8R1G: Dimeric ternary structure of E6AP-E6-p53

Dimeric ternary structure of E6AP-E6-p53. Determined by electron microscopy at 3.99 Å resolution. Released 6 Dec 2023.

Method: Electron microscopy
Resolution: 3.99 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae S288C, Human papillomavirus type 16
Chains: 6
Atoms: 16,732
Mol. weight: 363.66 kDa
Ligands: ZN
Released: 6 Dec 2023

Explore 8R1G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R1G contains 134 α-helices and 84 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.

Chains A and D: 49 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	130-142	13
α-helix	147-157	11
α-helix	160-166	7
α-helix	236-246	11
α-helix	250-269	20
α-helix	270-274	5
α-helix	276-279	4
α-helix	281-284	4
α-helix	285-291	7
α-helix	294-297	4
α-helix	299-300	2
α-helix	301-305	5
α-helix	306-313	8
α-helix	318-328	11
α-helix	333-353	21
β-strand	357	1	1
β-strand	360	1	1
α-helix	362-364	3
α-helix	366-385	20
β-strand	387-388	2	2
β-strand	394	1	3
α-helix	404-412	9
α-helix	427-432	6
α-helix	436-438	3
β-strand	439-441	3	2
α-helix	446-449	4
α-helix	452-457	6
α-helix	460-468	9
β-strand	469	1	4
α-helix	477-479	3
α-helix	481-483	3
α-helix	486-515	30
β-strand	522-527	6	5
α-helix	532-546	15
α-helix	550-552	3
β-strand	554-559	6	5
α-helix	569-583	15
α-helix	585-587	3
β-strand	590-593	4	6
β-strand	598-601	4	6
α-helix	609-624	16
α-helix	635-641	7
β-strand	644	1	3
α-helix	648-650	3
α-helix	651-654	4
α-helix	656-667	12
α-helix	672-676	5
β-strand	679	1	7
β-strand	681-685	5	8
β-strand	691-695	5	8
α-helix	700-702	3
β-strand	704	1	7
α-helix	710-719	10
α-helix	720-724	5
α-helix	727-741	15
α-helix	746-749	4
α-helix	752-760	9
β-strand	762	1	9
α-helix	767-773	7
β-strand	775-777	3	10
α-helix	785-796	12
α-helix	799-810	12
β-strand	815	1	9
α-helix	816	1
α-helix	820-822	3
β-strand	826-829	4	10
α-helix	836-838	3
β-strand	839-841	3	10
β-strand	846-849	4	10
α-helix	855-868	14

Chains B and E: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	19-25	7
β-strand	36-37	2	11
α-helix	42	1
β-strand	43	1	11
α-helix	44-45	2
α-helix	46-54	9
α-helix	58-59	2
β-strand	60-62	3	11
β-strand	65-68	4	11
α-helix	71-85	15
β-strand	86-91	6	4
α-helix	92-99	8
α-helix	103-105	3
β-strand	109-110	2	4
α-helix	115	1
β-strand	116	1	4
α-helix	117-118	2
α-helix	119-127	9
β-strand	131-135	5	4
β-strand	138-141	4	4
α-helix	144-147	4

