7KZF: Major capsid protein L1

High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and describes capsid flexibility. Determined by electron microscopy at 3.1 Å resolution. Released 24 Feb 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Human papillomavirus type 16
Chains: 6
Atoms: 22,491
Mol. weight: 336.59 kDa
Released: 24 Feb 2021

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

Secondary structure: helices and β-sheets

7KZF contains 124 α-helices and 231 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: 23 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
α-helix	24-26	3
β-strand	29-38	10	15
β-strand	41-46	6	15
β-strand	47	1	61
β-strand	52-53	2	62
β-strand	60-62	3	62
β-strand	64	1	61
β-strand	69	1	63
β-strand	71-76	6	64
α-helix	80-82	3
β-strand	87-88	2	6
β-strand	96-109	14	15
α-helix	112-113	2
β-strand	114	1	65
β-strand	118-123	6	66
α-helix	136-139	4
β-strand	145-149	5	66
β-strand	153	1	67
β-strand	155-160	6	64
β-strand	165-171	7	68
α-helix	180-181	2
α-helix	184-187	4
β-strand	188-194	7	68
α-helix	199	1
β-strand	200-201	2	63
α-helix	202	1
β-strand	208	1	68
β-strand	209	1	69
α-helix	210-213	4
β-strand	228	1	69
β-strand	229-230	2	63
β-strand	231-232	2	68
α-helix	234-238	5
β-strand	248	1	64
β-strand	251	1	64
β-strand	254	1	67
β-strand	259-261	3	70
α-helix	270-272	3
α-helix	281-283	3
α-helix	286-288	3
β-strand	292-294	3	70
α-helix	295	1
β-strand	310-311	2	15
β-strand	323-324	2	15
β-strand	328-335	8	64
β-strand	338	1	65
α-helix	340-341	2
β-strand	342	1	71
β-strand	345-347	3	72
β-strand	360-362	3	72
β-strand	365	1	71
β-strand	366-382	17	15
α-helix	385-394	10
α-helix	396-401	6
α-helix	407-409	3
β-strand	417-418	2	1
α-helix	440-442	3
β-strand	447-450	4	64
β-strand	456	1	15
α-helix	459-461	3
α-helix	463-472	10
α-helix	476-478	3

Chain B: 21 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	28-38	11	16
β-strand	42-46	5	16
β-strand	47	1	17
β-strand	52-53	2	18
β-strand	60-62	3	18
β-strand	64	1	17
β-strand	69	1	19
β-strand	71-76	6	13
α-helix	80-82	3
β-strand	83	1	20
α-helix	88-90	3
β-strand	96-109	14	16
α-helix	112-113	2
β-strand	114	1	21
β-strand	117-123	7	22
β-strand	128	1	23
β-strand	145-150	6	22
β-strand	153-160	8	13
β-strand	165-171	7	24
α-helix	179-181	3
α-helix	184-187	4
β-strand	188-194	7	24
α-helix	199	1
β-strand	200	1	19
β-strand	201	1	25
α-helix	202	1
β-strand	208	1	24
β-strand	209	1	26
α-helix	210-213	4
β-strand	214	1	14
β-strand	228	1	26
β-strand	230	1	25
β-strand	231-232	2	24
α-helix	234-237	4
β-strand	248-255	8	13
β-strand	256-262	7	23
β-strand	266-267	2	14
α-helix	270-272	3
α-helix	281-283	3
α-helix	286-288	3
β-strand	291-296	6	23
β-strand	300-301	2	27
β-strand	310-312	3	16
β-strand	323-324	2	16
β-strand	328-335	8	13
β-strand	338	1	21
α-helix	340-341	2
β-strand	342-347	6	28
α-helix	357-359	3
β-strand	360-365	6	28
β-strand	366-382	17	16
α-helix	385-394	10
α-helix	396-401	6
α-helix	434-436	3
β-strand	447-450	4	13
β-strand	456	1	16
α-helix	459-461	3
α-helix	463-472	10
α-helix	475-478	4

Chain C: 20 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	20
β-strand	28-38	11	29
β-strand	42-46	5	29
β-strand	47	1	30
β-strand	52-53	2	31
β-strand	60-62	3	31
β-strand	64	1	30
β-strand	69	1	32
β-strand	71-76	6	27
α-helix	80-82	3
β-strand	83	1	33
α-helix	88-90	3
β-strand	96-109	14	29
α-helix	112-113	2
β-strand	114	1	34
β-strand	118-123	6	35
β-strand	128	1	36
α-helix	136-139	4
β-strand	145-149	5	35
β-strand	153-160	8	27
β-strand	165-171	7	37
α-helix	179-181	3
α-helix	184-187	4
β-strand	188-194	7	37
α-helix	199	1
β-strand	200-201	2	32
α-helix	202	1
β-strand	208	1	37
β-strand	209	1	38
α-helix	210-213	4
β-strand	214	1	28
β-strand	228	1	38
β-strand	229-230	2	32
β-strand	231-232	2	37
α-helix	234-238	5
β-strand	248	1	27
β-strand	251-255	5	27
β-strand	256-261	6	36
β-strand	266-267	2	28
α-helix	270-272	3
α-helix	281-283	3
α-helix	286-288	3
β-strand	292-296	5	36
β-strand	300-301	2	39
β-strand	311-312	2	29
β-strand	323	1	29
β-strand	328-335	8	27
β-strand	338	1	34
α-helix	340-341	2
β-strand	342-347	6	40
α-helix	357-359	3
β-strand	360-365	6	40
β-strand	366-382	17	29
α-helix	385-394	10
α-helix	396-401	6
α-helix	431-433	3
β-strand	447-450	4	27
β-strand	456	1	29
α-helix	459-461	3
α-helix	463-472	10

