3JBA: H16.U4 antibody light chain

The U4 antibody epitope on human papillomavirus 16 identified by cryo-EM. Determined by electron microscopy at 12.0 Å resolution. Released 7 Oct 2015.

Method: Electron microscopy
Resolution: 12.0 Å
Organisms: Mus musculus, Human papillomavirus type 16
Chains: 8
Atoms: 13,253
Mol. weight: 346.08 kDa
Released: 7 Oct 2015

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

Secondary structure: helices and β-sheets

3JBA contains 68 α-helices and 238 β-strands across 8 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: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	21-23	3
β-strand	30-37	8	22
β-strand	42-46	5	23
α-helix	51	1
β-strand	52-53	2	24
α-helix	54	1
β-strand	60-62	3	24
β-strand	69	1	25
β-strand	71-76	6	26
β-strand	83	1	27
β-strand	96-108	13	22
β-strand	118-124	7	28
β-strand	128	1	29
β-strand	144-149	6	28
β-strand	153-160	8	26
β-strand	165-171	7	30
β-strand	188-194	7	30
α-helix	199	1
β-strand	200-201	2	25
β-strand	208	1	30
β-strand	209	1	31
β-strand	214	1	32
α-helix	223-225	3
β-strand	228	1	31
β-strand	229-230	2	25
β-strand	231-232	2	30
α-helix	234-238	5
β-strand	248-255	8	26
β-strand	256-262	7	29
β-strand	266-267	2	32
α-helix	281-284	4
β-strand	291-296	6	29
β-strand	300-301	2	15
β-strand	311	1	22
β-strand	323	1	22
β-strand	328-335	8	26
β-strand	341-342	2	23
β-strand	345-347	3	20
β-strand	360-362	3	20
β-strand	365-370	6	23
β-strand	371-382	12	22
α-helix	385-394	10
α-helix	397-402	6
β-strand	424	1	33
β-strand	447-450	4	26
β-strand	456	1	22
α-helix	463-472	10

Chain B: 11 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	7
β-strand	30-38	9	8
β-strand	42-46	5	9
β-strand	52-53	2	10
β-strand	60-62	3	10
β-strand	69	1	11
β-strand	71-76	6	12
α-helix	80-82	3
β-strand	96-108	13	8
α-helix	112	1
β-strand	118-123	6	13
β-strand	128	1	14
β-strand	145-149	5	13
β-strand	153-155	3	15
β-strand	156-160	5	12
α-helix	163-164	2
β-strand	165-167	3	16
β-strand	169-171	3	17
β-strand	182	1	18
β-strand	184	1	18
α-helix	185-187	3
β-strand	188-190	3	17
β-strand	193-194	2	16
α-helix	199	1
β-strand	200-201	2	11
β-strand	208	1	17
β-strand	209	1	19
α-helix	222-225	4
β-strand	228	1	19
β-strand	229-230	2	11
β-strand	231-232	2	16
α-helix	234-237	4
β-strand	248	1	12
β-strand	252-255	4	15
β-strand	256-262	7	14
β-strand	266-267	2	20
α-helix	281-283	3
β-strand	291-296	6	14
β-strand	300-301	2	21
β-strand	310-312	3	8
β-strand	328-334	7	12
β-strand	341-347	7	9
β-strand	360-370	11	9
β-strand	371-382	12	8
α-helix	385-395	11
α-helix	397-402	6
β-strand	447-450	4	12
α-helix	463-473	11

