4XR8: HPV16 E6/E6AP/p53 ternary complex

Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution. Determined by X-ray diffraction at 2.25 Å resolution. Released 3 Feb 2016.

Method: X-ray diffraction
Resolution: 2.25 Å
Organisms: Escherichia coli, HOMO SAPIENS, Homo sapiens
Chains: 6
Atoms: 12,034
Mol. weight: 166.67 kDa
Ligands: ZN
Released: 3 Feb 2016

Explore 4XR8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XR8 contains 81 α-helices and 95 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, 24 β-strands

Element	Residues	Length	Sheet
α-helix	4	1
β-strand	7-11	5	1
α-helix	18-32	15
β-strand	35-39	5	1
α-helix	44-52	9
β-strand	60-64	5	1
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	2
α-helix	78-80	3
α-helix	84-87	4
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	115-119	5	5
β-strand	129	1	6
α-helix	134-140	7
β-strand	146-148	3	5
α-helix	155-164	10
β-strand	168-173	6	7
β-strand	176-183	8	7
α-helix	187-197	11
α-helix	211-219	9
β-strand	223-228	6	5
α-helix	230-232	3
α-helix	233-239	7
β-strand	243-246	4	5
α-helix	247-249	3
β-strand	250	1	6
β-strand	251	1	8
β-strand	254	1	8
α-helix	258	1
β-strand	259-260	2	9
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	9
α-helix	331-332	2
α-helix	337-353	17
α-helix	358-369	12
α-helix	373-379	7

Chain B: 23 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	7-11	5	10
α-helix	18-32	15
β-strand	35-39	5	10
α-helix	44-52	9
β-strand	60-64	5	10
α-helix	65-67	3
α-helix	68-73	6
β-strand	77	1	11
α-helix	78-80	3
α-helix	84-87	4
β-strand	90	1	12
α-helix	92-97	6
β-strand	99-100	2	13
β-strand	103-104	2	13
β-strand	107-112	6	10
β-strand	115-119	5	14
β-strand	129	1	15
α-helix	132-138	7
β-strand	146-148	3	14
α-helix	155-164	10
β-strand	168-173	6	16
β-strand	176-183	8	16
α-helix	187-197	11
α-helix	211-219	9
β-strand	223-228	6	14
α-helix	230-232	3
α-helix	233-238	6
β-strand	243-246	4	14
α-helix	247-249	3
β-strand	250	1	15
β-strand	251	1	17
β-strand	254	1	17
β-strand	259-260	2	18
β-strand	261-267	7	10
β-strand	268	1	11
α-helix	274-280	7
α-helix	281-285	5
α-helix	288-297	10
β-strand	302-303	2	10
β-strand	305	1	12
α-helix	306-312	7
α-helix	316-327	12
β-strand	329-330	2	18
α-helix	331-332	2
α-helix	337-352	16
α-helix	358-367	10
α-helix	371-379	9

Chain C: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	103	1	19
β-strand	110-112	3	20
β-strand	124-127	4	19
β-strand	132-135	4	19
β-strand	140-146	7	20
α-helix	150-152	3
β-strand	156-163	8	19
α-helix	172-173	2
α-helix	177-181	5
β-strand	195-197	3	20
β-strand	204-207	4	19
β-strand	214-219	6	19
α-helix	222-224	3
β-strand	230-236	7	20
β-strand	251-258	8	19
β-strand	264-274	11	19
α-helix	278-291	14

Chain D: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	96-99	4
β-strand	103	1	21
β-strand	110-112	3	22
β-strand	124-127	4	21
β-strand	132-135	4	21
β-strand	141-146	6	22
α-helix	150-152	3
β-strand	156-163	8	21
α-helix	166-168	3
β-strand	172	1	21
α-helix	173	1
α-helix	177-180	4
β-strand	195-197	3	22
β-strand	204-207	4	21
β-strand	214-219	6	21
β-strand	230-236	7	22
β-strand	251-258	8	21
β-strand	264-274	11	21
α-helix	278-291	14

