8JRR: E6AP-E6 complex in Det2 state

Structure of E6AP-E6 complex in Det2 state. Determined by electron microscopy at 4.35 Å resolution. Released 5 Jun 2024.

Method: Electron microscopy
Resolution: 4.35 Å
Organisms: Homo sapiens, Human papillomavirus 16
Chains: 4
Atoms: 12,370
Mol. weight: 234.31 kDa
Ligands: ZN
Released: 5 Jun 2024

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

Secondary structure: helices and β-sheets

8JRR contains 94 α-helices and 50 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: 39 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	133-135	3
α-helix	136-139	4
α-helix	147-151	5
α-helix	153-156	4
α-helix	163-166	4
α-helix	236-245	10
α-helix	252-258	7
α-helix	260-269	10
α-helix	276-278	3
α-helix	284-287	4
α-helix	288-291	4
α-helix	299-314	16
α-helix	318-329	12
α-helix	333-342	10
α-helix	344-353	10
α-helix	371-384	14
β-strand	388	1	1
β-strand	393	1	2
α-helix	398-403	6
α-helix	404-409	6
α-helix	427-430	4
β-strand	439	1	1
α-helix	452-457	6
β-strand	469	1	3
α-helix	486-505	20
α-helix	509-512	4
β-strand	523-526	4	4
α-helix	532-545	14
α-helix	554	1
β-strand	555-558	4	4
α-helix	574-581	8
β-strand	590-593	4	5
β-strand	598-601	4	5
α-helix	608-610	3
α-helix	612-622	11
α-helix	635-641	7
β-strand	644	1	2
α-helix	651-654	4
α-helix	656-667	12
β-strand	682-684	3	6
β-strand	692-694	3	6
α-helix	710-719	10
α-helix	720-724	5
α-helix	729-741	13
α-helix	746-749	4
α-helix	752-759	8
β-strand	762	1	7
α-helix	767-770	4
α-helix	787-794	8
α-helix	806-809	4
β-strand	815	1	7
β-strand	826	1	8
β-strand	841	1	8
β-strand	846	1	8
α-helix	855-867	13

Chains B and D: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	19-25	7
β-strand	36	1	9
β-strand	37	1	10
β-strand	43	1	9
α-helix	47-50	4
α-helix	57-59	3
β-strand	60-62	3	11
β-strand	65-67	3	11
β-strand	68	1	10
α-helix	71-82	12
β-strand	86-91	6	3
α-helix	92-95	4
α-helix	115-118	4
α-helix	120-122	3
α-helix	123-126	4
β-strand	131-135	5	3
β-strand	138-140	3	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ubiquitin-protein ligase E3A	A, C	protein	875	Homo sapiens	Q05086 (AlphaFold model)
Protein E6	B, D	protein	135	Human papillomavirus 16	P03126 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>8JRR_1 Ubiquitin-protein ligase E3A (chains A, C)
MEKLHQCYWKSGEPQSDDIEASRMKRAAAKHLIERYYHQLTEGCGNEACTNEFCASCPTF
LRMDNNAAAIKALELYKINAKLCDPHPSKKGASSAYLENSKGAPNNSCSEIKMNKKGARI
DFKDVTYLTEEKVYEILELCREREDYSPLIRVIGRVFSSAEALVQSFRKVKQHTKEELKS
LQAKDEDKDEDEKEKAACSAAAMEEDSEASSSRIGDSSQGDNNLQKLGPDDVSVDIDAIR
RVYTRLLSNEKIETAFLNALVYLSPNVECDLTYHNVYSRDPNYLNLFIIVMENRNLHSPE
YLEMALPLFCKAMSKLPLAAQGKLIRLWSKYNADQIRRMMETFQQLITYKVISNEFNSRN
LVNDDDAIVAASKCLKMVYYANVVGGEVDTNHNEEDDEEPIPESSELTLQELLGEERRNK
KGPRVDPLETELGVKTLDCRKPLIPFEEFINEPLNEVLEMDKDYTFFKVETENKFSFMTC
PFILNAVTKNLGLYYDNRIRMYSERRITVLYSLVQGQQLNPYLRLKVRRDHIIDDALVRL
EMIAMENPADLKKQLYVEFEGEQGVDEGGVSKEFFQLVVEEIFNPDIGMFTYDESTKLFW
FNPSSFETEGQFTLIGIVLGLAIYNNCILDVHFPMVVYRKLMGKKGTFRDLGDSHPVLYQ
SLKDLLEYEGNVEDDMMITFQISQTDLFGNPMMYDLKENGDKIPITNENRKEFVNLYSDY
ILNKSVEKQFKAFRRGFHMVTNESPLKYLFRPEEIELLICGSRNLDFQALEETTEYDGGY
TRDSVLIREFWEIVHSFAAEQKRLFLQFTTGTDRAPVGGLGKLKMIIAKNGPDTERLPTS
HTAFNVLLLPEYSSKEKLKERLLKAITYAKGFGML

Sequence of entity 2 (B, D), FASTA

>8JRR_2 Protein E6 (chains B, D)
PQERPRKLPQLCTELQTTIHDIILECVYCKQQLLRREVYDFAFRDLCIVYRDGNPYAVCD
KCLKFYSKISEYRHYSYSLYGTTLEQQYNKPLSDLLIRCINCQKPLSPEEKQRHLDKKQR
FHNIRGRWTGRCMSC

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 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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