7UAJ: Apo HPV16 E6

Crystal structure of apo HPV16 E6. Determined by X-ray diffraction at 3.25 Å resolution. Released 15 Mar 2023.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Escherichia coli (strain K12), Human papillomavirus type 16
Chains: 4
Atoms: 16,217
Mol. weight: 245.54 kDa
Ligands: ZN
Released: 15 Mar 2023

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

Secondary structure: helices and β-sheets

7UAJ contains 125 α-helices and 129 β-strands across 4 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: 32 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	1
α-helix	18-31	14
β-strand	37-39	3	1
α-helix	44-53	10
β-strand	60-64	5	1
α-helix	65-73	9
β-strand	77	1	2
α-helix	84-89	6
β-strand	90	1	3
α-helix	92-97	6
β-strand	99-100	2	4
β-strand	103-104	2	4
β-strand	107-112	6	1
β-strand	115-118	4	5
β-strand	129	1	6
α-helix	132-142	11
β-strand	146	1	7
α-helix	155-162	8
β-strand	172	1	8
β-strand	177	1	8
α-helix	187-201	15
α-helix	211-219	9
β-strand	223	1	7
β-strand	225-228	4	5
α-helix	230-232	3
α-helix	233-238	6
β-strand	245-246	2	5
α-helix	247-249	3
β-strand	250	1	6
β-strand	251	1	9
β-strand	254	1	9
α-helix	258	1
β-strand	259-260	2	10
β-strand	261-267	7	1
β-strand	268	1	2
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	1
β-strand	305	1	3
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	10
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-368	11
α-helix	390-396	7
β-strand	407	1	11
β-strand	408	1	12
β-strand	414	1	11
α-helix	415-416	2
α-helix	417-425	9
α-helix	428-430	3
β-strand	431-433	3	13
β-strand	436-438	3	13
β-strand	439	1	12
α-helix	442-450	9
β-strand	460-461	2	14
α-helix	463-470	8
β-strand	480	1	14
α-helix	486	1
β-strand	487	1	14
α-helix	488-489	2
α-helix	490-498	9
α-helix	501-502	2
β-strand	503-506	4	14
β-strand	509-511	3	14
α-helix	515-518	4

Chain B: 32 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	15
α-helix	18-31	14
β-strand	36-39	4	15
α-helix	44-53	10
β-strand	60-64	5	15
α-helix	68-74	7
β-strand	77	1	16
α-helix	83-89	7
β-strand	90	1	17
α-helix	92-97	6
β-strand	99	1	18
β-strand	104	1	18
β-strand	107-112	6	15
β-strand	115-119	5	19
β-strand	129	1	20
α-helix	130-132	3
α-helix	133-142	10
β-strand	146-148	3	19
α-helix	155-162	8
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	19
α-helix	230-232	3
α-helix	233-238	6
β-strand	243-246	4	19
α-helix	247-249	3
β-strand	250-251	2	20
β-strand	254-255	2	20
α-helix	258-259	2
β-strand	260	1	21
β-strand	261-267	7	15
β-strand	268	1	16
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	15
β-strand	305	1	17
α-helix	306-308	3
α-helix	316-327	12
β-strand	330	1	21
α-helix	331-332	2
α-helix	337-352	16
α-helix	359-369	11
α-helix	390-396	7
β-strand	407	1	22
β-strand	408	1	23
α-helix	413	1
β-strand	414	1	22
α-helix	415-416	2
α-helix	417-425	9
α-helix	428-430	3
β-strand	431-433	3	24
β-strand	436-438	3	24
β-strand	439	1	23
α-helix	442-450	9
β-strand	459-461	3	25
α-helix	463-470	8
β-strand	480-481	2	25
β-strand	487	1	25
α-helix	488-489	2
α-helix	490-499	10
β-strand	503-506	4	25
β-strand	509-512	4	25
α-helix	515-518	4

Chain C: 30 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	26
α-helix	18-32	15
β-strand	37-39	3	26
α-helix	44-54	11
β-strand	60-64	5	26
α-helix	65-74	10
α-helix	84-89	6
α-helix	92-97	6
β-strand	99-100	2	27
β-strand	103-104	2	27
β-strand	107-112	6	26
β-strand	115-119	5	28
β-strand	129	1	29
α-helix	132-142	11
β-strand	146-148	3	28
α-helix	155-162	8
β-strand	169	1	30
β-strand	183	1	30
α-helix	187-201	15
α-helix	211-219	9
β-strand	223-228	6	28
α-helix	230-232	3
α-helix	233-238	6
β-strand	243-246	4	28
α-helix	247-249	3
β-strand	250	1	29
β-strand	251	1	31
β-strand	254	1	31
β-strand	259-260	2	32
β-strand	261-267	7	26
α-helix	274-282	9
α-helix	288-297	10
β-strand	302-303	2	26
α-helix	306-309	4
α-helix	312-314	3
α-helix	316-327	12
β-strand	329-330	2	32
α-helix	331-332	2
α-helix	337-352	16
α-helix	358-370	13
α-helix	390-396	7
β-strand	407	1	33
β-strand	408	1	34
α-helix	413	1
β-strand	414	1	33
α-helix	415-416	2
α-helix	417-425	9
α-helix	428-430	3
β-strand	431-433	3	35
β-strand	436-438	3	35
β-strand	439	1	34
α-helix	442-450	9
β-strand	461-462	2	36
α-helix	463-469	7
β-strand	480	1	37
β-strand	487	1	37
α-helix	488-489	2
α-helix	490-498	9
β-strand	502-503	2	36
β-strand	505-506	2	38
β-strand	509-510	2	38
α-helix	515-518	4

