8GCR: HPV16 E6-E6AP-p53 complex

HPV16 E6-E6AP-p53 complex. Determined by electron microscopy at 3.38 Å resolution. Released 6 Mar 2024.

Method: Electron microscopy
Resolution: 3.38 Å
Organisms: Escherichia coli O157:H7, Human papillomavirus type 16, Homo sapiens
Chains: 3
Atoms: 7,206
Mol. weight: 190.34 kDa
Ligands: ZN
Released: 6 Mar 2024

Explore 8GCR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GCR contains 47 α-helices and 30 β-strands across 3 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: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	19-25	7
β-strand	36-37	2	1
β-strand	43	1	1
α-helix	46-54	9
α-helix	58-59	2
β-strand	60-62	3	1
β-strand	65-68	4	1
α-helix	71-85	15
β-strand	86-91	6	2
α-helix	92-99	8
α-helix	103-105	3
β-strand	109-110	2	2
α-helix	115	1
β-strand	116	1	2
α-helix	117-118	2
α-helix	119-127	9
β-strand	131-135	5	2
β-strand	138-141	4	2

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	103	1	3
β-strand	110-113	4	4
β-strand	124-127	4	3
β-strand	132-136	5	3
β-strand	141-146	6	4
α-helix	150-152	3
β-strand	156-163	8	3
α-helix	174-176	3
β-strand	195-197	3	4
β-strand	204-207	4	3
β-strand	214-219	6	3
β-strand	230-236	7	4
β-strand	251-258	8	3
β-strand	264-275	12	3
α-helix	280-289	10

Chain R: 35 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	130-142	13
α-helix	147-156	10
α-helix	160-165	6
α-helix	236-246	11
α-helix	250-263	14
α-helix	265-271	7
α-helix	281-288	8
α-helix	294-296	3
α-helix	299-301	3
α-helix	305-314	10
α-helix	318-329	12
α-helix	333-353	21
α-helix	362-364	3
α-helix	366-385	20
α-helix	406-413	8
α-helix	446-449	4
α-helix	452-455	4
α-helix	460-468	9
β-strand	469	1	2
α-helix	481-483	3
α-helix	486-513	28
β-strand	522-527	6	5
α-helix	533-546	14
α-helix	548-550	3
β-strand	554-559	6	5
α-helix	569-582	14
β-strand	590-593	4	6
β-strand	598-601	4	6
α-helix	609-624	16
α-helix	635-640	6
α-helix	645-647	3
α-helix	648-650	3
α-helix	651-654	4
α-helix	656-666	11
β-strand	679	1	7
β-strand	685	1	8
β-strand	691	1	8
β-strand	704	1	7
α-helix	710-719	10
α-helix	720-724	5
α-helix	727-738	12
α-helix	746-749	4
α-helix	752-754	3
α-helix	756-759	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Maltose/maltodextrin-binding periplasmic protein,Protein E6	A	protein	541	Escherichia coli O157:H7, Human papillomavirus type 16	P03126 (AlphaFold model), P0AEX9 (AlphaFold model)
Cellular tumor antigen p53	B	protein	220	Homo sapiens	P04637 (AlphaFold model)
Ubiquitin-protein ligase E3A	R	protein	903	Homo sapiens	Q05086 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8GCR_1 Maltose/maltodextrin-binding periplasmic protein,Protein E6 (chains A)
MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDI
IFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNK
DLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIK
DVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSK
VNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPL
GAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDE
ALKDAQTRITKGGGGSENLYFQGMHQKRTAMFQDPQERPRKLPQLCTELQTTIHDIILEC
VYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCDKCLKFYSKISEYRHYSYSLYGTTLEQ
QYNKPLSDLLIRCINCQKPLSPEEKQRHLDKKQRFHNIRGRWTGRCMSCSRSSRTRRETQ
L

Sequence of entity 2 (B), FASTA

>8GCR_2 Cellular tumor antigen p53 (chains B)
GSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPP
PGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTF
RHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEV
RVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

Sequence of entity 3 (R), FASTA

>8GCR_3 Ubiquitin-protein ligase E3A (chains R)
MEKLHQCYWKSGEPQSDDIEASRMKRAAAKHLIERYYHQLTEGCGNEACTNEFCASCPTF
LRMDNNAAAIKALELYKINAKLCDPHPSKKGASSAYLENSKGAPNNSCSEIKMNKKGARI
DFKDVTYLTEEKVYEILELCREREDYSPLIRVIGRVFSSAEALVQSFRKVKQHTKEELKS
LQAKDEDKDEDEKEKAACSAAAMEEDSEASSSRIGDSSQGDNNLQKLGPDDVSVDIDAIR
RVYTRLLSNEKIETAFLNALVYLSPNVECDLTYHNVYSRDPNYLNLFIIVMENRNLHSPE
YLEMALPLFCKAMSKLPLAAQGKLIRLWSKYNADQIRRMMETFQQLITYKVISNEFNSRN
LVNDDDAIVAASKCLKMVYYANVVGGEVDTNHNEEDDEEPIPESSELTLQELLGEERRNK
KGPRVDPLETELGVKTLDCRKPLIPFEEFINEPLNEVLEMDKDYTFFKVETENKFSFMTC
PFILNAVTKNLGLYYDNRIRMYSERRITVLYSLVQGQQLNPYLRLKVRRDHIIDDALVRL
EMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQLVVEEIFNPDIGMFTYDESTKLFW
FNPSSFETEGQFTLIGIVLGLAIYNNCILDVHFPMVVYRKLMGKKGTFRDLGDSHPVLYQ
SLKDLLEYEGNVEDDMMITFQISQTDLFGNPMMYDLKENGDKIPITNENRKEFVNLYSDY
ILNKSVEKQFKAFRRGFHMVTNESPLKYLFRPEEIELLICGSRNLDFQALEETTEYDGGY
TRDSVLIREFWEIVHSFTDEQKRLFLQFTTGTDRAPVGGLGKLKMIIAKNGPDTERLPTS
HTCFNVLLLPEYSSKEKLKERLLKAITYAKGFGMLENLYFQGHHHHHHGLNDIFEAQKIE
WHE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Structure of the p53 degradation complex from HPV16. Wang, J.C.K., Baddock, H.T., Mafi, A. et al. Nat Commun (2024) 15:1842-1842. DOI 10.1038/s41467-024-45920-w · PubMed

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

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