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- EMDB-36604: Structure of human full-length E6AP -

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Basic information

Entry
Database: EMDB / ID: EMD-36604
TitleStructure of human full-length E6AP
Map data
Sample
  • Complex: E6AP
    • Protein or peptide: Ubiquitin-protein ligase E3A
KeywordsUbiquitin / LIGASE
Function / homology
Function and homology information


sperm entry / positive regulation of Golgi lumen acidification / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / androgen receptor signaling pathway / progesterone receptor signaling pathway / postsynaptic cytosol / protein K48-linked ubiquitination / protein autoubiquitination ...sperm entry / positive regulation of Golgi lumen acidification / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / androgen receptor signaling pathway / progesterone receptor signaling pathway / postsynaptic cytosol / protein K48-linked ubiquitination / protein autoubiquitination / ovarian follicle development / negative regulation of TORC1 signaling / proteasome complex / response to progesterone / positive regulation of protein ubiquitination / regulation of circadian rhythm / brain development / regulation of synaptic plasticity / protein polyubiquitination / ubiquitin-protein transferase activity / synaptic vesicle / ubiquitin protein ligase activity / rhythmic process / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / proteolysis / zinc ion binding / nucleus / 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 / 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
Ubiquitin-protein ligase E3A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsWang Z / Yu X
Funding support China, 6 items
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, 2023-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36604.png

Downloads & links

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Map

FileDownload / File: emd_36604.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.176 Å		1.07 Å/pix.
x 256 pix.
= 274.176 Å		1.07 Å/pix.
x 256 pix.
= 274.176 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.021160373 - 0.0496162
Average (Standard dev.)0.0000052515475 (±0.0014650471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.176 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36604_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36604_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E6AP

EntireName: E6AP
Components
  • Complex: E6AP
    • Protein or peptide: Ubiquitin-protein ligase E3A

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Supramolecule #1: E6AP

SupramoleculeName: E6AP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ubiquitin-protein ligase E3A

MacromoleculeName: Ubiquitin-protein ligase E3A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: HECT-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.811508 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEKLHQCYWK SGEPQSDDIE ASRMKRAAAK HLIERYYHQL TEGCGNEACT NEFCASCPTF LRMDNNAAAI KALELYKINA KLCDPHPSK KGASSAYLEN SKGAPNNSCS EIKMNKKGAR IDFKDVTYLT EEKVYEILEL CREREDYSPL IRVIGRVFSS A EALVQSFR ...String:
MEKLHQCYWK SGEPQSDDIE ASRMKRAAAK HLIERYYHQL TEGCGNEACT NEFCASCPTF LRMDNNAAAI KALELYKINA KLCDPHPSK KGASSAYLEN SKGAPNNSCS EIKMNKKGAR IDFKDVTYLT EEKVYEILEL CREREDYSPL IRVIGRVFSS A EALVQSFR KVKQHTKEEL KSLQAKDEDK DEDEKEKAAC SAAAMEEDSE ASSSRIGDSS QGDNNLQKLG PDDVSVDIDA IR RVYTRLL SNEKIETAFL NALVYLSPNV ECDLTYHNVY SRDPNYLNLF IIVMENRNLH SPEYLEMALP LFCKAMSKLP LAA QGKLIR LWSKYNADQI RRMMETFQQL ITYKVISNEF NSRNLVNDDD AIVAASKCLK MVYYANVVGG EVDTNHNEED DEEP IPESS ELTLQELLGE ERRNKKGPRV DPLETELGVK TLDCRKPLIP FEEFINEPLN EVLEMDKDYT FFKVETENKF SFMTC PFIL NAVTKNLGLY YDNRIRMYSE RRITVLYSLV QGQQLNPYLR LKVRRDHIID DALVRLEMIA MENPADLKKQ LYVEFE GEQ GVDEGGVSKE FFQLVVEEIF NPDIGMFTYD ESTKLFWFNP SSFETEGQFT LIGIVLGLAI YNNCILDVHF PMVVYRK LM GKKGTFRDLG DSHPVLYQSL KDLLEYEGNV EDDMMITFQI SQTDLFGNPM MYDLKENGDK IPITNENRKE FVNLYSDY I LNKSVEKQFK AFRRGFHMVT NESPLKYLFR PEEIELLICG SRNLDFQALE ETTEYDGGYT RDSVLIREFW EIVHSFTDE QKRLFLQFTT GTDRAPVGGL GKLKMIIAKN GPDTERLPTS HTCFNVLLLP EYSSKEKLKE RLLKAITYAK GFGML

UniProtKB: Ubiquitin-protein ligase E3A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 168999
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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