Chain D: 18 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	33
α-helix	13-18	6
β-strand	28-38	11	41
β-strand	42-46	5	41
β-strand	47	1	42
β-strand	52-53	2	43
β-strand	60-62	3	43
β-strand	64	1	42
β-strand	69	1	44
β-strand	71-76	6	39
β-strand	96-109	14	41
α-helix	112-113	2
β-strand	114	1	45
β-strand	117-123	7	46
β-strand	128	1	47
β-strand	145-150	6	46
β-strand	153-160	8	39
β-strand	165-171	7	48
α-helix	172-175	4
α-helix	180-181	2
α-helix	184-187	4
β-strand	188-194	7	48
α-helix	195-196	2
α-helix	199	1
β-strand	200-201	2	44
α-helix	202	1
β-strand	208	1	48
β-strand	209	1	49
β-strand	228	1	49
β-strand	229-230	2	44
β-strand	231-232	2	48
α-helix	234-237	4
β-strand	248-255	8	39
β-strand	256-262	7	47
β-strand	266-267	2	40
α-helix	270-272	3
α-helix	281-284	4
α-helix	286-288	3
β-strand	291-296	6	47
β-strand	300-301	2	50
β-strand	310-312	3	41
β-strand	323	1	41
β-strand	328-335	8	39
β-strand	338	1	45
β-strand	342-347	6	51
α-helix	357-359	3
β-strand	360-365	6	51
β-strand	366-382	17	41
α-helix	385-394	10
α-helix	398-401	4
α-helix	440-442	3
β-strand	447-450	4	39
β-strand	456	1	41
α-helix	459-461	3
α-helix	463-471	9

Chain E: 21 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	14-17	4
α-helix	24-27	4
β-strand	29-38	10	52
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	50
α-helix	80-82	3
β-strand	96-109	14	52
α-helix	112-113	2
β-strand	114	1	56
β-strand	118-123	6	57
β-strand	128	1	58
β-strand	145-149	5	57
β-strand	153-160	8	50
β-strand	165-171	7	59
α-helix	172-175	4
α-helix	184-187	4
β-strand	188-194	7	59
α-helix	199	1
β-strand	200-201	2	55
α-helix	202	1
β-strand	208	1	59
β-strand	209	1	60
α-helix	210-213	4
β-strand	214	1	51
β-strand	228	1	60
β-strand	229-230	2	55
β-strand	231-232	2	59
α-helix	234-238	5
β-strand	248-255	8	50
β-strand	256-262	7	58
β-strand	266-267	2	51
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	58
β-strand	300-301	2	5
β-strand	310-312	3	52
β-strand	323	1	52
β-strand	328-335	8	50
β-strand	338	1	56
α-helix	340-341	2
β-strand	342-347	6	11
α-helix	357-359	3
β-strand	360-365	6	11
β-strand	366-382	17	52
α-helix	385-394	10
α-helix	396-401	6
α-helix	440-442	3
β-strand	447-450	4	50
β-strand	455-456	2	52
α-helix	459-461	3
α-helix	463-472	10

Chain F: 21 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	13-17	5
α-helix	21-23	3
α-helix	24-26	3
β-strand	28-38	11	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
α-helix	80-82	3
β-strand	87-88	2	6
β-strand	96-109	14	1
α-helix	112-113	2
β-strand	114	1	7
β-strand	117-123	7	8
β-strand	145-150	6	8
β-strand	153-160	8	5
β-strand	165-171	7	9
α-helix	173-175	3
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	222-224	3
β-strand	228	1	10
β-strand	229-230	2	4
β-strand	231-232	2	9
α-helix	234-238	5
β-strand	248-255	8	5
β-strand	256-261	6	12
β-strand	266-267	2	11
α-helix	270-272	3
α-helix	282-284	3
α-helix	286-288	3
β-strand	292-296	5	12
β-strand	300-301	2	13
β-strand	310-312	3	1
β-strand	323-324	2	1
β-strand	328-335	8	5
β-strand	338	1	7
β-strand	342-347	6	14
α-helix	357-359	3
β-strand	360-365	6	14
β-strand	366-382	17	1
α-helix	385-394	10
α-helix	396-402	7
β-strand	416-418	3	15
β-strand	447-450	4	5
β-strand	455-456	2	1
α-helix	459-461	3
α-helix	463-472	10
α-helix	475-478	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Major capsid protein L1	A, B, C, D, E, F	protein	503	Human papillomavirus type 16	P03101 (AlphaFold model)

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

>7KZF_1 Major capsid protein L1 (chains A, B, C, D, E, F)
MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKI
LVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGH
PLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAV
NPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSE
PYGDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMV
TSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNF
KEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRF
VTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKF
TLGKRKATPTTSSTSTTAKRKKR

Primary citation

High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and describes capsid flexibility. Goetschius, D.J., Hartmann, S.R., Subramanian, S. et al. Sci Rep (2021) 11:3498-3498. DOI 10.1038/s41598-021-83076-5 · 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
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
3J8W 13.0 Å, Cryo-EM reconstruction of quasi-HPV16 complex with H263.A2 Fab

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