[English] 日本語
Yorodumi
- EMDB-40407: Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-40407
TitleCryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 2)
Map data
Sample
  • Complex: Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 2)
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 7
    • Protein or peptide: Ubiquitin-like protein ISG15
    • Protein or peptide: Ubiquitin/ISG15-conjugating enzyme E2 L6
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsLigase / Signaling Protein
Function / homology
Function and homology information


ISG15 activating enzyme activity / ISG15 transferase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / protein localization to mitochondrion / NS1 Mediated Effects on Host Pathways / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway ...ISG15 activating enzyme activity / ISG15 transferase activity / Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases / positive regulation of protein oligomerization / ISG15-protein conjugation / regulation of type II interferon production / protein localization to mitochondrion / NS1 Mediated Effects on Host Pathways / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / E2 ubiquitin-conjugating enzyme / RSV-host interactions / ubiquitin conjugating enzyme activity / positive regulation of interleukin-10 production / positive regulation of bone mineralization / ubiquitin ligase complex / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / ubiquitin binding / integrin-mediated signaling pathway / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / PKR-mediated signaling / protein modification process / ISG15 antiviral mechanism / modification-dependent protein catabolic process / protein polyubiquitination / positive regulation of type II interferon production / ubiquitin-protein transferase activity / protein tag activity / Interferon alpha/beta signaling / integrin binding / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / defense response to bacterium / Amyloid fiber formation / innate immune response / ubiquitin protein ligase binding / DNA damage response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain ...: / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin/ISG15-conjugating enzyme E2 L6 / Ubiquitin-like protein ISG15 / Ubiquitin-like modifier-activating enzyme 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsAfsar M / Jia L / Ruben EA / Olsen SK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2023
Title: Cryo-EM structures of Uba7 reveal the molecular basis for ISG15 activation and E1-E2 thioester transfer.
Authors: Mohammad Afsar / GuanQun Liu / Lijia Jia / Eliza A Ruben / Digant Nayak / Zuberwasim Sayyad / Priscila Dos Santos Bury / Kristin E Cano / Anindita Nayak / Xiang Ru Zhao / Ankita Shukla / ...Authors: Mohammad Afsar / GuanQun Liu / Lijia Jia / Eliza A Ruben / Digant Nayak / Zuberwasim Sayyad / Priscila Dos Santos Bury / Kristin E Cano / Anindita Nayak / Xiang Ru Zhao / Ankita Shukla / Patrick Sung / Elizabeth V Wasmuth / Michaela U Gack / Shaun K Olsen /
Abstract: ISG15 plays a crucial role in the innate immune response and has been well-studied due to its antiviral activity and regulation of signal transduction, apoptosis, and autophagy. ISG15 is a ubiquitin- ...ISG15 plays a crucial role in the innate immune response and has been well-studied due to its antiviral activity and regulation of signal transduction, apoptosis, and autophagy. ISG15 is a ubiquitin-like protein that is activated by an E1 enzyme (Uba7) and transferred to a cognate E2 enzyme (UBE2L6) to form a UBE2L6-ISG15 intermediate that functions with E3 ligases that catalyze conjugation of ISG15 to target proteins. Despite its biological importance, the molecular basis by which Uba7 catalyzes ISG15 activation and transfer to UBE2L6 is unknown as there is no available structure of Uba7. Here, we present cryo-EM structures of human Uba7 in complex with UBE2L6, ISG15 adenylate, and ISG15 thioester intermediate that are poised for catalysis of Uba7-UBE2L6-ISG15 thioester transfer. Our structures reveal a unique overall architecture of the complex compared to structures from the ubiquitin conjugation pathway, particularly with respect to the location of ISG15 thioester intermediate. Our structures also illuminate the molecular basis for Uba7 activities and for its exquisite specificity for ISG15 and UBE2L6. Altogether, our structural, biochemical, and human cell-based data provide significant insights into the functions of Uba7, UBE2L6, and ISG15 in cells.
History
DepositionApr 8, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_40407.png

Downloads & links

-
Map

FileDownload / File: emd_40407.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 299.952 Å		0.83 Å/pix.
x 360 pix.
= 299.952 Å		0.83 Å/pix.
x 360 pix.
= 299.952 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.94834894 - 1.4205289
Average (Standard dev.)-0.00011660488 (±0.023266155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 299.952 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_40407_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_40407_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_40407_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thio...

EntireName: Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 2)
Components
  • Complex: Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 2)
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 7
    • Protein or peptide: Ubiquitin-like protein ISG15
    • Protein or peptide: Ubiquitin/ISG15-conjugating enzyme E2 L6
  • Ligand: ADENOSINE MONOPHOSPHATE

-
Supramolecule #1: Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thio...

