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- PDB-8yym: Cryo-EM structure of cylindrical fiber of MyD88 TIR -

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基本情報

登録情報
データベース: PDB / ID: 8yym
タイトルCryo-EM structure of cylindrical fiber of MyD88 TIR
要素Myeloid differentiation primary response protein MyD88
キーワードIMMUNE SYSTEM / signaling protein / innate immunity
機能・相同性
機能・相同性情報


regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / TIR domain binding / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / regulation of chemokine (C-X-C motif) ligand 2 production / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response ...regulation of chemokine (C-X-C motif) ligand 1 production / MyD88 deficiency (TLR5) / TIR domain binding / ATP-dependent histone chaperone activity / Toll binding / toll-like receptor 5 signaling pathway / induced systemic resistance / regulation of chemokine (C-X-C motif) ligand 2 production / neutrophil-mediated killing of bacterium / leukocyte activation involved in inflammatory response / response to molecule of fungal origin / positive regulation of lymphocyte proliferation / response to peptidoglycan / toll-like receptor 8 signaling pathway / positive regulation of interleukin-23 production / regulation of neutrophil migration / IRAK4 deficiency (TLR5) / establishment of endothelial intestinal barrier / MyD88 dependent cascade initiated on endosome / TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation / MyD88 cascade initiated on plasma membrane / cellular response to oxidised low-density lipoprotein particle stimulus / Toll signaling pathway / Toll-like receptor binding / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / toll-like receptor TLR6:TLR2 signaling pathway / interleukin-33-mediated signaling pathway / neutrophil activation involved in immune response / microglia differentiation / RIP-mediated NFkB activation via ZBP1 / interleukin-1 receptor binding / positive regulation of cytokine production involved in inflammatory response / MyD88 deficiency (TLR2/4) / death receptor binding / interleukin-1-mediated signaling pathway / IRAK4 deficiency (TLR2/4) / positive regulation of macrophage cytokine production / extrinsic component of cytoplasmic side of plasma membrane / MyD88-dependent toll-like receptor signaling pathway / 3'-UTR-mediated mRNA stabilization / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extrinsic component of plasma membrane / toll-like receptor 4 signaling pathway / skin development / type I interferon-mediated signaling pathway / response to amine / defense response to protozoan / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of interleukin-17 production / immunoglobulin mediated immune response / positive regulation of type I interferon production / phagocytosis / response to amino acid / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / positive regulation of chemokine production / JNK cascade / signaling adaptor activity / positive regulation of smooth muscle cell proliferation / response to interleukin-1 / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / cellular response to mechanical stimulus / positive regulation of NF-kappaB transcription factor activity / Interleukin-1 signaling / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / PIP3 activates AKT signaling / ER-Phagosome pathway / cellular response to lipopolysaccharide / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / response to ethanol / molecular adaptor activity / defense response to virus / gene expression / cell surface receptor signaling pathway / endosome membrane / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-positive bacterium / defense response to bacterium / innate immune response / apoptotic process / positive regulation of gene expression / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
Myeloid differentiation primary response protein MyD88 / MyD88, death domain / TIR domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Myeloid differentiation primary response protein MyD88 / MyD88, death domain / TIR domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Death-like domain superfamily
類似検索 - ドメイン・相同性
Myeloid differentiation primary response protein MyD88
類似検索 - 構成要素
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: 3.3 Å
データ登録者Kasai, K. / Imamura, K. / Narita, A. / Makino, F. / Miyata, T. / Kato, T. / Namba, K. / Onishi, H. / Tochio, H.
資金援助 日本, 2件
組織認可番号国
Japan Science and TechnologyJPMJCR1762 日本
Japan Society for the Promotion of Science (JSPS)16H04752 日本
引用ジャーナル: Biorxiv / 年: 2024
タイトル: From Monomers to Oligomers: Structural Mechanism of Receptor-Triggered MyD88 Assembly in Innate Immune Signaling
著者: Kasai, K. / Imamura, K. / Uno, M. / Sekiyama, N. / Miyata, T. / Makino, F. / Yamada, R. / Takahashi, Y. / Kodera, N. / Namba, K. / Ohnishi, H. / Narita, A. / Konno, H. / Tochio, H.
履歴
登録2024年4月4日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02025年3月26日Provider: repository / タイプ: Initial release

