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- PDB-8ivq: Cryo-EM structure of mouse BIRC6, Global map -

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Basic information

Entry
Database: PDB / ID: 8ivq
TitleCryo-EM structure of mouse BIRC6, Global map
ComponentsIsoform 2 of Baculoviral IAP repeat-containing protein 6
KeywordsAPOPTOSIS / Inhibitor of apoptosis protein / BIRC6 / Smac
Function / homology
Function and homology information


spongiotrophoblast layer development / labyrinthine layer development / Flemming body / microtubule organizing center / cysteine-type endopeptidase inhibitor activity / ubiquitin conjugating enzyme activity / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway / trans-Golgi network / RING-type E3 ubiquitin transferase ...spongiotrophoblast layer development / labyrinthine layer development / Flemming body / microtubule organizing center / cysteine-type endopeptidase inhibitor activity / ubiquitin conjugating enzyme activity / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway / trans-Golgi network / RING-type E3 ubiquitin transferase / placenta development / spindle pole / regulation of cell population proliferation / midbody / cell population proliferation / endosome / protein ubiquitination / cell division / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / apoptotic process / membrane / nucleus
Similarity search - Function
Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues ...Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / 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 / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLiu, S. / Jiang, T. / Bu, F. / Zhao, J. / Wang, G. / Li, N. / Gao, N. / Qiu, X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Nat Commun / Year: 2024
Title: Molecular mechanisms underlying the BIRC6-mediated regulation of apoptosis and autophagy.
Authors: Shuo-Shuo Liu / Tian-Xia Jiang / Fan Bu / Ji-Lan Zhao / Guang-Fei Wang / Guo-Heng Yang / Jie-Yan Kong / Yun-Fan Qie / Pei Wen / Li-Bin Fan / Ning-Ning Li / Ning Gao / Xiao-Bo Qiu /
Abstract: Procaspase 9 is the initiator caspase for apoptosis, but how its levels and activities are maintained remains unclear. The gigantic Inhibitor-of-Apoptosis Protein BIRC6/BRUCE/Apollon inhibits both ...Procaspase 9 is the initiator caspase for apoptosis, but how its levels and activities are maintained remains unclear. The gigantic Inhibitor-of-Apoptosis Protein BIRC6/BRUCE/Apollon inhibits both apoptosis and autophagy by promoting ubiquitylation of proapoptotic factors and the key autophagic protein LC3, respectively. Here we show that BIRC6 forms an anti-parallel U-shaped dimer with multiple previously unannotated domains, including a ubiquitin-like domain, and the proapoptotic factor Smac/DIABLO binds BIRC6 in the central cavity. Notably, Smac outcompetes the effector caspase 3 and the pro-apoptotic protease HtrA2, but not procaspase 9, for binding BIRC6 in cells. BIRC6 also binds LC3 through its LC3-interacting region, probably following dimer disruption of this BIRC6 region. Mutation at LC3 ubiquitylation site promotes autophagy and autophagic degradation of BIRC6. Moreover, induction of autophagy promotes autophagic degradation of BIRC6 and caspase 9, but not of other effector caspases. These results are important to understand how the balance between apoptosis and autophagy is regulated under pathophysiological conditions.
History
DepositionMar 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Baculoviral IAP repeat-containing protein 6
B: Isoform 2 of Baculoviral IAP repeat-containing protein 6


Theoretical massNumber of molelcules
Total (without water)1,070,0422
Polymers1,070,0422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Isoform 2 of Baculoviral IAP repeat-containing protein 6 / BIR repeat-containing ubiquitin-conjugating enzyme / BRUCE / RING-type E3 ubiquitin transferase ...BIR repeat-containing ubiquitin-conjugating enzyme / BRUCE / RING-type E3 ubiquitin transferase BIRC6 / Ubiquitin-conjugating BIR domain enzyme apollon / APOLLON


Mass: 535020.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The plasmid used for BIRC6 protein expression in this deposition is originated from Dr. Stefan Jentsch lab, and the Birc6 sequence in that plasmid is available from GenBank under accession ...Details: The plasmid used for BIRC6 protein expression in this deposition is originated from Dr. Stefan Jentsch lab, and the Birc6 sequence in that plasmid is available from GenBank under accession number GenBank: Y17267.1. No identical sequence could be identified in Uniprot. Here is the citation of the used Birc6 sequence: Hauser, H.P., et al., A giant ubiquitin-conjugating enzyme related to IAP apoptosis inhibitors. Journal of Cell Biology, 1998. 141(6): p. 1415-1422.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Birc6, Kiaa1289 / Production host: Homo sapiens (human)
References: UniProt: O88738, RING-type E3 ubiquitin transferase
Has protein modificationY

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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: Baculoviral IAP repeat-containing protein 6, Dimer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
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: 2000 nm
Image recordingElectron dose: 68.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00946000
ELECTRON MICROSCOPYf_angle_d1.48462480
ELECTRON MICROSCOPYf_dihedral_angle_d6.9156122
ELECTRON MICROSCOPYf_chiral_restr0.077536
ELECTRON MICROSCOPYf_plane_restr0.0147850

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