9NZU: Atomic resolution cryoEM structure of HPV16

Name: PDB 9NZU: Atomic resolution cryoEM structure of HPV16 bound to heparin
Published: 2026-04-29
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Atomic resolution cryoEM structure of HPV16 bound to heparin. Determined by electron microscopy at 1.9 Å resolution. Released 29 Apr 2026.

Method: Electron microscopy
Resolution: 1.9 Å
Organism: Human papillomavirus 16
Chains: 6
Atoms: 24,050
Mol. weight: 329.56 kDa
Ligands: MG
Released: 29 Apr 2026

Explore 9NZU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NZU contains 157 α-helices and 230 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: 25 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	13-18	6
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	77-78	2
β-strand	96-109	14	15
β-strand	114	1	65
β-strand	118-123	6	66
β-strand	127-128	2	67
α-helix	135-139	5
β-strand	145-149	5	66
β-strand	153-160	8	64
β-strand	165-171	7	68
α-helix	173-175	3
α-helix	179-181	3
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
α-helix	222-225	4
β-strand	228	1	69
β-strand	229-230	2	63
β-strand	231-232	2	68
α-helix	234-239	6
β-strand	248-254	7	64
β-strand	256-262	7	67
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	67
α-helix	302-304	3
β-strand	311-312	2	15
β-strand	323	1	15
β-strand	328-335	8	64
β-strand	338	1	65
α-helix	340-341	2
β-strand	342-347	6	70
α-helix	357-359	3
β-strand	360-365	6	70
β-strand	366-382	17	15
α-helix	385-394	10
α-helix	396-402	7
α-helix	406-409	4
β-strand	416-418	3	2
β-strand	426	1	24
β-strand	447-450	4	64
β-strand	455-456	2	15
α-helix	459-461	3
α-helix	463-471	9
α-helix	476-478	3

Chain B: 24 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	24-26	3
β-strand	29-38	10	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
β-strand	96-109	14	16
β-strand	114	1	21
β-strand	118-123	6	22
β-strand	128	1	23
β-strand	145-149	5	22
α-helix	150-152	3
β-strand	153-160	8	13
β-strand	165-171	7	24
α-helix	173-175	3
α-helix	184-187	4
β-strand	188-194	7	24
α-helix	195-196	2
α-helix	199	1
β-strand	200-201	2	19
α-helix	202	1
β-strand	208	1	24
β-strand	209	1	25
α-helix	210-213	4
β-strand	214	1	14
β-strand	228	1	25
β-strand	229-230	2	19
β-strand	231-232	2	24
α-helix	234-239	6
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	273-275	3
β-strand	278	1	26
α-helix	281-283	3
α-helix	286-288	3
β-strand	291-296	6	23
β-strand	300-301	2	27
α-helix	302-304	3
β-strand	310-312	3	16
β-strand	323	1	16
α-helix	325-327	3
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	406-408	3
β-strand	447-450	4	13
β-strand	455-456	2	16
α-helix	459-461	3
α-helix	463-472	10
α-helix	476-478	3

Chain C: 28 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	20
α-helix	13-17	5
α-helix	24-26	3
β-strand	29-38	10	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	77-78	2
α-helix	80-82	3
β-strand	83	1	33
β-strand	96-109	14	29
β-strand	114	1	34
β-strand	118-123	6	35
β-strand	127-128	2	36
α-helix	135-139	5
β-strand	145-149	5	35
α-helix	150-152	3
β-strand	153-160	8	27
β-strand	165-171	7	37
α-helix	173-175	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
α-helix	222-225	4
β-strand	228	1	38
β-strand	229-230	2	32
β-strand	231-232	2	37
α-helix	234-239	6
β-strand	248-255	8	27
β-strand	256-262	7	36
β-strand	266-267	2	28
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	36
β-strand	300-301	2	39
α-helix	302-304	3
β-strand	310-312	3	29
β-strand	323	1	29
α-helix	325-327	3
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	408-409	2
α-helix	436-439	4
β-strand	447-450	4	27
β-strand	455-456	2	29
α-helix	459-461	3
α-helix	463-471	9
α-helix	476-478	3

