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- PDB-9m5r: ES-type (short pitch) amyloid fibril (40) of Tottori (D7N) mutant -

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基本情報

登録情報
データベース: PDB / ID: 9m5r
タイトルES-type (short pitch) amyloid fibril (40) of Tottori (D7N) mutant
要素Amyloid-beta protein 40
キーワードPROTEIN FIBRIL / Amyloid
機能・相同性
機能・相同性情報


amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of Wnt signaling pathway / regulation of synapse structure or activity / axo-dendritic transport ...amyloid-beta complex / negative regulation of presynapse assembly / cytosolic mRNA polyadenylation / collateral sprouting in absence of injury / microglia development / synaptic assembly at neuromuscular junction / Formyl peptide receptors bind formyl peptides and many other ligands / regulation of Wnt signaling pathway / regulation of synapse structure or activity / axo-dendritic transport / axon midline choice point recognition / smooth endoplasmic reticulum calcium ion homeostasis / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / mating behavior / regulation of spontaneous synaptic transmission / ciliary rootlet / Golgi-associated vesicle / Lysosome Vesicle Biogenesis / PTB domain binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / neuron remodeling / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / nuclear envelope lumen / COPII-coated ER to Golgi transport vesicle / suckling behavior / dendrite development / positive regulation of protein metabolic process / modulation of excitatory postsynaptic potential / TRAF6 mediated NF-kB activation / presynaptic active zone / signaling receptor activator activity / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / neuromuscular process controlling balance / negative regulation of long-term synaptic potentiation / regulation of multicellular organism growth / transition metal ion binding / intracellular copper ion homeostasis / regulation of presynapse assembly / negative regulation of neuron differentiation / ECM proteoglycans / spindle midzone / positive regulation of T cell migration / smooth endoplasmic reticulum / Purinergic signaling in leishmaniasis infection / forebrain development / positive regulation of chemokine production / clathrin-coated pit / Notch signaling pathway / positive regulation of G2/M transition of mitotic cell cycle / extracellular matrix organization / neuron projection maintenance / Mitochondrial protein degradation / ionotropic glutamate receptor signaling pathway / positive regulation of mitotic cell cycle / response to interleukin-1 / cholesterol metabolic process / protein serine/threonine kinase binding / positive regulation of calcium-mediated signaling / axonogenesis / platelet alpha granule lumen / learning / adult locomotory behavior / positive regulation of glycolytic process / central nervous system development / dendritic shaft / positive regulation of long-term synaptic potentiation / positive regulation of interleukin-1 beta production / trans-Golgi network membrane / endosome lumen / locomotory behavior / astrocyte activation / positive regulation of JNK cascade / Post-translational protein phosphorylation / microglial cell activation / serine-type endopeptidase inhibitor activity / regulation of long-term neuronal synaptic plasticity / positive regulation of non-canonical NF-kappaB signal transduction / synapse organization / TAK1-dependent IKK and NF-kappa-B activation / visual learning / neuromuscular junction / recycling endosome / positive regulation of interleukin-6 production / Golgi lumen / cognition / neuron cellular homeostasis / endocytosis / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / cellular response to amyloid-beta / G2/M transition of mitotic cell cycle / positive regulation of tumor necrosis factor production / apical part of cell / synaptic vesicle / Platelet degranulation / cell-cell junction
類似検索 - 分子機能
Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site ...Amyloidogenic glycoprotein, copper-binding / Amyloidogenic glycoprotein, copper-binding domain conserved site / Amyloidogenic glycoprotein, copper-binding domain superfamily / Copper-binding of amyloid precursor, CuBD / Amyloid precursor protein (APP) copper-binding (CuBD) domain signature. / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide / Beta-amyloid precursor protein C-terminal / Amyloidogenic glycoprotein, intracellular domain, conserved site / Beta-amyloid precursor protein C-terminus / Amyloid precursor protein (APP) intracellular domain signature. / Amyloidogenic glycoprotein, extracellular / Amyloidogenic glycoprotein, heparin-binding / Amyloidogenic glycoprotein, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / Amyloid A4 N-terminal heparin-binding / E2 domain of amyloid precursor protein / Amyloid precursor protein (APP) E1 domain profile. / Amyloid precursor protein (APP) E2 domain profile. / amyloid A4 / Amyloidogenic glycoprotein / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / PH-like domain superfamily
類似検索 - ドメイン・相同性
Amyloid-beta precursor protein
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å
データ登録者Burton-Smith, R.N. / Murata, K.
