PDB-9ixu: Overall reconstruction of the Bax line

基本情報

• 登録情報: データベース: PDB / ID: 9ixu
• タイトル: Overall reconstruction of the Bax line
• 要素: Apoptosis regulator BAX
• キーワード: APOPTOSIS / Pore forming Bax proteins

機能・相同性

分子機能:

T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / Activation, translocation and oligomerization of BAX / spermatid differentiation / Sertoli cell proliferation / NTRK3 as a dependence receptor / positive regulation of apoptotic DNA fragmentation / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell homeostatic proliferation / B cell negative selection / BAK complex / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / mitochondrial fragmentation involved in apoptotic process / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / endoplasmic reticulum calcium ion homeostasis / positive regulation of epithelial cell apoptotic process / fertilization / calcium ion transport into cytosol / mitochondrial fusion / epithelial cell apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / motor neuron apoptotic process / execution phase of apoptosis / thymocyte apoptotic process / pore complex / hypothalamus development / positive regulation of IRE1-mediated unfolded protein response / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / germ cell development / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / positive regulation of calcium ion transport into cytosol / BH3 domain binding / vagina development / negative regulation of mitochondrial membrane potential / B cell homeostasis / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / ectopic germ cell programmed cell death / response to axon injury / negative regulation of fibroblast proliferation / negative regulation of protein binding / ovarian follicle development / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / extrinsic apoptotic signaling pathway / response to salt stress / release of sequestered calcium ion into cytosol / Hsp70 protein binding / extrinsic apoptotic signaling pathway in absence of ligand / regulation of mitochondrial membrane potential / homeostasis of number of cells within a tissue / intrinsic apoptotic signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / response to gamma radiation / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / kidney development / cerebral cortex development / cellular response to virus / response to toxic substance / neuron migration / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / nuclear envelope / positive regulation of neuron apoptotic process / retina development in camera-type eye / channel activity / regulation of apoptotic process

ドメイン・相同性:

Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily

構成要素:

Apoptosis regulator BAX

• 生物種: Homo sapiens (ヒト)
• 手法: 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.19 Å
• データ登録者: Zhang, Y. / Tian, L. / Ge, X. / Huang, G. / Shi, Y.

資金援助

中国, 3件

組織	認可番号	国
Ministry of Science and Technology (MoST, China)	2020YFA0509300	中国
National Natural Science Foundation of China (NSFC)	81920108015	中国
National Natural Science Foundation of China (NSFC)	31930059	中国

• 引用: ジャーナル: Science / 年: 2025; タイトル: Structural basis of BAX pore formation.; 著者: Ying Zhang / Lu Tian / Gaoxingyu Huang / Xiaofei Ge / Fang Kong / Pengqi Wang / Yige Xu / Yigong Shi / ; 要旨: During apoptosis, cytosolic BAX monomers are translocated to the mitochondria to permeabilize the outer membrane. Here, we identified a dimer of BAX dimers as the basic repeating unit of its various oligomeric forms: arcs, lines, and rings. Cryo-electron microscopy structure of the BAX repeating unit at 3.2-angstrom resolution revealed the interactions within and between dimers. End-to-end stacking of the repeating units through the protruding α9 pairs yielded lines, arcs, polygons, and rings. We structurally characterized the tetragon, pentagon, hexagon, and heptagon, which comprise 16, 20, 24, and 28 BAX protomers, respectively. Missense mutations at the BAX inter-protomer interface damage pore formation and cripple its proapoptotic function. The assembly principle of the various BAX oligomers reported here provides the structural basis of membrane permeabilization by BAX.

履歴

登録	2024年7月29日	登録サイト: PDBJ / 処理サイト: PDBC
改定 1.0	2025年6月18日	Provider: repository / タイプ: Initial release
改定 1.1	2025年7月9日	Group: Data collection / Database references / カテゴリ: citation / citation_author / em_admin Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

集合体

登録構造単位

A: Apoptosis regulator BAX

B: Apoptosis regulator BAX

E: Apoptosis regulator BAX

F: Apoptosis regulator BAX

C: Apoptosis regulator BAX

D: Apoptosis regulator BAX

G: Apoptosis regulator BAX

H: Apoptosis regulator BAX

概要:

• 170 kDa, 8 ポリマー

構成要素の詳細:

	分子量 (理論値)	分子数
合計 (水以外)	169,635	8
ポリマ－	169,635	8
非ポリマー	0	0
水	0	0

1

概要:

• 登録構造と同一
• 登録者が定義した集合体
• 根拠: 電子顕微鏡法, not applicable

対称操作:

タイプ	名称	対称操作	数
identity operation	1_555		1

要素

#1: タンパク質

A B E F C D G H
Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4

詳細:

分子量: 21204.355 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BAX, BCL2L4 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q07812

• Has protein modification: N

実験情報

実験

• 実験: 手法: 電子顕微鏡法
• EM実験: 試料の集合状態: FILAMENT / ３次元再構成法: 単粒子再構成法

試料調製

• 構成要素: 名称: Bax line / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
• 分子量: 実験値: NO
• 由来(天然): 生物種: Homo sapiens (ヒト)
• 由来(組換発現): 生物種: Homo sapiens (ヒト)
• 緩衝液: pH: 8
• 試料: 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
• 急速凍結: 凍結剤: ETHANE

電子顕微鏡撮影

• 実験機器: モデル: Titan Krios / 画像提供: FEI Company
• 顕微鏡: モデル: TFS KRIOS
• 電子銃: 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
• 電子レンズ: モード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 18000 nm / 最小 デフォーカス（公称値）: 13000 nm
• 撮影: 電子線照射量: 50 e/Ų; フィルム・検出器のモデル: FEI FALCON IV (4k x 4k)

解析

• EMソフトウェア: 名称: PHENIX / バージョン: 1.17.1_3660: / カテゴリ: モデル精密化
• CTF補正: タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
• 対称性: 点対称性: C₁ (非対称)
• 3次元再構成: 解像度: 3.19 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 190916 / 対称性のタイプ: POINT