PDB-8xer: Cryo-EM structure of integrin ITGAV, ITGB3 and Cilengitide TFA co...

基本情報

• 登録情報: データベース: PDB / ID: 8xer
• タイトル: Cryo-EM structure of integrin ITGAV, ITGB3 and Cilengitide TFA complex, conformation 1

要素

• Integrin alpha-V
• Integrin beta-3

• キーワード: MEMBRANE PROTEIN

機能・相同性

分子機能:

integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / Laminin interactions / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / regulation of phagocytosis / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / transforming growth factor beta binding / positive regulation of small GTPase mediated signal transduction / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / apoptotic cell clearance / integrin complex / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / endodermal cell differentiation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of intracellular signal transduction / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / positive regulation of bone resorption / positive regulation of T cell migration / voltage-gated calcium channel activity / negative regulation of endothelial cell apoptotic process / vasculogenesis / specific granule membrane / coreceptor activity / extrinsic apoptotic signaling pathway in absence of ligand / cell adhesion molecule binding / phagocytic vesicle / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / ERK1 and ERK2 cascade / positive regulation of cell adhesion

ドメイン・相同性:

Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2.

構成要素:

: / Integrin beta-3 / Integrin alpha-V

• 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 Å
• データ登録者: Xi, Z.

資金援助

中国, 1件

組織	認可番号	国
National Natural Science Foundation of China (NSFC)		中国

• 引用: ジャーナル: To Be Published; タイトル: Cryo-EM structure of integrin ITGAV, ITGB3 and Cilengitide TFA complex, conformation 1; 著者: Xi, Z.

履歴

登録	2023年12月12日	登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.0	2024年12月18日	Provider: repository / タイプ: Initial release

集合体

登録構造単位

A: Integrin alpha-V

B: Integrin beta-3

ヘテロ分子

概要:

• 204 kDa, 2 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)	203,895	3
ポリマ－	203,306	2
非ポリマー	589	1
水	0	0

1

概要:

• 登録構造と同一
• 登録者・ソフトウェアが定義した集合体
• 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	x,y,z	1

要素

#1: タンパク質

A Integrin alpha-V

詳細:

分子量: 116155.445 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGAV / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P06756

#2: タンパク質

B Integrin beta-3

詳細:

分子量: 87150.773 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGB3 / 細胞株 (発現宿主): HEK293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P05106

#3: 化合物

B-801 ChemComp-A1LU4 / 2-[(2~{R},5~{R},8~{S},11~{S})-11-(3-carbamimidamidopropyl)-7-methyl-3,6,9,12,15-pentakis(oxidanylidene)-5-(phenylmethyl)-8-propan-2-yl-1,4,7,10,13-pentazacyclopentadec-2-yl]ethanoic acid

詳細:

分子量: 588.656 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C₂₇H₄₀N₈O₇

• 研究の焦点であるリガンドがあるか: N
• Has protein modification: Y

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: PARTICLE / ３次元再構成法: 単粒子再構成法

試料調製

• 構成要素: 名称: The complex of integrin ITGAV/ITGB3 with Cilengitide TFA; タイプ: COMPLEX / Entity ID: #1-#2 / 由来: RECOMBINANT
• 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: 7.4
• 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: FEI TITAN 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）: 5000 nm / 最小 デフォーカス（公称値）: 1200 nm
• 撮影: 電子線照射量: 50 e/Ų / フィルム・検出器のモデル: GATAN K3 (6k x 4k)

解析

• CTF補正: タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
• 3次元再構成: 解像度: 3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 103938 / 対称性のタイプ: POINT