資金援助 日本, 1件
組織認可番号国
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP24ama121005 日本
引用ジャーナル: ACS Chem Neurosci / 年: 2025
タイトル: Microgravity-Assisted Exploration of the Conformational Space of Amyloid β Affected by Tottori-Type Familial Mutation D7N.
著者: Maho Yagi-Utsumi / Saeko Yanaka / Raymond N Burton-Smith / Chihong Song / Christian Ganser / Chiaki Yamazaki / Haruo Kasahara / Toru Shimazu / Takayuki Uchihashi / Kazuyoshi Murata / Koichi Kato /
要旨: The amyloid β (Aβ) Tottori variant (D7N) exhibits unique aggregation behaviors and altered fibril formation, posing challenges for structural characterization. To overcome this, the microgravity ...The amyloid β (Aβ) Tottori variant (D7N) exhibits unique aggregation behaviors and altered fibril formation, posing challenges for structural characterization. To overcome this, the microgravity environment on the International Space Station was employed to study Tottori-type Aβ40 fibril formation and structure. Under Earth gravity, Tottori-type Aβ40 primarily formed nonfibrillar aggregates, hindering detailed structural analysis. In contrast, microgravity significantly enhanced fibril formation and minimized amorphous aggregates. Cryo-electron microscopy revealed two structurally distinct fibril types, each comprising different protomer conformations. In both types, the N-terminal segment was disordered and nor resolved in the density maps. The D7N mutation disrupts the protection of the core by the N-terminal segment often observed in wild-type Aβ40 fibrils, enhancing the hydrophobicity-mediated aggregation propensity. However, microgravity suppressed kinetic traps and facilitated high-quality fibril formation suitable for structural studies that can explore the free energy landscape of Aβ fibril formation. These findings demonstrate the utility of microgravity for studying familial Aβ variants and potentially accelerate our understanding of Aβ aggregation mechanisms in Alzheimer's disease.
履歴
登録2025年3月6日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02025年7月9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
0: Amyloid-beta protein 40
A: Amyloid-beta protein 40
B: Amyloid-beta protein 40
C: Amyloid-beta protein 40
D: Amyloid-beta protein 40
E: Amyloid-beta protein 40
F: Amyloid-beta protein 40
G: Amyloid-beta protein 40
H: Amyloid-beta protein 40
I: Amyloid-beta protein 40
J: Amyloid-beta protein 40
K: Amyloid-beta protein 40
L: Amyloid-beta protein 40
M: Amyloid-beta protein 40
N: Amyloid-beta protein 40
O: Amyloid-beta protein 40
P: Amyloid-beta protein 40
Q: Amyloid-beta protein 40
R: Amyloid-beta protein 40
S: Amyloid-beta protein 40
T: Amyloid-beta protein 40
U: Amyloid-beta protein 40
V: Amyloid-beta protein 40
W: Amyloid-beta protein 40
X: Amyloid-beta protein 40
Y: Amyloid-beta protein 40
Z: Amyloid-beta protein 40
a: Amyloid-beta protein 40
b: Amyloid-beta protein 40
c: Amyloid-beta protein 40
d: Amyloid-beta protein 40
e: Amyloid-beta protein 40
f: Amyloid-beta protein 40
