
α-helix	112-113	2
β-strand	118-123	6	42
β-strand	145-149	5	42
α-helix	150-152	3
β-strand	153-160	8	35
β-strand	165-171	7	43
α-helix	179-181	3
β-strand	188-194	7	43
β-strand	200	1	41
β-strand	209	1	44
α-helix	210-213	4
β-strand	214	1	36
α-helix	222-225	4
β-strand	228	1	44
β-strand	231-232	2	43
α-helix	234-238	5
β-strand	248-255	8	35
β-strand	256-262	7	45
β-strand	266-267	2	36
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	45
β-strand	300-301	2	46
β-strand	323	1	37
α-helix	325-327	3
β-strand	328-335	8	35
β-strand	341-347	7	38
α-helix	357-359	3
β-strand	360-370	11	38
β-strand	371-382	12	37
α-helix	385-394	10
α-helix	396-401	6
α-helix	440-443	4
β-strand	448-450	3	35
β-strand	456	1	37
α-helix	463-472	10

Chain E: 21 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	14-17	4
β-strand	29-38	10	47
β-strand	42-46	5	48
β-strand	47	1	49
β-strand	52-53	2	50
β-strand	60-62	3	50
β-strand	64	1	49
β-strand	69	1	51
β-strand	71-76	6	46
α-helix	80-82	3
β-strand	96-101	6	47
β-strand	105-108	4	47
α-helix	112-113	2
β-strand	118-123	6	52
β-strand	145-149	5	52
α-helix	150-152	3
β-strand	153-160	8	46
α-helix	163-164	2
β-strand	165-170	6	53
α-helix	173-175	3
α-helix	179-181	3
α-helix	184-187	4
β-strand	189-194	6	53
β-strand	200	1	51
β-strand	209	1	54
α-helix	210-213	4
β-strand	214	1	38
α-helix	222-225	4
β-strand	228	1	54
β-strand	231-232	2	53
α-helix	234-238	5
β-strand	248-255	8	46
β-strand	256-262	7	55
β-strand	267	1	38
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	55
β-strand	300-301	2	56
β-strand	323	1	47
α-helix	325-327	3
β-strand	328-335	8	46
β-strand	341-347	7	48
α-helix	357-359	3
β-strand	360-370	11	48
β-strand	371-382	12	47
α-helix	385-394	10
α-helix	396-401	6
α-helix	440-443	4
β-strand	448-450	3	46
β-strand	455-456	2	47
α-helix	463-472	10

Chain F: 20 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	28-38	11	57
β-strand	42-46	5	22
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	56
α-helix	80-82	3
β-strand	83	1	7
β-strand	97-101	5	57
β-strand	105-108	4	57
α-helix	112-113	2
β-strand	119-123	5	61
β-strand	145-148	4	61
α-helix	150-152	3
β-strand	153-160	8	56
α-helix	163-164	2
β-strand	165-170	6	62
α-helix	171-175	5
α-helix	179-181	3
α-helix	184-187	4
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	48
α-helix	222-225	4
β-strand	228	1	63
β-strand	231-232	2	62
α-helix	234-238	5
β-strand	248-255	8	56
β-strand	256-262	7	64
β-strand	266-267	2	48
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	64
β-strand	300-301	2	18
β-strand	323	1	57
α-helix	325-327	3
β-strand	328-335	8	56
β-strand	341-347	7	22
α-helix	357-359	3
β-strand	360-370	11	22
β-strand	371-381	11	57
α-helix	385-394	10
α-helix	397-401	5
α-helix	429	1
β-strand	448-450	3	56
β-strand	456	1	57
α-helix	463-472	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Major capsid protein L1	A, B, C, D, E, F	protein	483	Human papillomavirus type 16	P03101 (AlphaFold model)

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

>5KEP_1 Major capsid protein L1 (chains A, B, C, D, E, F)
LWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILV
PKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPL
LNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAVNP
GDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPY
GDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTS
DAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKE
YLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVT
SQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKFTL
GKR

Primary citation

Cryoelectron Microscopy Maps of Human Papillomavirus 16 Reveal L2 Densities and Heparin Binding Site. Guan, J., Bywaters, S.M., Brendle, S.A. et al. Structure (2017) 25:253-263. DOI 10.1016/j.str.2016.12.001 · 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
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

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