PDB-6q0k: Structure of a MAPK pathway complex

基本情報

• 登録情報: データベース: PDB / ID: 6q0k
• タイトル: Structure of a MAPK pathway complex

要素

• 14-3-3 protein zeta/delta
• Serine/threonine-protein kinase B-raf

• キーワード: SIGNALING PROTEIN/Transferase / TRANSFERASE (転移酵素) / SIGNALING PROTEIN-Transferase complex

機能・相同性

分子機能:

Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / trehalose metabolism in response to stress / CD4-positive, alpha-beta T cell differentiation / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / establishment of Golgi localization / head morphogenesis / Signalling to p38 via RIT and RIN / myeloid progenitor cell differentiation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endothelial cell apoptotic process / Rap1 signalling / negative regulation of fibroblast migration / positive regulation of glucose transmembrane transport / establishment of protein localization to membrane / negative regulation of protein localization to nucleus / mitogen-activated protein kinase kinase binding / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / positive regulation of axonogenesis / Frs2-mediated activation / stress fiber assembly / positive regulation of axon regeneration / face development / synaptic vesicle exocytosis / somatic stem cell population maintenance / MAP kinase kinase activity / thyroid gland development / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / MAP kinase kinase kinase activity / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / positive regulation of stress fiber assembly / response to cAMP / ERK1 and ERK2 cascade / cellular response to calcium ion / negative regulation of innate immune response / substrate adhesion-dependent cell spreading / protein sequestering activity / cellular response to nerve growth factor stimulus / regulation of ERK1 and ERK2 cascade / thymus development / long-term synaptic potentiation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / animal organ morphogenesis / Spry regulation of FGF signaling / RAF activation / Signaling by high-kinase activity BRAF mutants / visual learning / MAP2K and MAPK activation / epidermal growth factor receptor signaling pathway / response to peptide hormone / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / メラノソーム / 分裂促進因子活性化タンパク質キナーゼ / Signaling by BRAF and RAF1 fusions / cellular response to xenobiotic stimulus / presynapse / cell body / positive regulation of peptidyl-serine phosphorylation / T cell differentiation in thymus / regulation of cell population proliferation / T cell receptor signaling pathway / scaffold protein binding / blood microparticle / DNA-binding transcription factor binding / negative regulation of neuron apoptotic process / vesicle / transmembrane transporter binding / positive regulation of ERK1 and ERK2 cascade / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / cadherin binding / protein phosphorylation / focal adhesion / protein serine kinase activity / intracellular membrane-bounded organelle

ドメイン・相同性:

Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3タンパク質 / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3タンパク質 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ubiquitin-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily

構成要素:

Serine/threonine-protein kinase B-raf / 14-3-3 protein zeta/delta

• 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: 6.8 Å
• データ登録者: Park, E. / Rawson, S. / Jeon, H. / Eck, M.J.

資金援助

米国, 2件

組織	認可番号	国
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	P50CA165962	米国
National Institutes of Health/National Cancer Institute (NIH/NCI)	R50CA221830	米国

• 引用: ジャーナル: Nature / 年: 2019; タイトル: Architecture of autoinhibited and active BRAF-MEK1-14-3-3 complexes.; 著者: Eunyoung Park / Shaun Rawson / Kunhua Li / Byeong-Won Kim / Scott B Ficarro / Gonzalo Gonzalez-Del Pino / Humayun Sharif / Jarrod A Marto / Hyesung Jeon / Michael J Eck / ; 要旨: RAF family kinases are RAS-activated switches that initiate signalling through the MAP kinase cascade to control cellular proliferation, differentiation and survival. RAF activity is tightly regulated and inappropriate activation is a frequent cause of cancer; however, the structural basis for RAF regulation is poorly understood at present. Here we use cryo-electron microscopy to determine autoinhibited and active-state structures of full-length BRAF in complexes with MEK1 and a 14-3-3 dimer. The reconstruction reveals an inactive BRAF-MEK1 complex restrained in a cradle formed by the 14-3-3 dimer, which binds the phosphorylated S365 and S729 sites that flank the BRAF kinase domain. The BRAF cysteine-rich domain occupies a central position that stabilizes this assembly, but the adjacent RAS-binding domain is poorly ordered and peripheral. The 14-3-3 cradle maintains autoinhibition by sequestering the membrane-binding cysteine-rich domain and blocking dimerization of the BRAF kinase domain. In the active state, these inhibitory interactions are released and a single 14-3-3 dimer rearranges to bridge the C-terminal pS729 binding sites of two BRAFs, which drives the formation of an active, back-to-back BRAF dimer. Our structural snapshots provide a foundation for understanding normal RAF regulation and its mutational disruption in cancer and developmental syndromes.

履歴

登録	2019年8月1日	登録サイト: RCSB / 処理サイト: RCSB
改定 1.0	2019年10月9日	Provider: repository / タイプ: Initial release
改定 1.1	2019年12月4日	Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.2	2020年4月22日	Group: Database references / カテゴリ: citation / citation_author Item: _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

集合体

登録構造単位

A: Serine/threonine-protein kinase B-raf

B: Serine/threonine-protein kinase B-raf

X: 14-3-3 protein zeta/delta

Y: 14-3-3 protein zeta/delta

概要:

• 234 kDa, 4 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)	234,200	4
ポリマ－	234,200	4
非ポリマー	0	0
水	0

1

概要:

• 登録構造と同一
• 登録者が定義した集合体
• 根拠: light scattering

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 Serine/threonine-protein kinase B-raf / Proto-oncogene B-Raf / p94 / v-Raf murine sarcoma viral oncogene homolog B1

詳細:

分子量: 89322.812 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BRAF, BRAF1, RAFB1 / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: P15056, non-specific serine/threonine protein kinase

#2: タンパク質

X Y 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1

詳細:

分子量: 27777.092 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P63104

• 研究の焦点であるリガンドがあるか: 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: ERK pathway complexMAPK/ERK pathway / タイプ: COMPLEX / Entity ID: all / 由来: MULTIPLE SOURCES
• 分子量: 値: 233 kDa/nm / 実験値: YES
• 由来(天然): 生物種: Homo sapiens (ヒト)
• 由来(組換発現): 生物種: Spodoptera frugiperda (ツマジロクサヨトウ)
• 緩衝液: pH: 7.5
• 試料: 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
• 試料支持: 詳細: unspecified
• 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: OTHER
• 電子レンズ: モード: OTHER
• 撮影: 電子線照射量: 60 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: NONE
• 3次元再構成: 解像度: 6.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 66215 / 対称性のタイプ: POINT
• 原子モデル構築: プロトコル: RIGID BODY FIT / 空間: REAL

原子モデル構築

ID	PDB-ID	PDB chain-ID	3D fitting-ID
1	4MNE 4mne	A	1
2	4MNE 4mne	B	1
3	3NKX 3nkx	X	1
4	3NKX 3nkx	Y	1