Chain F: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	12-18	7
β-strand	29	1	23
β-strand	30	1	24
α-helix	35	1
β-strand	36	1	23
α-helix	37-38	2
α-helix	39-47	9
β-strand	53-55	3	25
β-strand	58-60	3	25
β-strand	61	1	24
α-helix	64-78	15
β-strand	79-83	5	26
α-helix	85-92	8
α-helix	96-98	3
β-strand	101-103	3	26
α-helix	108	1
β-strand	109	1	26
α-helix	110-111	2
α-helix	112-120	9
α-helix	123-124	2
β-strand	125-128	4	26
β-strand	131-134	4	26

Chain H: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	12-18	7
β-strand	29	1	27
β-strand	30	1	28
α-helix	35	1
β-strand	36	1	27
α-helix	37-38	2
α-helix	39-47	9
β-strand	53-55	3	29
β-strand	58-60	3	29
β-strand	61	1	28
α-helix	64-78	15
β-strand	79-83	5	30
α-helix	85-92	8
α-helix	96-98	3
β-strand	101-103	3	30
α-helix	108	1
β-strand	109	1	30
α-helix	110-111	2
α-helix	112-121	10
α-helix	123-124	2
β-strand	125-128	4	30
β-strand	131-134	4	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose-binding periplasmic protein, ubiquitin ligase E6AP	A, B	protein	383	Escherichia coli, HOMO SAPIENS	P0AEX9 (AlphaFold model), Q05086 (AlphaFold model)
Cellular tumor antigen p53	C, D	protein	199	Homo sapiens	P04637 (AlphaFold model)
Protein E6	F, H	protein	151	Human papillomavirus type 16	P03126 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4XR8_1 Maltose-binding periplasmic protein, ubiquitin ligase E6AP (chains A, B)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSA
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDA
ALAAAQTNAAAELTLQELLGEER

Sequence of entity 2 (C, D), FASTA

>4XR8_2 Cellular tumor antigen p53 (chains C, D)
SSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPP
GTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFR
HSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVR
VCACPGRDRRTEEENLRKK

Sequence of entity 3 (F, H), FASTA

>4XR8_3 Protein E6 (chains F, H)
MFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPY
AVCDKCLKFYSKISEYRHYSYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPEEKQRHLD
KKQRFHNIRGRWTGRCMSCSRSSRTRRETQL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Water and common crystallization additives (PEG, EDO) are not listed.

Primary citation

Structure of the E6/E6AP/p53 complex required for HPV-mediated degradation of p53. Martinez-Zapien, D., Ruiz, F.X., Poirson, J. et al. Nature (2016) 529:541-545. DOI 10.1038/nature16481 · PubMed

Other PDB entries of the same protein (UniProt P0AEX9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8C8F 1.15 Å, Crystal structure of the E. coli maltodextrin-binding protein
4EXK 1.28 Å, A chimera protein containing MBP fused to the C-terminal domain of the uncharacterized…
3Q27 1.3 Å, Cyrstal structure of human alpha-synuclein (32-57) fused to maltose binding protein (MBP)
7KD4 1.31 Å, Structure of the C-terminal domain of the Menangle virus phosphoprotein (residues 329…
5M13 1.37 Å, Synthetic nanobody in complex with MBP
5HZ7 1.43 Å, High-resolution crystal structure of the minor DNA-binding pilin ComP from Neisseria…
5H7Q 1.45 Å, Crystal structure of human MNDA PYD domain with MBP tag
6XDS 1.47 Å, Crystal structure of MBP-TREM2 Ig domain fusion with fragment,…
4IRL 1.47 Å, X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein
8SVY 1.47 Å, MBP-Mcl1 in complex with ligand 10
3MP6 1.48 Å, Complex Structure of Sgf29 and dimethylated H3K4
9CLC 1.48 Å, Crystal structure of maltose binding protein (Apo), mutant Trp10 to 4-Cyanotryptophan

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