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Myeloid differentiation primary response protein MyD88
AA: Myeloid differentiation primary response protein MyD88
AB: Myeloid differentiation primary response protein MyD88
AC: Myeloid differentiation primary response protein MyD88
B: Myeloid differentiation primary response protein MyD88
BA: Myeloid differentiation primary response protein MyD88
BB: Myeloid differentiation primary response protein MyD88
BC: Myeloid differentiation primary response protein MyD88
C: Myeloid differentiation primary response protein MyD88
CA: Myeloid differentiation primary response protein MyD88
CB: Myeloid differentiation primary response protein MyD88
CC: Myeloid differentiation primary response protein MyD88
D: Myeloid differentiation primary response protein MyD88
DA: Myeloid differentiation primary response protein MyD88
DB: Myeloid differentiation primary response protein MyD88
DC: Myeloid differentiation primary response protein MyD88
E: Myeloid differentiation primary response protein MyD88
EA: Myeloid differentiation primary response protein MyD88
EB: Myeloid differentiation primary response protein MyD88
EC: Myeloid differentiation primary response protein MyD88
F: Myeloid differentiation primary response protein MyD88
FA: Myeloid differentiation primary response protein MyD88
FB: Myeloid differentiation primary response protein MyD88
FC: Myeloid differentiation primary response protein MyD88
G: Myeloid differentiation primary response protein MyD88
GA: Myeloid differentiation primary response protein MyD88
GB: Myeloid differentiation primary response protein MyD88
GC: Myeloid differentiation primary response protein MyD88
H: Myeloid differentiation primary response protein MyD88
HA: Myeloid differentiation primary response protein MyD88
HB: Myeloid differentiation primary response protein MyD88
HC: Myeloid differentiation primary response protein MyD88
I: Myeloid differentiation primary response protein MyD88
IA: Myeloid differentiation primary response protein MyD88
IB: Myeloid differentiation primary response protein MyD88
IC: Myeloid differentiation primary response protein MyD88
J: Myeloid differentiation primary response protein MyD88
JA: Myeloid differentiation primary response protein MyD88
JB: Myeloid differentiation primary response protein MyD88
JC: Myeloid differentiation primary response protein MyD88
K: Myeloid differentiation primary response protein MyD88
KA: Myeloid differentiation primary response protein MyD88
KB: Myeloid differentiation primary response protein MyD88
KC: Myeloid differentiation primary response protein MyD88
L: Myeloid differentiation primary response protein MyD88
LA: Myeloid differentiation primary response protein MyD88
LB: Myeloid differentiation primary response protein MyD88
LC: Myeloid differentiation primary response protein MyD88
M: Myeloid differentiation primary response protein MyD88
MA: Myeloid differentiation primary response protein MyD88
MB: Myeloid differentiation primary response protein MyD88
MC: Myeloid differentiation primary response protein MyD88
N: Myeloid differentiation primary response protein MyD88
NA: Myeloid differentiation primary response protein MyD88
NB: Myeloid differentiation primary response protein MyD88
NC: Myeloid differentiation primary response protein MyD88
O: Myeloid differentiation primary response protein MyD88
OA: Myeloid differentiation primary response protein MyD88
OB: Myeloid differentiation primary response protein MyD88
OC: Myeloid differentiation primary response protein MyD88
P: Myeloid differentiation primary response protein MyD88
PA: Myeloid differentiation primary response protein MyD88
PB: Myeloid differentiation primary response protein MyD88
PC: Myeloid differentiation primary response protein MyD88
Q: Myeloid differentiation primary response protein MyD88
QA: Myeloid differentiation primary response protein MyD88
QB: Myeloid differentiation primary response protein MyD88
QC: Myeloid differentiation primary response protein MyD88
R: Myeloid differentiation primary response protein MyD88
RA: Myeloid differentiation primary response protein MyD88
RB: Myeloid differentiation primary response protein MyD88
RC: Myeloid differentiation primary response protein MyD88
S: Myeloid differentiation primary response protein MyD88
SA: Myeloid differentiation primary response protein MyD88
SB: Myeloid differentiation primary response protein MyD88
SC: Myeloid differentiation primary response protein MyD88
T: Myeloid differentiation primary response protein MyD88
TA: Myeloid differentiation primary response protein MyD88
TB: Myeloid differentiation primary response protein MyD88
TC: Myeloid differentiation primary response protein MyD88
U: Myeloid differentiation primary response protein MyD88
UA: Myeloid differentiation primary response protein MyD88
UB: Myeloid differentiation primary response protein MyD88
UC: Myeloid differentiation primary response protein MyD88
V: Myeloid differentiation primary response protein MyD88
VA: Myeloid differentiation primary response protein MyD88
VB: Myeloid differentiation primary response protein MyD88
VC: Myeloid differentiation primary response protein MyD88
W: Myeloid differentiation primary response protein MyD88
WA: Myeloid differentiation primary response protein MyD88
WB: Myeloid differentiation primary response protein MyD88
WC: Myeloid differentiation primary response protein MyD88
X: Myeloid differentiation primary response protein MyD88
XA: Myeloid differentiation primary response protein MyD88
XB: Myeloid differentiation primary response protein MyD88
XC: Myeloid differentiation primary response protein MyD88
Y: Myeloid differentiation primary response protein MyD88
YA: Myeloid differentiation primary response protein MyD88
YB: Myeloid differentiation primary response protein MyD88
YC: Myeloid differentiation primary response protein MyD88
Z: Myeloid differentiation primary response protein MyD88
ZA: Myeloid differentiation primary response protein MyD88
ZB: Myeloid differentiation primary response protein MyD88
ZC: Myeloid differentiation primary response protein MyD88