SupramoleculeName: Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 160 KDa

-
Macromolecule #1: Ubiquitin-like modifier-activating enzyme 7

MacromoleculeName: Ubiquitin-like modifier-activating enzyme 7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 111.822102 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDALDASKLL DEELYSRQLY VLGSPAMQRI QGARVLVSGL QGLGAEVAKN LVLMGVGSLT LHDPHPTCWS DLAAQFLLSE QDLERSRAE ASQELLAQLN RAVQVVVHTG DITEDLLLDF QVVVLTAAKL EEQLKVGTLC HKHGVCFLAA DTRGLVGQLF C DFGEDFTV ...String:
MDALDASKLL DEELYSRQLY VLGSPAMQRI QGARVLVSGL QGLGAEVAKN LVLMGVGSLT LHDPHPTCWS DLAAQFLLSE QDLERSRAE ASQELLAQLN RAVQVVVHTG DITEDLLLDF QVVVLTAAKL EEQLKVGTLC HKHGVCFLAA DTRGLVGQLF C DFGEDFTV QDPTEAEPLT AAIQHISQGS PGILTLRKGA NTHYFRDGDL VTFSGIEGMV ELNDCDPRSI HVREDGSLEI GD TTTFSRY LRGGAITEVK RPKTVRHKSL DTALLQPHVV AQSSQEVHHA HCLHQAFCAL HKFQHLHGRP PQPWDPVDAE TVV GLARDL EPLKRTEEEP LEEPLDEALV RTVALSSAGV LSPMVAMLGA VAAQEVLKAI SRKFMPLDQW LYFDALDCLP EDGE LLPSP EDCALRGSRY DGQIAVFGAG FQEKLRRQHY LLVGAGAIGC ELLKVFALVG LGAGNSGGLT VVDMDHIERS NLSRQ FLFR SQDVGRPKAE VAAAAARGLN PDLQVIPLTY PLDPTTEHIY GDNFFSRVDG VAAALDSFQA RRYVAARCTH YLKPLL EAG TSGTWGSATV FMPHVTEAYR APASAAASED APYPVCTVRY FPSTAEHTLQ WARHEFEELF RLSAETINHH QQAHTSL AD MDEPQTLTLL KPVLGVLRVR PQNWQDCVAW ALGHWKLCFH YGIKQLLRHF PPNKVLEDGT PFWSGPKQCP QPLEFDTN Q DTHLLYVLAA ANLYAQMHGL PGSQDWTALR ELLKLLPQPD PQQMAPIFAS NLELASASAE FGPEQQKELN KALEVWSVG PPLKPLMFEK DDDSNFHVDF VVAAASLRCQ NYGIPPVNRA QSKRIVGQII PAIATTTAAV AGLLGLELYK VVSGPRPRSA FRHSYLHLA ENYLIRYMPF APAIQTFHHL KWTSWDRLKV PAGQPERTLE SLLAHLQEQH GLRVRILLHG SALLYAAGWS P EKQAQHLP LRVTELVQQL TGQAPAPGQR VLVLELSCEG DDEDTAFPPL HYEL

UniProtKB: Ubiquitin-like modifier-activating enzyme 7

-
Macromolecule #2: Ubiquitin-like protein ISG15

MacromoleculeName: Ubiquitin-like protein ISG15 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.163701 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGWDLTVKML AGNEFQVSLS SSMSVSELKA QITQKIGVHA FQQRLAVHPS GVALQDRVPL ASQGLGPGST VLLVVDKCDE PLSILVRNN KGRSSTYEVR LTQTVAHLKQ QVSGLEGVQD DLFWLTFEGK PLEDQLPLGE YGLKPLSTVF MNLRLRGG

UniProtKB: Ubiquitin-like protein ISG15

-
Macromolecule #3: Ubiquitin/ISG15-conjugating enzyme E2 L6

MacromoleculeName: Ubiquitin/ISG15-conjugating enzyme E2 L6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.643377 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MASMRVVKEL EDLQKKPPPY LRNLSSDDAN VLVWHALLLP DQPPYHLKAF NLRISFPPEY PFKPPMIKFT TKIYHPNVDE NGQICLPII SSENWKPSTK TSQVLEALNV LVNRPNIREP KRMDLADLLT QNPELFRKNA EEFTLRFGVD RPS

UniProtKB: Ubiquitin/ISG15-conjugating enzyme E2 L6

-
Macromolecule #4: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.888 µm / Nominal defocus min: 0.1 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 149051
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 10
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more