g: Amyloid-beta protein 40
h: Amyloid-beta protein 40
i: Amyloid-beta protein 40
j: Amyloid-beta protein 40
k: Amyloid-beta protein 40
l: Amyloid-beta protein 40
m: Amyloid-beta protein 40
n: Amyloid-beta protein 40
o: Amyloid-beta protein 40
p: Amyloid-beta protein 40
q: Amyloid-beta protein 40
r: Amyloid-beta protein 40
s: Amyloid-beta protein 40
t: Amyloid-beta protein 40
u: Amyloid-beta protein 40
v: Amyloid-beta protein 40
w: Amyloid-beta protein 40
x: Amyloid-beta protein 40
y: Amyloid-beta protein 40
z: Amyloid-beta protein 40
1: Amyloid-beta protein 40
2: Amyloid-beta protein 40
3: Amyloid-beta protein 40
4: Amyloid-beta protein 40
5: Amyloid-beta protein 40
6: Amyloid-beta protein 40
7: Amyloid-beta protein 40
8: Amyloid-beta protein 40
9: Amyloid-beta protein 40
AA: Amyloid-beta protein 40
AB: Amyloid-beta protein 40
AC: Amyloid-beta protein 40
AD: Amyloid-beta protein 40
AE: Amyloid-beta protein 40
AF: Amyloid-beta protein 40
AG: Amyloid-beta protein 40
AH: Amyloid-beta protein 40
AI: Amyloid-beta protein 40
AJ: Amyloid-beta protein 40
AK: Amyloid-beta protein 40
AL: Amyloid-beta protein 40
AM: Amyloid-beta protein 40
AN: Amyloid-beta protein 40
AO: Amyloid-beta protein 40
AP: Amyloid-beta protein 40
AQ: Amyloid-beta protein 40
AR: Amyloid-beta protein 40
AS: Amyloid-beta protein 40
AT: Amyloid-beta protein 40
AU: Amyloid-beta protein 40
AV: Amyloid-beta protein 40
AW: Amyloid-beta protein 40
AX: Amyloid-beta protein 40
AY: Amyloid-beta protein 40
AZ: Amyloid-beta protein 40
Aa: Amyloid-beta protein 40
Ab: Amyloid-beta protein 40
Ac: Amyloid-beta protein 40
Ad: Amyloid-beta protein 40
Ae: Amyloid-beta protein 40
Af: Amyloid-beta protein 40
Ag: Amyloid-beta protein 40
Ah: Amyloid-beta protein 40
Ai: Amyloid-beta protein 40
Aj: Amyloid-beta protein 40
Ak: Amyloid-beta protein 40
Al: Amyloid-beta protein 40
Am: Amyloid-beta protein 40
An: Amyloid-beta protein 40
Ao: Amyloid-beta protein 40
Ap: Amyloid-beta protein 40
Aq: Amyloid-beta protein 40
Ar: Amyloid-beta protein 40
As: Amyloid-beta protein 40
At: Amyloid-beta protein 40
Au: Amyloid-beta protein 40
Av: Amyloid-beta protein 40
Aw: Amyloid-beta protein 40
Ax: Amyloid-beta protein 40
Ay: Amyloid-beta protein 40
Az: Amyloid-beta protein 40
A0: Amyloid-beta protein 40
A1: Amyloid-beta protein 40
A2: Amyloid-beta protein 40
A3: Amyloid-beta protein 40
A4: Amyloid-beta protein 40
A5: Amyloid-beta protein 40
A6: Amyloid-beta protein 40
A7: Amyloid-beta protein 40
A8: Amyloid-beta protein 40
A9: Amyloid-beta protein 40
BA: Amyloid-beta protein 40
BB: Amyloid-beta protein 40
BC: Amyloid-beta protein 40
BD: Amyloid-beta protein 40
BE: Amyloid-beta protein 40
BF: Amyloid-beta protein 40
BG: Amyloid-beta protein 40
BH: Amyloid-beta protein 40
BI: Amyloid-beta protein 40
BJ: Amyloid-beta protein 40
BK: Amyloid-beta protein 40
BL: Amyloid-beta protein 40
BM: Amyloid-beta protein 40
BN: Amyloid-beta protein 40
BO: Amyloid-beta protein 40
BP: Amyloid-beta protein 40
BQ: Amyloid-beta protein 40