分子量 (理論値)分子数
合計 (水以外)1,751,545104
ポリマ－1,751,545104
非ポリマー00
水00
1


  • 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
タイプ名称対称操作数
identity operation1_5551

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要素

#1: タンパク質 ...
Myeloid differentiation primary response protein MyD88


分子量: 16841.775 Da / 分子数: 104 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MYD88 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q99836
Has protein modificationN

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実験情報

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実験

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

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試料調製

構成要素名称: signaling adopter protein in a self-assembled form / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
分子量値: 5.7 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: Escherichia coli BL21(DE3) (大腸菌)
緩衝液pH: 7
緩衝液成分
ID濃度名称式Buffer-ID
120.0 mMHEPES-NaOH1
250.0 mMsodium chlorideNaCl1
310.0 mMdithiothreitolDTT1
試料濃度: 3.4 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K

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電子顕微鏡撮影

顕微鏡モデル: JEOL CRYO ARM 300
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）: 2500 nm / 最小 デフォーカス（公称値）: 1000 nm / Cs: 2.7 mm
撮影平均露光時間: 3.2 sec. / 電子線照射量: 1 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 実像数: 5325

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解析

EMソフトウェア名称: Gctf / カテゴリ: CTF補正
CTF補正タイプ: NONE
3次元再構成解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 26680 / 対称性のタイプ: POINT
精密化立体化学のターゲット値: CDL v1.2
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.0058118352
ELECTRON MICROSCOPYf_angle_d0.6726159640
ELECTRON MICROSCOPYf_chiral_restr0.051317888
ELECTRON MICROSCOPYf_plane_restr0.007219760
ELECTRON MICROSCOPYf_dihedral_angle_d10.374573112

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