Chain C: 7 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	28-38	11	57
β-strand	42-46	5	56
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	21
β-strand	96-108	13	57
β-strand	117-124	8	61
β-strand	128	1	62
β-strand	144-150	7	61
β-strand	153-160	8	21
β-strand	165-171	7	63
α-helix	185-187	3
β-strand	188-194	7	63
α-helix	199	1
β-strand	200-201	2	60
β-strand	208	1	63
β-strand	209	1	64
β-strand	228	1	64
β-strand	229-230	2	60
β-strand	231-232	2	63
α-helix	234-238	5
β-strand	248-255	8	21
β-strand	256-262	7	62
α-helix	281-284	4
β-strand	291-296	6	62
β-strand	300-301	2	48
β-strand	310-311	2	57
β-strand	323	1	57
β-strand	328-335	8	21
β-strand	340-347	8	56
β-strand	356	1	51
β-strand	360-370	11	56
β-strand	371-382	12	57
α-helix	385-395	11
α-helix	397-400	4
β-strand	447-450	4	21
β-strand	456	1	57
α-helix	463-472	10

Chain D: 14 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	28-38	11	44
β-strand	42-46	5	43
β-strand	47	1	45
β-strand	52-53	2	46
β-strand	60-62	3	46
β-strand	64	1	45
β-strand	69	1	47
β-strand	71-76	6	48
α-helix	80-82	3
β-strand	96-108	13	44
β-strand	118-124	7	49
β-strand	128	1	50
α-helix	135-137	3
β-strand	141	1	51
β-strand	144-149	6	49
β-strand	153-160	8	48
α-helix	163-164	2
β-strand	165-170	6	52
α-helix	173-174	2
β-strand	175	1	53
β-strand	180	1	53
β-strand	182	1	54
β-strand	184	1	54
α-helix	185-187	3
β-strand	189-194	6	52
α-helix	199	1
β-strand	200	1	47
α-helix	201	1
β-strand	208	1	52
β-strand	209	1	55
β-strand	214	1	56
α-helix	222-225	4
β-strand	228	1	55
β-strand	229	1	47
β-strand	231-232	2	52
α-helix	234-239	6
β-strand	248-255	8	48
β-strand	259-262	4	50
α-helix	281-283	3
β-strand	291-294	4	50
α-helix	295	1
β-strand	299-301	3	37
β-strand	309-311	3	44
β-strand	328-335	8	48
β-strand	341-346	6	43
β-strand	361-370	10	43
β-strand	371-382	12	44
α-helix	385-395	11
α-helix	397-402	6
β-strand	447-450	4	48
α-helix	463-471	9

Chain E: 11 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	28-38	11	34
β-strand	42-46	5	32
β-strand	52-53	2	35
β-strand	60-62	3	35
β-strand	69	1	36
β-strand	71-76	6	37
β-strand	96-108	13	34
β-strand	119-124	6	38
β-strand	128	1	37
β-strand	129	1	39
β-strand	132	1	39
β-strand	144-148	5	38
β-strand	153-160	8	37
α-helix	163-164	2
β-strand	165-171	7	40
α-helix	172-174	3
β-strand	181	1	41
β-strand	184	1	41
β-strand	188-194	7	40
α-helix	195-196	2
α-helix	199	1
β-strand	200	1	36
α-helix	201	1
β-strand	208	1	40
β-strand	209	1	42
β-strand	214	1	43
α-helix	222-226	5
β-strand	228	1	42
β-strand	229	1	36
β-strand	231-232	2	40
α-helix	234-238	5
β-strand	248-262	15	37
α-helix	281-284	4
β-strand	291-296	6	37
β-strand	300-301	2	26
β-strand	311-312	2	34
β-strand	323	1	34
β-strand	328-335	8	37
β-strand	341-347	7	32
β-strand	360-370	11	32
β-strand	371-382	12	34
α-helix	385-394	10
α-helix	397-402	6
β-strand	447-450	4	37
β-strand	456	1	34
α-helix	463-471	9