BR: Amyloid-beta protein 40
BS: Amyloid-beta protein 40
BT: Amyloid-beta protein 40
BU: Amyloid-beta protein 40
BV: Amyloid-beta protein 40
BW: Amyloid-beta protein 40
BX: Amyloid-beta protein 40
BY: Amyloid-beta protein 40
BZ: Amyloid-beta protein 40
Ba: Amyloid-beta protein 40
Bb: Amyloid-beta protein 40
Bc: Amyloid-beta protein 40
Bd: Amyloid-beta protein 40
Be: Amyloid-beta protein 40
Bf: Amyloid-beta protein 40
Bg: Amyloid-beta protein 40
Bh: Amyloid-beta protein 40
Bi: Amyloid-beta protein 40
Bj: Amyloid-beta protein 40
Bk: Amyloid-beta protein 40
Bl: Amyloid-beta protein 40
Bm: Amyloid-beta protein 40
Bn: Amyloid-beta protein 40
Bo: Amyloid-beta protein 40
Bp: Amyloid-beta protein 40
Bq: Amyloid-beta protein 40
Br: Amyloid-beta protein 40
Bs: Amyloid-beta protein 40
Bt: Amyloid-beta protein 40
Bu: Amyloid-beta protein 40
Bv: Amyloid-beta protein 40


分子量 (理論値)分子数
合計 (水以外)745,597172
ポリマ－745,597172
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
タイプ名称対称操作数
identity operation1_5551
非結晶学的対称性 (NCS)NCS oper:
IDCodeMatrixベクター
1given(0.555962, 0.831208), (-0.831208, 0.555962), (1)-82.51361, 271.78036, -121.48455
2given(-0.520265, -0.854005), (0.854005, -0.520265), (1)506.00435, 141.99321, -119.1025
3given(0.483634, 0.87527), (-0.87527, 0.483634), (1)-76.48967, 296.5856, -116.72045
4given(-0.446135, -0.894966), (0.894966, -0.446135), (1)498.9354, 117.46531, -114.3384
5given(0.407837, 0.913055), (-0.913055, 0.407837), (1)-68.38839, 320.79215, -111.95635
6given(-0.368806, -0.929506), (0.929506, -0.368806), (1)489.81633, 93.62353, -109.5743
7given(0.329114, 0.94429), (-0.94429, 0.329114), (1)-58.26788, 344.22638, -107.19225
8given(-0.288831, -0.95738), (0.95738, -0.288831), (1)478.71254, 70.63889, -104.8102
9given(0.248031, 0.968752), (-0.968752, 0.248031), (1)-46.20074, 366.7202, -102.42815
10given(-0.206785, -0.978386), (0.978386, -0.206785), (1)465.70369, 48.67626, -100.0461
11given(0.165168, 0.986265), (-0.986265, 0.165168), (1)-32.27351, 388.11225, -97.66405
12given(-0.123255, -0.992375), (0.992375, -0.123255), (1)450.88308, 27.89316, -95.282
13given(0.081121, 0.996704), (-0.996704, 0.081121), (1)-16.58611, 408.24911, -92.89995
14given(-0.038841, -0.999245), (0.999245, -0.038841), (1)434.35702, 8.43867, -90.5179
15given(-0.003508, 0.999994), (-0.999994, -0.003508), (1)0.74896, 426.98633, -88.13585
16given(0.045851, -0.998948), (0.998948, 0.045851), (1)416.24405, -9.54766, -85.7538
17given(-0.088112, 0.996111), (-0.996111, -0.088112), (1)19.60734, 444.1895, -83.37175
18given(0.130215, -0.991486), (0.991486, 0.130215), (1)396.67409, -25.93682, -80.9897
19given(-0.172084, 0.985082), (-0.985082, -0.172084), (1)39.85377, 459.73524, -78.60765
20given(0.213644, -0.976912), (0.976912, 0.213644), (1)375.78752, -40.61124, -76.2256
21given(-0.254821, 0.966988), (-0.966988, -0.254821), (1)61.34301, 473.51203, -73.84355
22given(0.295541, -0.95533), (0.95533, 0.295541), (1)353.73415, -53.46569, -71.4615
23given(-0.335731, 0.941958), (-0.941958, -0.335731), (1)83.92094, 485.42106, -69.07945
