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- PDB-8jrn: Structure of E6AP-E6 complex in Att1 state -

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Basic information

Entry
Database: PDB / ID: 8jrn
TitleStructure of E6AP-E6 complex in Att1 state
Components
  • Protein E6
  • Ubiquitin-protein ligase E3A
KeywordsLIGASE/ONCOPROTEIN / Complex / Viral protein / Tumor / LIGASE-ONCOPROTEIN complex
Function / homology
Function and homology information


sperm entry / positive regulation of Golgi lumen acidification / symbiont-mediated suppression of host transcription / motor learning / negative regulation of dendritic spine morphogenesis / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / regulation of proteolysis / activation of GTPase activity ...sperm entry / positive regulation of Golgi lumen acidification / symbiont-mediated suppression of host transcription / motor learning / negative regulation of dendritic spine morphogenesis / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / regulation of proteolysis / activation of GTPase activity / progesterone receptor signaling pathway / androgen receptor signaling pathway / locomotory exploration behavior / protein autoubiquitination / protein K48-linked ubiquitination / ovarian follicle development / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of TORC1 signaling / proteasome complex / response to cocaine / positive regulation of protein ubiquitination / PDZ domain binding / response to progesterone / regulation of synaptic plasticity / response to hydrogen peroxide / regulation of circadian rhythm / brain development / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / proteasome-mediated ubiquitin-dependent protein catabolic process / host cell cytoplasm / transcription coactivator activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / DNA-templated transcription / glutamatergic synapse / host cell nucleus / positive regulation of transcription by RNA polymerase II / proteolysis / DNA binding / identical protein binding / nucleus / metal ion binding / cytosol
Similarity search - Function
Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain superfamily / Amino-terminal Zinc-binding domain of ubiquitin ligase E3A / Ubiquitin-protein ligase E3B/C / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / HECT domain / HECT, E3 ligase catalytic domain ...Ubiquitin-protein ligase E3A / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain / Ubiquitin-protein ligase E3A, N-terminal zinc-binding domain superfamily / Amino-terminal Zinc-binding domain of ubiquitin ligase E3A / Ubiquitin-protein ligase E3B/C / E6 early regulatory protein / E6 superfamily / Early Protein (E6) / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with
Similarity search - Domain/homology
Protein E6 / Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesHuman papillomavirus 16
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsWang, Z. / Yu, X.
Funding support China, 6items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000896 China
National Natural Science Foundation of China (NSFC)81821005 China
National Natural Science Foundation of China (NSFC)92253303 China
Ministry of Science and Technology (MoST, China)2022YFC3400500 China
Ministry of Science and Technology (MoST, China)2021ZD0203900 China
Ministry of Science and Technology (MoST, China)2022YFC2804800 China
CitationJournal: Nat Commun / Year: 2024
Title: Structural insights into the functional mechanism of the ubiquitin ligase E6AP.
Authors: Zhen Wang / Fengying Fan / Zhihai Li / Fei Ye / Qingxia Wang / Rongchao Gao / Jiaxuan Qiu / Yixin Lv / Min Lin / Wenwen Xu / Cheng Luo / Xuekui Yu /
Abstract: E6AP dysfunction is associated with Angelman syndrome and Autism spectrum disorder. Additionally, the host E6AP is hijacked by the high-risk HPV E6 to aberrantly ubiquitinate the tumor suppressor ...E6AP dysfunction is associated with Angelman syndrome and Autism spectrum disorder. Additionally, the host E6AP is hijacked by the high-risk HPV E6 to aberrantly ubiquitinate the tumor suppressor p53, which is linked with development of multiple types of cancer, including most cervical cancers. Here we show that E6AP and the E6AP/E6 complex exist, respectively, as a monomer and a dimer of the E6AP/E6 protomer. The short α1-helix of E6AP transforms into a longer helical structure when in complex with E6. The extended α1-helices of the dimer intersect symmetrically and contribute to the dimerization. The two protomers sway around the crossed region of the two α1-helices to promote the attachment and detachment of substrates to the catalytic C-lobe of E6AP, thus facilitating ubiquitin transfer. These findings, complemented by mutagenesis analysis, suggest that the α1-helix, through conformational transformations, controls the transition between the inactive monomer and the active dimer of E6AP.
History
DepositionJun 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
D: Protein E6
C: Ubiquitin-protein ligase E3A
B: Protein E6
A: Ubiquitin-protein ligase E3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,1358
Polymers239,8734
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein E6


Mass: 19157.135 Da / Num. of mol.: 2 / Mutation: C87S/C104S/C118S/C147S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus 16 / Gene: E6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P03126
#2: Protein Ubiquitin-protein ligase E3A / E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6- ...E6AP ubiquitin-protein ligase / HECT-type ubiquitin transferase E3A / Human papillomavirus E6-associated protein / Oncogenic protein-associated protein E6-AP / Renal carcinoma antigen NY-REN-54


Mass: 100779.445 Da / Num. of mol.: 2 / Mutation: C843A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3A, E6AP, EPVE6AP, HPVE6A / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q05086, HECT-type E3 ubiquitin transferase
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: E6AP-E6 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233242 / Symmetry type: POINT

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