Chain D: 27 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	33
α-helix	13-17	5
α-helix	24-27	4
β-strand	29-38	10	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
α-helix	77-78	2
α-helix	80-82	3
β-strand	96-109	14	41
β-strand	114	1	45
β-strand	118-123	6	46
β-strand	128	1	47
α-helix	135-139	5
β-strand	145-149	5	46
α-helix	150-152	3
β-strand	153-160	8	39
β-strand	165-171	7	48
α-helix	173-175	3
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
α-helix	210-213	4
β-strand	214	1	40
α-helix	222-225	4
β-strand	228	1	49
β-strand	229-230	2	44
β-strand	231-232	2	48
α-helix	234-239	6
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	273-275	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
α-helix	325-327	3
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	396-402	7
α-helix	408-409	2
α-helix	440-443	4
β-strand	447-450	4	39
β-strand	456	1	41
α-helix	459-461	3
α-helix	463-471	9
α-helix	476-479	4

Chain E: 27 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	14-17	4
α-helix	19-21	3
α-helix	24-26	3
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	77-78	2
α-helix	80-82	3
β-strand	83	1	1
β-strand	96-109	14	52
β-strand	114	1	56
β-strand	118-123	6	57
β-strand	127-128	2	58
α-helix	135-139	5
β-strand	145-149	5	57
α-helix	150-152	3
β-strand	153-160	8	50
β-strand	165-171	7	59
α-helix	184-187	4
β-strand	188-194	7	59
α-helix	195-196	2
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	234-239	6
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	6
α-helix	302-304	3
β-strand	310-312	3	52
β-strand	323	1	52
α-helix	325-327	3
β-strand	328-335	8	50
β-strand	338	1	56
β-strand	342-347	6	12
β-strand	354	1	26
α-helix	357-359	3
β-strand	360-365	6	12
β-strand	366-382	17	52
α-helix	385-401	17
α-helix	427-429	3
α-helix	433-437	5
α-helix	440-443	4
β-strand	447-450	4	50
β-strand	455-456	2	52
α-helix	459-461	3
α-helix	463-472	10
α-helix	476-478	3

Chain F: 26 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	1
α-helix	13-19	7
α-helix	24-26	3
β-strand	29-38	10	2
β-strand	41-46	6	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
α-helix	77-78	2
α-helix	80-83	4
β-strand	96-109	14	2
β-strand	114	1	7
β-strand	118-123	6	8
β-strand	127-128	2	9
α-helix	135-139	5
β-strand	145-149	5	8
α-helix	150-152	3
β-strand	153-160	8	6
β-strand	165-171	7	10
α-helix	173-175	3
α-helix	180-181	2
α-helix	184-187	4
β-strand	188-194	7	10
α-helix	199	1
β-strand	200-201	2	5
α-helix	202	1
β-strand	208	1	10
β-strand	209	1	11
α-helix	210-213	4
β-strand	214	1	12
α-helix	222-225	4
β-strand	228	1	11
β-strand	229-230	2	5
β-strand	231-232	2	10
α-helix	234-239	6
β-strand	248-255	8	6
β-strand	256-262	7	9
β-strand	266-267	2	12
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	9
β-strand	300-301	2	13
α-helix	302-304	3
β-strand	310-312	3	2
β-strand	323	1	2
β-strand	328-335	8	6
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	2
α-helix	385-394	10
α-helix	396-402	7
α-helix	407-409	3
β-strand	416-418	3	15
β-strand	447-450	4	6
β-strand	456	1	2
α-helix	459-461	3
α-helix	463-472	10
α-helix	476-478	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Major capsid protein L1	A, B, C, D, E, F	protein	485	Human papillomavirus 16	P03101 (AlphaFold model)

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

>9NZU_1 Major capsid protein L1 (chains A, B, C, D, E, F)
MSLWLPSEATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKI
LVPKVSGLQYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGH
PLLNKLDDTENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTNVAV
NPGDCPPLELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSE
PYGDSLFFYLRREQMFVRHLFNRAGAVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMV
TSDAQIFNKPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNF
KEYLRHGEEYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRF
VTSQAIACQKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQAGLKAKPKF
TLGKR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	189

Primary citation

Atomic resolution structure of human papillomavirus bound to heparin. Langley, C.H., Hafenstein, S.L. To be published.

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
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
3J8W 13.0 Å, Cryo-EM reconstruction of quasi-HPV16 complex with H263.A2 Fab

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