24given(0.375319, -0.926896), (0.926896, 0.375319), (1)330.67217, -64.40793, -66.6974
25given(-0.414233, 0.910171), (-0.910171, -0.414233), (1)107.4256, 495.3769, -64.31535
26given(0.452404, -0.891813), (0.891813, 0.452404), (1)306.767, -73.3595, -61.9333
27given(-0.489763, 0.871856), (-0.871856, -0.489763), (1)131.68839, 503.30814, -59.55125
28given(0.526244, -0.850334), (0.850334, 0.526244), (1)282.19011, -80.25619, -57.1692
29given(-0.56178, 0.827287), (-0.827287, -0.56178), (1)156.53529, 509.15789, -54.78715
30given(0.596309, -0.802755), (0.802755, 0.596309), (1)257.11779, -85.04851, -52.4051
31given(-0.629768, 0.776783), (-0.776783, -0.629768), (1)181.78806, 512.88419, -50.02305
32given(0.662097, -0.749418), (0.749418, 0.662097), (1)231.72987, -87.70211, -47.641
33given(-0.693238, 0.720708), (-0.720708, -0.693238), (1)207.26557, 514.46032, -45.25895
34given(0.723136, -0.690706), (0.690706, 0.723136), (1)206.20847, -88.19794, -42.8769
35given(-0.751736, 0.659464), (-0.659464, -0.751736), (1)232.78507, 513.87496, -40.49485
36given(0.778988, -0.627039), (0.627039, 0.778988), (1)180.73665, -86.53244, -38.1128
37given(-0.804842, 0.593489), (-0.593489, -0.804842), (1)258.16352, 511.13232, -35.73075
38given(0.829252, -0.558875), (0.558875, 0.829252), (1)155.4971, -82.71757, -33.3487
39given(-0.852175, 0.523257), (-0.523257, -0.852175), (1)283.21888, 506.25207, -30.96665
40given(0.873568, -0.486701), (0.486701, 0.873568), (1)130.67088, -76.78069, -28.5846
41given(-0.893395, 0.449272), (-0.449272, -0.893395), (1)307.77142, 499.26921, -26.20255
42given(0.911619, -0.411037), (0.411037, 0.911619), (1)106.43606, -68.76438, -23.8205
43given(-0.928207, 0.372065), (-0.372065, -0.928207), (1)331.64504, 490.23383, -21.43845
44given(0.94313, -0.332425), (0.332425, 0.94313), (1)82.96647, -58.72615, -19.0564
45given(-0.956361, 0.292188), (-0.292188, -0.956361), (1)354.66849, 479.21075, -16.67435
46given(0.967876, -0.251427), (0.251427, 0.967876), (1)60.43046, -46.73799, -14.2923
47given(-0.977655, 0.210216), (-0.210216, -0.977655), (1)376.67663, 466.27902, -11.91025
48given(0.98568, -0.168627), (0.168627, 0.98568), (1)38.98968, -32.88589, -9.5282
49given(-0.991937, 0.126736), (-0.126736, -0.991937), (1)397.5116, 451.53141, -7.14615
50given(0.996414, -0.084617), (0.084617, 0.996414), (1)18.79791, -17.26923, -4.7641
51given(-0.999103, 0.042346), (-0.042346, -0.999103), (1)417.02394, 435.0737, -2.38205
53given(-0.999103, -0.042346), (0.042346, -0.999103), (1)435.0737, 417.02394, 2.38205
54given(0.996414, 0.084617), (-0.084617, 0.996414), (1)-17.26923, 18.79791, 4.7641
55given(-0.991937, -0.126736), (0.126736, -0.991937), (1)451.53141, 397.5116, 7.14615
56given(0.98568, 0.168627), (-0.168627, 0.98568), (1)-32.88589, 38.98968, 9.5282
57given(-0.977655, -0.210216), (0.210216, -0.977655), (1)466.27902, 376.67663, 11.91025
58given(0.967876, 0.251427), (-0.251427, 0.967876), (1)-46.73799, 60.43046, 14.2923
