8JRP: E6AP-E6 complex in Att3 state

Structure of E6AP-E6 complex in Att3 state. Determined by electron microscopy at 3.58 Å resolution. Released 5 Jun 2024.

Method: Electron microscopy
Resolution: 3.58 Å
Organisms: Human papillomavirus 16, Homo sapiens
Chains: 4
Atoms: 13,630
Mol. weight: 235.9 kDa
Ligands: ZN
Released: 5 Jun 2024

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

Secondary structure: helices and β-sheets

8JRP contains 116 α-helices and 52 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: 47 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	132-142	11
α-helix	147-158	12
α-helix	160-165	6
α-helix	236-246	11
α-helix	254-269	16
α-helix	270-274	5
α-helix	276-279	4
α-helix	282-284	3
α-helix	285-291	7
α-helix	294-297	4
α-helix	299-302	4
α-helix	305-314	10
α-helix	318-328	11
α-helix	333-352	20
α-helix	366-385	20
β-strand	393	1	4
α-helix	394-401	8
α-helix	404-413	10
α-helix	427-432	6
α-helix	446-449	4
α-helix	452-455	4
α-helix	460-468	9
β-strand	469	1	3
α-helix	477-479	3
α-helix	481-483	3
α-helix	486-510	25
α-helix	511-515	5
β-strand	522-525	4	5
α-helix	532-546	15
α-helix	548-552	5
β-strand	554-557	4	5
α-helix	570-582	13
α-helix	585-587	3
β-strand	590-591	2	6
β-strand	600-601	2	6
α-helix	610-625	16
α-helix	635-642	8
β-strand	644	1	4
α-helix	648-650	3
α-helix	651-654	4
α-helix	656-666	11
β-strand	679	1	7
β-strand	681-684	4	8
β-strand	692-695	4	8
β-strand	704	1	7
α-helix	711-719	9
α-helix	720-724	5
α-helix	727-740	14
α-helix	746-749	4
α-helix	752-759	8
β-strand	762	1	9
α-helix	767-773	7
β-strand	775-777	3	10
α-helix	785-795	11
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	837-838	2
β-strand	839-841	3	10
α-helix	842-844	3
β-strand	846-849	4	10
α-helix	855-866	12

Chains B and D: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	19-25	7
α-helix	30-32	3
β-strand	36	1	1
β-strand	37	1	2
β-strand	43	1	1
α-helix	46-55	10
α-helix	58-60	3
β-strand	68	1	2
α-helix	71-84	14
β-strand	86-90	5	3
α-helix	92-99	8
β-strand	109-110	2	3
α-helix	115	1
β-strand	116	1	3
α-helix	117-118	2
α-helix	119-128	10
α-helix	130-131	2
β-strand	132-135	4	3
β-strand	138-141	4	3
α-helix	145-147	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein E6	B, D	protein	141	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

>8JRP_1 Protein E6 (chains B, D)
FQDPQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYA
VCDKCLKFYSKISEYRHYSYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPEEKQRHLDK
KQRFHNIRGRWTGRCMSCSRS

Sequence of entity 2 (A, C), FASTA

>8JRP_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…
8JRN 2.6 Å, Structure of E6AP-E6 complex in Att1 state

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