9CHT: Human E3 ligase E6AP

Name: PDB 9CHT: Human E3 ligase E6AP in complex with HPV16-E6 and p53
Published: 2025-01-08
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Human E3 ligase E6AP in complex with HPV16-E6 and p53. Determined by electron microscopy at 3.54 Å resolution. Released 8 Jan 2025.

Method: Electron microscopy
Resolution: 3.54 Å
Organisms: Homo sapiens, Streptococcus sp. group G, Human papillomavirus 16
Chains: 3
Atoms: 8,445
Mol. weight: 165.15 kDa
Released: 8 Jan 2025

Explore 9CHT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9CHT contains 44 α-helices and 19 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: 34 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	130-143	14
α-helix	147-156	10
α-helix	160-164	5
α-helix	238-245	8
α-helix	251-272	22
α-helix	276-279	4
α-helix	286-292	7
α-helix	305-314	10
α-helix	318-329	12
α-helix	333-353	21
α-helix	366-385	20
α-helix	405-413	9
α-helix	427-432	6
α-helix	436-438	3
α-helix	446-449	4
α-helix	452-455	4
α-helix	463-468	6
α-helix	477-479	3
α-helix	486-514	29
α-helix	532-546	15
α-helix	548-550	3
α-helix	569-583	15
β-strand	590-593	4	1
β-strand	598-601	4	1
α-helix	611-625	15
α-helix	635-640	6
α-helix	648-651	4
α-helix	656-666	11
α-helix	711-720	10
α-helix	727-740	14
α-helix	756-759	4
β-strand	762	1	2
α-helix	767-772	6
β-strand	775-776	2	3
α-helix	785-795	11
α-helix	799-810	12
β-strand	815	1	2
α-helix	819-821	3
β-strand	826-827	2	3
β-strand	841	1	3
β-strand	846	1	3
α-helix	855-867	13

Chain B: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	103	1	4
β-strand	157-163	7	5
α-helix	166-168	3
α-helix	171-173	3
α-helix	177-181	5
β-strand	217-218	2	5
β-strand	251-256	6	5
β-strand	267	1	4
α-helix	283-289	7

Chain C: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-18	7
β-strand	29	1	6
β-strand	36	1	6
α-helix	39-46	8
β-strand	54-55	2	7
β-strand	58-59	2	7
α-helix	65-68	4
α-helix	72-74	3
α-helix	112-114	3
β-strand	128	1	8
β-strand	131	1	8
α-helix	137-139	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-protein ligase E3A	A	protein	895	Homo sapiens	Q05086 (AlphaFold model)
Immunoglobulin G-binding protein G/Cellular tumor antigen p53 fusion protein	B	protein	396	Streptococcus sp. group G, Homo sapiens	P04637 (AlphaFold model)
Protein E6	C	protein	151	Human papillomavirus 16	P03126 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9CHT_1 Ubiquitin-protein ligase E3A (chains A)
MGSSHHHHHHSSGLVPRGSHMEKLHQCYWKSGEPQSDDIEASRMKRAAAKHLIERYYHQL
TEGCGNEACTNEFCASCPTFLRMDNNAAAIKALELYKINAKLCDPHPSKKGASSAYLENS
KGAPNNSCSEIKMNKKGARIDFKDVTYLTEEKVYEILELCREREDYSPLIRVIGRVFSSA
EALVQSFRKVKQHTKEELKSLQAKDEDKDEDEKEKAACSAAAMEEDSEASSSRIGDSSQG
DNNLQKLGPDDVSVDIDAIRRVYTRLLSNEKIETAFLNALVYLSPNVECDLTYHNVYSRD
PNYLNLFIIVMENRNLHSPEYLEMALPLFCKAMSKLPLAAQGKLIRLWSKYNADQIRRMM
ETFQQLITYKVISNEFNSRNLVNDDDAIVAASKCLKMVYYANVVGGEVDTNHNEEDDEEP
IPESSELTLQELLGEERRNKKGPRVDPLETELGVKTLDCRKPLIPFEEFINEPLNEVLEM
DKDYTFFKVETENKFSFMTCPFILNAVTKNLGLYYDNRIRMYSERRITVLYSLVQGQQLN
PYLRLKVRRDHIIDDALVRLEMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQLVVE
EIFNPDIGMFTYDESTKLFWFNPSSFETEGQFTLIGIVLGLAIYNNCILDVHFPMVVYRK
LMGKKGTFRDLGDSHPVLYQSLKDLLEYEGNVEDDMMITFQISQTDLFGNPMMYDLKENG
DKIPITNENRKEFVNLYSDYILNKSVEKQFKAFRRGFHMVTNESPLKYLFRPEEIELLIC
GSRNLDFQALEETTEYDGGYTRDSVLIREFWEIVHSFTDEQKRLFLQFTTGTDRAPVGGL
GKLKMIIAKNGPDTERLPTSHTCFNVLLLPEYSSKEKLKERLLKAITYAKGFGML

Sequence of entity 2 (B), FASTA

>9CHT_2 Immunoglobulin G-binding protein G/Cellular tumor antigen p53 fusion protein (chains B)
MGHHHHHHSSGMTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDAT
KTFTVTEEFSSGSSGENLYFQGSHMEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLP
SQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSS
VPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKLFCQLAKTCPVQLWVDSTPPPGTR
VRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRAEYLDDRNTFRHSV
VVPYEPPEVGSDCTTIHYNYMCYSSCMGGMNRRPILTIITLEDSSGNLLGRDSFEVRVCA
CPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNT

Sequence of entity 3 (C), FASTA

>9CHT_3 Protein E6 (chains C)
MFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPY
AVCDKCLKFYSKISEYRHYCYSLYGTTLEQQYNKPLCDLLIRCINCQKPLCPEEKQRHLD
KKQRFHNIRGRWTGRCMSCCRSSRTRRETQL

Primary citation

Structure of E6AP in complex with HPV16-E6 and p53 reveals a novel ordered domain important for E3 ligase activation. Kenny, S., Iyer, S., Gabel, C.A. et al. Structure (2025) 33:504-516.e4. DOI 10.1016/j.str.2024.12.013 · PubMed

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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