- EMDB-4862: Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC ch... -
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データベース: EMDB / ID: EMD-4862
タイトル
Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule
マップデータ
Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 13-protofilament GDP-microtubule
試料
複合体: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chimera (human doublecortin sequence) bound to 13-protofilament GDP-microtubule lattice site composed of 4 tubulin subunits (two alpha-subunits and two beta-subunits)
複合体: human doublecortin
タンパク質・ペプチド: Neuronal migration protein doublecortin
複合体: tubulin
タンパク質・ペプチド: Tubulin beta-2B chain
タンパク質・ペプチド: Tubulin alpha-1B chain
リガンド: GUANOSINE-5'-DIPHOSPHATE
リガンド: GUANOSINE-5'-TRIPHOSPHATE
リガンド: MAGNESIUM ION
キーワード
Microtubule-associated protein / neuronal migration protein / ubiquitin-like fold / microtubule nucleation and stabilisation / CYTOSOLIC PROTEIN
機能・相同性
機能・相同性情報
axoneme assembly / Neurofascin interactions / positive regulation of axon guidance / microtubule associated complex / microtubule organizing center / microtubule-based process / central nervous system development / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / neuron migration / structural constituent of cytoskeleton ...axoneme assembly / Neurofascin interactions / positive regulation of axon guidance / microtubule associated complex / microtubule organizing center / microtubule-based process / central nervous system development / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / neuron migration / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / retina development in camera-type eye / nervous system development / mitotic cell cycle / microtubule binding / microtubule / cytoskeleton / intracellular signal transduction / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / protein kinase binding / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能
ジャーナル: J Struct Biol / 年: 2020 タイトル: A microtubule RELION-based pipeline for cryo-EM image processing. 著者: Alexander D Cook / Szymon W Manka / Su Wang / Carolyn A Moores / Joseph Atherton / 要旨: Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall ...Microtubules are polar filaments built from αβ-tubulin heterodimers that exhibit a range of architectures in vitro and in vivo. Tubulin heterodimers are arranged helically in the microtubule wall but many physiologically relevant architectures exhibit a break in helical symmetry known as the seam. Noisy 2D cryo-electron microscopy projection images of pseudo-helical microtubules therefore depict distinct but highly similar views owing to the high structural similarity of α- and β-tubulin. The determination of the αβ-tubulin register and seam location during image processing is essential for alignment accuracy that enables determination of biologically relevant structures. Here we present a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing near-atomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins.
A: 123.71 Å / B: 111.2 Å / C: 129.27 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
1.39
1.39
1.39
M x/y/z
89
80
93
origin x/y/z
0.000
0.000
0.000
length x/y/z
123.710
111.200
129.270
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
63
61
81
NX/NY/NZ
131
135
92
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
89
80
93
D min/max/mean
-0.223
0.507
0.011
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添付データ
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試料の構成要素
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全体 : 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chim...
全体
名称: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chimera (human doublecortin sequence) bound to 13-protofilament GDP-microtubule lattice site composed of 4 tubulin subunits (two ...名称: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chimera (human doublecortin sequence) bound to 13-protofilament GDP-microtubule lattice site composed of 4 tubulin subunits (two alpha-subunits and two beta-subunits)
要素
複合体: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chimera (human doublecortin sequence) bound to 13-protofilament GDP-microtubule lattice site composed of 4 tubulin subunits (two alpha-subunits and two beta-subunits)
複合体: human doublecortin
タンパク質・ペプチド: Neuronal migration protein doublecortin
複合体: tubulin
タンパク質・ペプチド: Tubulin beta-2B chain
タンパク質・ペプチド: Tubulin alpha-1B chain
リガンド: GUANOSINE-5'-DIPHOSPHATE
リガンド: GUANOSINE-5'-TRIPHOSPHATE
リガンド: MAGNESIUM ION
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超分子 #1: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chim...
超分子
名称: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chimera (human doublecortin sequence) bound to 13-protofilament GDP-microtubule lattice site composed of 4 tubulin subunits (two ...名称: 5-component complex of N-terminal DC domain (NDC) of NDC-NDC chimera (human doublecortin sequence) bound to 13-protofilament GDP-microtubule lattice site composed of 4 tubulin subunits (two alpha-subunits and two beta-subunits) タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#3