Chain F: 10 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	28-38	11	65
β-strand	42-46	5	33
β-strand	47	1	66
β-strand	52-53	2	67
β-strand	60-62	3	67
β-strand	64	1	66
β-strand	69	1	68
β-strand	71-76	6	69
β-strand	85	1	27
β-strand	96-108	13	65
β-strand	114	1	70
β-strand	118-124	7	71
β-strand	128	1	72
β-strand	144-149	6	71
α-helix	150-152	3
β-strand	153-160	8	69
β-strand	165-171	7	73
α-helix	185-187	3
β-strand	188-194	7	73
β-strand	200	1	68
β-strand	208	1	73
α-helix	222-225	4
β-strand	229	1	68
β-strand	231-232	2	73
α-helix	234-238	5
β-strand	248-254	7	69
β-strand	256-262	7	72
α-helix	281-284	4
β-strand	291-296	6	72
β-strand	311-312	2	65
β-strand	323-324	2	65
β-strand	328-334	7	69
β-strand	338	1	70
β-strand	341-347	7	33
β-strand	360-370	11	33
β-strand	371-382	12	65
α-helix	385-394	10
α-helix	397-402	6
β-strand	405	1	7
α-helix	433	1
α-helix	435	1
β-strand	447-450	4	69
α-helix	463-472	10

Chain H: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	4
β-strand	18-23	6	5
α-helix	29-31	3
β-strand	34-39	6	4
β-strand	45-51	7	4
β-strand	57-58	2	4
β-strand	64	1	6
β-strand	67	1	6
β-strand	68-72	5	5
β-strand	77-82	6	5
α-helix	84-86	3
β-strand	88-98	11	4
β-strand	100C-103	7	4
β-strand	107-111	5	4

Chain L: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	30-30A	2	3
β-strand	30F-31	2	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H16.U4 antibody light chain	L	protein	115	Mus musculus
H16.U4 antibody heavy chain	H	protein	115	Mus musculus
Major capsid protein L1	A, B, C, D, E, F	protein	478	Human papillomavirus type 16	P03101 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>3JBA_1 H16.U4 antibody light chain (chains L)
DIVMSQSPSSLAVSVGEKVTMSCKSSQSLLYSNTQKNYLAWYQQKPGQSPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTISSVKAEDLAVYYCQQYYSYPLTFGAGTKLELKRA

Sequence of entity 2 (H), FASTA

>3JBA_2 H16.U4 antibody heavy chain (chains H)
SGGGLVKPGGSLKLSCEASGFTFSSYAMSWVRQTPEKRLEWVASISSGGNTHYPDSVKGR
FTISRDNARNILYLQMSSLRSEDTAMYYCARGLYYGYDEGSDFDYWGQGTTLTVS

Sequence of entity 3 (A, B, C, D, E, F), FASTA

>3JBA_3 Major capsid protein L1 (chains A, B, C, D, E, F)
ATVYLPPVPVSKVVSTDEYVARTNIYYHAGTSRLLAVGHPYFPIKKPNNNKILVPKVSGL
QYRVFRIHLPDPNKFGFPDTSFYNPDTQRLVWACVGVEVGRGQPLGVGISGHPLLNKLDD
TENASAYAANAGVDNRECISMDYKQTQLCLIGCKPPIGEHWGKGSPCTQVAVQPGDCPPL
ELINTVIQDGDMVDTGFGAMDFTTLQANKSEVPLDICTSICKYPDYIKMVSEPYGDSLFF
YLRREQMFVRHLFNRAGTVGENVPDDLYIKGSGSTANLASSNYFPTPSGSMVTSDAQIFN
KPYWLQRAQGHNNGICWGNQLFVTVVDTTRSTNMSLCAAISTSETTYKNTNFKEYLRHGE
EYDLQFIFQLCKITLTADVMTYIHSMNSTILEDWNFGLQPPPGGTLEDTYRFVTSQAIAC
QKHTPPAPKEDPLKKYTFWEVNLKEKFSADLDQFPLGRKFLLQLGLKAKPKFTLGKRK

Primary citation

The U4 Antibody Epitope on Human Papillomavirus 16 Identified by Cryo-electron Microscopy. Guan, J., Bywaters, S.M., Brendle, S.A. et al. J Virol (2015) 89:12108-12117. DOI 10.1128/JVI.02020-15 · 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
3J8W 13.0 Å, Cryo-EM reconstruction of quasi-HPV16 complex with H263.A2 Fab

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