5KEQ: 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 5KEQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KEQ contains 115 α-helices and 201 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	24-26	3
β-strand	28-37	10	1
β-strand	43	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	105-108	4	1
α-helix	112-113	2
β-strand	118-123	6	8
β-strand	145-149	5	8
α-helix	150-152	3
β-strand	153-160	8	6
β-strand	165-171	7	9
α-helix	185-187	3
β-strand	188-194	7	9
α-helix	199	1
β-strand	200	1	5
β-strand	201	1	10
α-helix	202	1
β-strand	209	1	11
α-helix	210-213	4
α-helix	222-225	4
β-strand	228	1	11
β-strand	230	1	10
β-strand	231-232	2	9
α-helix	234-238	5
β-strand	248-254	7	6
β-strand	256-262	7	12
α-helix	270-272	3
α-helix	273-275	3
α-helix	281-284	4
β-strand	291-296	6	12
β-strand	323	1	1
α-helix	325-327	3
β-strand	328-335	8	6
α-helix	340	1
β-strand	341-347	7	13
α-helix	357-359	3
β-strand	360-366	7	13
β-strand	369	1	2
β-strand	371-382	12	1
α-helix	385-394	10
α-helix	396-399	4
β-strand	448	1	6
β-strand	456	1	1
α-helix	463-472	10

Chain B: 20 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	14
β-strand	42-46	5	15
β-strand	47	1	16
β-strand	52-53	2	17
β-strand	60-62	3	17
β-strand	64	1	16
β-strand	69	1	18
β-strand	72-76	5	19
α-helix	80-82	3
β-strand	97-101	5	14
β-strand	105-108	4	14
α-helix	112-113	2
β-strand	118-123	6	20
β-strand	145-149	5	20
α-helix	150-152	3
β-strand	153-160	8	19
α-helix	163-164	2
β-strand	165-171	7	21
α-helix	173-175	3
α-helix	179-181	3
β-strand	188-194	7	21
β-strand	200	1	18
β-strand	209	1	22
α-helix	210-213	4
β-strand	214	1	23
α-helix	222-225	4
β-strand	228	1	22
β-strand	231-232	2	21
α-helix	234-238	5
β-strand	248-255	8	19
β-strand	256-262	7	24
β-strand	266-267	2	23
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	24
β-strand	300-301	2	25
β-strand	323	1	14
α-helix	325-327	3
β-strand	328-335	8	19
β-strand	341-347	7	15
α-helix	357-359	3
β-strand	360-370	11	15
β-strand	371-381	11	14
α-helix	385-394	10
α-helix	397-401	5
α-helix	426-428	3
α-helix	440-443	4
β-strand	448-450	3	19
β-strand	456	1	14
α-helix	463-472	10

Chain C: 19 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	26
β-strand	42-44	3	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	25
α-helix	80-82	3
α-helix	88-90	3
β-strand	96-101	6	26
β-strand	104-108	5	26
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	25
α-helix	163-164	2
β-strand	165-171	7	32
α-helix	173-175	3
α-helix	179-181	3
β-strand	188-194	7	32
β-strand	200	1	30
β-strand	209	1	33
α-helix	210-213	4
β-strand	214	1	15
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	25
β-strand	256-262	7	34
β-strand	266-267	2	15
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	34
β-strand	300-301	2	35
β-strand	311-312	2	26
β-strand	323	1	26
α-helix	325-327	3
β-strand	328-335	8	25
β-strand	342-347	6	36
α-helix	357-359	3
β-strand	360-365	6	36
β-strand	368-370	3	27
β-strand	371-382	12	26
α-helix	385-394	10
α-helix	396-400	5
β-strand	448-450	3	25
β-strand	456	1	26
α-helix	465-472	8

Chain D: 18 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	29-38	10	37
β-strand	42-45	4	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	80-82	3
β-strand	96-101	6	37
β-strand	104-108	5	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
α-helix	163-164	2
β-strand	165-170	6	43
α-helix	179-181	3
β-strand	189-194	6	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	311-312	2	37
β-strand	323	1	37
α-helix	325-327	3
β-strand	328-335	8	35
β-strand	342-347	6	47
α-helix	357-359	3
β-strand	360-365	6	47
β-strand	367-370	4	38
β-strand	371-382	12	37
α-helix	385-394	10
α-helix	397-401	5
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, 33 β-strands

Element	Residues	Length	Sheet
α-helix	13-17	5
β-strand	29-38	10	48
β-strand	42-46	5	49
β-strand	47	1	50
β-strand	52-53	2	51
β-strand	60-62	3	51
β-strand	64	1	50
β-strand	69	1	52
β-strand	71-76	6	46
α-helix	80-82	3
β-strand	96-101	6	48
β-strand	104-108	5	48
α-helix	112-113	2
β-strand	118-123	6	53
β-strand	145-149	5	53
α-helix	150-152	3
β-strand	153-160	8	46
β-strand	165-170	6	54
α-helix	173-175	3
α-helix	179-181	3
α-helix	184-187	4
β-strand	189-194	6	54
β-strand	200	1	52
β-strand	209	1	55
α-helix	210-213	4
β-strand	214	1	47
α-helix	222-226	5
β-strand	228	1	55
β-strand	231-232	2	54
α-helix	234-238	5
β-strand	248-255	8	46
β-strand	256-262	7	56
β-strand	266-267	2	47
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	56
β-strand	300-301	2	57
β-strand	311-312	2	48
β-strand	323	1	48
α-helix	325-327	3
β-strand	328-335	8	46
β-strand	341-347	7	49
α-helix	357-359	3
β-strand	360-370	11	49
β-strand	371-382	12	48
α-helix	385-394	10
α-helix	396-400	5
α-helix	413-415	3
α-helix	440-443	4
β-strand	448-450	3	46
β-strand	455-456	2	48
α-helix	463-472	10

Chain F: 19 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	28-38	11	58
β-strand	42-46	5	59
β-strand	47	1	60
β-strand	52-53	2	61
β-strand	60-62	3	61
β-strand	64	1	60
β-strand	69	1	62
β-strand	71-76	6	57
α-helix	80-82	3
β-strand	83	1	7
β-strand	97-101	5	58
β-strand	104-108	5	58
α-helix	112-113	2
β-strand	118-123	6	63
β-strand	145-149	5	63
α-helix	150-152	3
β-strand	153-160	8	57
α-helix	163-164	2
β-strand	165-170	6	64
α-helix	173-175	3
α-helix	179-181	3
β-strand	189-194	6	64
β-strand	200	1	62
β-strand	209	1	65
α-helix	210-213	4
β-strand	214	1	49
α-helix	222-225	4
β-strand	228	1	65
β-strand	231-232	2	64
α-helix	234-239	6
β-strand	248-255	8	57
β-strand	256-262	7	66
β-strand	266-267	2	49
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	66
β-strand	300-301	2	19
β-strand	311-312	2	58
β-strand	323	1	58
α-helix	325-327	3
β-strand	328-335	8	57
β-strand	342-347	6	23
α-helix	357-359	3
β-strand	360-365	6	23
β-strand	366-370	5	59
β-strand	371-381	11	58
α-helix	385-394	10
α-helix	397-401	5
α-helix	440-443	4
β-strand	448-450	3	57
β-strand	456	1	58
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

>5KEQ_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
5KEP 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 5KEQ 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.