8JRN: E6AP-E6 complex in Att1 state

Structure of E6AP-E6 complex in Att1 state. Determined by electron microscopy at 2.6 Å resolution. Released 5 Jun 2024.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Human papillomavirus 16, Homo sapiens
Chains: 4
Atoms: 13,672
Mol. weight: 240.13 kDa
Ligands: ZN
Released: 5 Jun 2024

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

Secondary structure: helices and β-sheets

8JRN contains 116 α-helices and 64 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.

Chains A and C: 46 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	132-139	8
α-helix	147-156	10
α-helix	160-164	5
β-strand	168	1	18
β-strand	234	1	18
α-helix	236-246	11
α-helix	252-269	18
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	305-313	9
α-helix	318-329	12
α-helix	333-353	21
α-helix	366-384	19
β-strand	387-388	2	19
β-strand	393	1	20
α-helix	394-397	4
α-helix	399-403	5
α-helix	404-412	9
α-helix	427-432	6
β-strand	439-441	3	19
α-helix	446-449	4
α-helix	452-455	4
α-helix	460-468	9
β-strand	469	1	17
α-helix	477-479	3
α-helix	481-483	3
α-helix	486-514	29
β-strand	522-527	6	21
α-helix	529-531	3
α-helix	532-546	15
α-helix	548-552	5
β-strand	554-559	6	21
α-helix	569-582	14
α-helix	585-587	3
β-strand	590-593	4	22
β-strand	598-601	4	22
α-helix	609-624	16
α-helix	635-641	7
β-strand	644	1	20
α-helix	648-650	3
α-helix	651-654	4
α-helix	656-666	11
α-helix	672-675	4
β-strand	679	1	23
β-strand	681-685	5	24
β-strand	691-695	5	24
β-strand	704	1	23
α-helix	710-719	10
α-helix	720-724	5
α-helix	727-741	15
α-helix	746-749	4
α-helix	752-759	8
β-strand	762	1	25
α-helix	767-773	7
β-strand	775-777	3	26
α-helix	785-795	11
α-helix	799-810	12
β-strand	815	1	25
β-strand	826-829	4	26
α-helix	836-838	3
β-strand	839-841	3	26
α-helix	842-844	3
β-strand	846-849	4	26
α-helix	855-866	12

Chains B and D: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	19-25	7
β-strand	36	1	14
β-strand	37	1	15
α-helix	42	1
β-strand	43	1	14
α-helix	44-45	2
α-helix	46-54	9
β-strand	60-61	2	16
β-strand	66-67	2	16
β-strand	68	1	15
α-helix	71-85	15
β-strand	86-90	5	17
α-helix	92-99	8
α-helix	103-105	3
β-strand	109-110	2	17
α-helix	115	1
β-strand	116	1	17
α-helix	117-118	2
α-helix	119-127	9
α-helix	130-131	2
β-strand	132-135	4	17
β-strand	138-141	4	17
α-helix	144-147	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein E6	B, D	protein	158	Human papillomavirus 16	P03126 (AlphaFold model)
Ubiquitin-protein ligase E3A	A, C	protein	875	Homo sapiens	Q05086 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>8JRN_1 Protein E6 (chains B, D)
MHQKRTAMFQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIV
YRDGNPYAVCDKCLKFYSKISEYRHYSYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPE
EKQRHLDKKQRFHNIRGRWTGRCMSCSRSSRTRRETQL

Sequence of entity 2 (A, C), FASTA

>8JRN_2 Ubiquitin-protein ligase E3A (chains A, C)
MEKLHQCYWKSGEPQSDDIEASRMKRAAAKHLIERYYHQLTEGCGNEACTNEFCASCPTF
LRMDNNAAAIKALELYKINAKLCDPHPSKKGASSAYLENSKGAPNNSCSEIKMNKKGARI
DFKDVTYLTEEKVYEILELCREREDYSPLIRVIGRVFSSAEALVQSFRKVKQHTKEELKS
LQAKDEDKDEDEKEKAACSAAAMEEDSEASSSRIGDSSQGDNNLQKLGPDDVSVDIDAIR
RVYTRLLSNEKIETAFLNALVYLSPNVECDLTYHNVYSRDPNYLNLFIIVMENRNLHSPE
YLEMALPLFCKAMSKLPLAAQGKLIRLWSKYNADQIRRMMETFQQLITYKVISNEFNSRN
LVNDDDAIVAASKCLKMVYYANVVGGEVDTNHNEEDDEEPIPESSELTLQELLGEERRNK
KGPRVDPLETELGVKTLDCRKPLIPFEEFINEPLNEVLEMDKDYTFFKVETENKFSFMTC
PFILNAVTKNLGLYYDNRIRMYSERRITVLYSLVQGQQLNPYLRLKVRRDHIIDDALVRL
EMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQLVVEEIFNPDIGMFTYDESTKLFW
FNPSSFETEGQFTLIGIVLGLAIYNNCILDVHFPMVVYRKLMGKKGTFRDLGDSHPVLYQ
SLKDLLEYEGNVEDDMMITFQISQTDLFGNPMMYDLKENGDKIPITNENRKEFVNLYSDY
ILNKSVEKQFKAFRRGFHMVTNESPLKYLFRPEEIELLICGSRNLDFQALEETTEYDGGY
TRDSVLIREFWEIVHSFTDEQKRLFLQFTTGTDRAPVGGLGKLKMIIAKNGPDTERLPTS
HTAFNVLLLPEYSSKEKLKERLLKAITYAKGFGML

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Structural insights into the functional mechanism of the ubiquitin ligase E6AP. Wang, Z., Fan, F., Li, Z. et al. Nat Commun (2024) 15:3531-3531. DOI 10.1038/s41467-024-47586-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…
6TWQ 2.65 Å, MAGI1_2 complexed with a 16E6 peptide

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