Chains C and F: 6 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	103	1	12
α-helix	105-107	3
β-strand	110-113	4	13
β-strand	124-127	4	12
β-strand	132-135	4	12
β-strand	141-146	6	13
α-helix	150-152	3
β-strand	156-163	8	12
α-helix	166-168	3
α-helix	177-180	4
β-strand	195-198	4	13
β-strand	204-207	4	12
β-strand	214-219	6	12
α-helix	222-224	3
β-strand	230-236	7	13
β-strand	251-258	8	12
β-strand	264-274	11	12
α-helix	278-291	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-protein ligase E3A	A, D	protein	899	Homo sapiens	Q05086 (AlphaFold model)
Ubiquitin-like protein SMT3,Protein E6	B, E	protein	266	Saccharomyces cerevisiae S288C, Human papillomavirus type 16	P03126 (AlphaFold model), Q12306 (AlphaFold model)
Cellular tumor antigen p53	C, F	protein	417	Homo sapiens	P04637 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8R1G_1 Ubiquitin-protein ligase E3A (chains A, D)
MDWSHPQFEKSAVDENLYFQGGGRMEKLHQCYWKSGEPQSDDIEASRMKRAAAKHLIERY
YHQLTEGCGNEACTNEFCASCPTFLRMDNNAAAIKALELYKINAKLCDPHPSKKGASSAY
LENSKGAPNNSCSEIKMNKKGARIDFKDVTYLTEEKVYEILELCREREDYSPLIRVIGRV
FSSAEALVQSFRKVKQHTKEELKSLQAKDEDKDEDEKEKAACSAAAMEEDSEASSSRIGD
SSQGDNNLQKLGPDDVSVDIDAIRRVYTRLLSNEKIETAFLNALVYLSPNVECDLTYHNV
YSRDPNYLNLFIIVMENRNLHSPEYLEMALPLFCKAMSKLPLAAQGKLIRLWSKYNADQI
RRMMETFQQLITYKVISNEFNSRNLVNDDDAIVAASKCLKMVYYANVVGGEVDTNHNEED
DEEPIPESSELTLQELLGEERRNKKGPRVDPLETELGVKTLDCRKPLIPFEEFINEPLNE
VLEMDKDYTFFKVETENKFSFMTCPFILNAVTKNLGLYYDNRIRMYSERRITVLYSLVQG
QQLNPYLRLKVRRDHIIDDALVRLEMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQ
LVVEEIFNPDIGMFTYDESTKLFWFNPSSFETEGQFTLIGIVLGLAIYNNCILDVHFPMV
VYRKLMGKKGTFRDLGDSHPVLYQSLKDLLEYEGNVEDDMMITFQISQTDLFGNPMMYDL
KENGDKIPITNENRKEFVNLYSDYILNKSVEKQFKAFRRGFHMVTNESPLKYLFRPEEIE
LLICGSRNLDFQALEETTEYDGGYTRDSVLIREFWEIVHSFTDEQKRLFLQFTTGTDRAP
VGGLGKLKMIIAKNGPDTERLPTSHTCFNVLLLPEYSSKEKLKERLLKAITYAKGFGML

Sequence of entity 2 (B, E), FASTA

>8R1G_2 Ubiquitin-like protein SMT3,Protein E6 (chains B, E)
MSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEM
DSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSADENLYFQGMHQKRTAMFQDP
QERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCDK
CLKFYSKISEYRHYSYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPEEKQRHLDKKQRF
HNIRGRWTGRCMSCSRSSRTRRETQL

Sequence of entity 3 (C, F), FASTA

>8R1G_3 Cellular tumor antigen p53 (chains C, F)
MDWSHPQFEKSAVDENLYFQGGGRMEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLP
SQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSS
VPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTR
VRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSV
VVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCA
CPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRE
RFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

Structural insights into viral hijacking of p53 by E6 and E6AP. Sandate, C.R., Chakraborty, D., Kater, L. et al. bioRxiv (2023). DOI 10.1101/2023.11.01.565136

Other PDB entries of the same protein (UniProt Q05086 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TGK 1.3 Å, Domain swapped E6AP C-lobe dimer
6SJV 2.03 Å, Structure of HPV18 E6 oncoprotein in complex with mutant E6AP LxxLL motif
4XR8 2.25 Å, Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution
7QPB 2.34 Å, Catalytic C-lobe of the HECT-type ubiquitin ligase E6AP in complex with a hybrid…
4GIZ 2.55 Å, Crystal structure of full-length human papillomavirus oncoprotein E6 in complex with…
9L3L 2.59 Å, Crystal structure of the C lobe of E6AP in complex with K48-linked diUb
1C4Z 2.6 Å, Structure of an E6AP-UBCH7 complex: insights into the ubiquitination pathway
8JRN 2.6 Å, Structure of E6AP-E6 complex in Att1 state
1D5F 2.8 Å, Structure of E6AP: insights into ubiquitination pathway
6SLM 2.8 Å, Crystal structure of full-length HPV31 E6 oncoprotein in complex with LXXLL peptide of…
8JRO 3.01 Å, Structure of E6AP-E6 complex in Att2 state
7Q41 3.01 Å, Crystal structure of RCC1-Like domain 2 of ubiquitin ligase HERC2 in complex with…

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