Chain D: 31 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	39
α-helix	18-31	14
β-strand	36-39	4	39
α-helix	44-54	11
β-strand	60-64	5	39
α-helix	65-73	9
β-strand	77	1	40
α-helix	78-80	3
α-helix	85-89	5
α-helix	92-97	6
β-strand	107-112	6	39
β-strand	115-119	5	41
β-strand	129	1	42
α-helix	133-142	10
β-strand	146-148	3	41
α-helix	155-163	9
α-helix	187-201	15
α-helix	211-220	10
β-strand	223-228	6	41
α-helix	230-232	3
α-helix	233-238	6
β-strand	243-246	4	41
α-helix	247-249	3
β-strand	250	1	42
β-strand	251	1	43
β-strand	254	1	43
β-strand	259-260	2	44
β-strand	261-267	7	39
β-strand	268	1	40
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	39
α-helix	306-311	6
α-helix	316-327	12
β-strand	329-330	2	44
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-370	13
α-helix	390-396	7
β-strand	407	1	45
β-strand	408	1	46
β-strand	414	1	45
α-helix	415-416	2
α-helix	417-425	9
α-helix	428-430	3
β-strand	431-433	3	47
β-strand	436-438	3	47
β-strand	439	1	46
α-helix	442-449	8
β-strand	459-461	3	48
α-helix	463-470	8
β-strand	481	1	49
α-helix	486-489	4
α-helix	490-499	10
α-helix	501-502	2
β-strand	503-505	3	48
β-strand	510-511	2	48
β-strand	512	1	49
α-helix	515-518	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose/maltodextrin-binding periplasmic protein,Protein E6	A, B, C, D	protein	537	Escherichia coli (strain K12), Human papillomavirus type 16	P03126 (AlphaFold model), P0AEX9 (AlphaFold model)

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

>7UAJ_1 Maltose/maltodextrin-binding periplasmic protein,Protein E6 (chains A, B, C, D)
MGHHHHHHMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVA
ATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVE
ALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKY
ENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWA
WSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLE
AVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAA
SGRQTVDEALKDAQTNSSSENLYFQGMFQDPQERPRKLPQLCTELQTTIHDIILECVYCK
QQLLRREVYDFAFRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHYSYSLYGTTLEQQYNK
PLSDLLIRCINCQKPLSPEEKQRHLDKKQRFHNIRGRWTGRCMSCSRSSRTRRETQL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

Disorder-to-order transition of the interdomain linker of HPV E6 upon E6AP binding reshapes p53 binding pocket. Shen, Q., Leonard, P.G., Cross, J.B. To be published.

Other PDB entries of the same protein (UniProt P03126 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6SJA 1.5 Å, Structure of HPV16 E6 oncoprotein in complex with IRF3 LxxLL motif
6SIV 1.75 Å, Structure of HPV16 E6 oncoprotein in complex with mutant IRF3 LxxLL motif
4JOP 1.8 Å, CFTR Associated Ligand (CAL) PDZ bound to HPV16 E6 oncoprotein C-terminal peptide…
8B87 2.0 Å, Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide
6HKS 2.19 Å, Crystal structure of the PTPN3 PDZ domain bound to the HPV16 E6 oncoprotein C-terminal…
4XR8 2.25 Å, Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution
6TWX 2.3 Å, MAGI1_2 complexed with a phosphorylated 16E6 peptide
9W6A 2.35 Å, Crystal structure of 18-3 TCR in complex with HLA-A*11:01 bound to HPV16-E6(93-101)
6TWU 2.4 Å, MAGI1_2 complexed with a phosphomimetic 16E6 peptide
8B9T 2.5 Å, Crystal structure of Scribble PDZ1 with human papillomavirus strain 16 E6 peptide
4GIZ 2.55 Å, Crystal structure of full-length human papillomavirus oncoprotein E6 in complex with…
8JRN 2.6 Å, Structure of E6AP-E6 complex in Att1 state

Browse structure collections

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