59given(-0.956361, -0.292188), (0.292188, -0.956361), (1)479.21075, 354.66849, 16.67435
60given(0.94313, 0.332425), (-0.332425, 0.94313), (1)-58.72615, 82.96647, 19.0564
61given(-0.928207, -0.372065), (0.372065, -0.928207), (1)490.23383, 331.64504, 21.43845
62given(0.911619, 0.411037), (-0.411037, 0.911619), (1)-68.76438, 106.43606, 23.8205
63given(-0.893395, -0.449272), (0.449272, -0.893395), (1)499.26921, 307.77142, 26.20255
64given(0.873568, 0.486701), (-0.486701, 0.873568), (1)-76.78069, 130.67088, 28.5846
65given(-0.852175, -0.523257), (0.523257, -0.852175), (1)506.25207, 283.21888, 30.96665
66given(0.829252, 0.558875), (-0.558875, 0.829252), (1)-82.71757, 155.4971, 33.3487
67given(-0.804842, -0.593489), (0.593489, -0.804842), (1)511.13232, 258.16352, 35.73075
68given(0.778988, 0.627039), (-0.627039, 0.778988), (1)-86.53244, 180.73665, 38.1128
69given(-0.751736, -0.659464), (0.659464, -0.751736), (1)513.87496, 232.78507, 40.49485
70given(0.723136, 0.690706), (-0.690706, 0.723136), (1)-88.19794, 206.20847, 42.8769
71given(-0.693238, -0.720708), (0.720708, -0.693238), (1)514.46032, 207.26557, 45.25895
72given(0.662097, 0.749418), (-0.749418, 0.662097), (1)-87.70211, 231.72987, 47.641
73given(-0.629768, -0.776783), (0.776783, -0.629768), (1)512.88419, 181.78806, 50.02305
74given(0.596309, 0.802755), (-0.802755, 0.596309), (1)-85.04851, 257.11779, 52.4051
75given(-0.56178, -0.827287), (0.827287, -0.56178), (1)509.15789, 156.53529, 54.78715
76given(0.526244, 0.850334), (-0.850334, 0.526244), (1)-80.25619, 282.19011, 57.1692
77given(-0.489763, -0.871856), (0.871856, -0.489763), (1)503.30814, 131.68839, 59.55125
78given(0.452404, 0.891813), (-0.891813, 0.452404), (1)-73.3595, 306.767, 61.9333
79given(-0.414233, -0.910171), (0.910171, -0.414233), (1)495.3769, 107.4256, 64.31535
80given(0.375319, 0.926896), (-0.926896, 0.375319), (1)-64.40793, 330.67217, 66.6974
81given(-0.335731, -0.941958), (0.941958, -0.335731), (1)485.42106, 83.92094, 69.07945
82given(0.295541, 0.95533), (-0.95533, 0.295541), (1)-53.46569, 353.73415, 71.4615
83given(-0.254821, -0.966988), (0.966988, -0.254821), (1)473.51203, 61.34301, 73.84355
84given(0.213644, 0.976912), (-0.976912, 0.213644), (1)-40.61124, 375.78752, 76.2256
85given(-0.172084, -0.985082), (0.985082, -0.172084), (1)459.73524, 39.85377, 78.60765
86given(0.130215, 0.991486), (-0.991486, 0.130215), (1)-25.93682, 396.67409, 80.9897
87given(-0.088112, -0.996111), (0.996111, -0.088112), (1)444.1895, 19.60734, 83.37175
88given(0.045851, 0.998948), (-0.998948, 0.045851), (1)-9.54766, 416.24405, 85.7538
89given(-0.003508, -0.999994), (0.999994, -0.003508), (1)426.98633, 0.74896, 88.13585
90given(-0.038841, 0.999245), (-0.999245, -0.038841), (1)8.43867, 434.35702, 90.5179
91given(0.081121, -0.996704), (0.996704, 0.081121), (1)408.24911, -16.58611, 92.89995
92given(-0.123255, 0.992375), (-0.992375, -0.123255), (1)27.89316, 450.88308, 95.282
93given(0.165168, -0.986265), (0.986265, 0.165168), (1)388.11225, -32.27351, 97.66405
94given(-0.206785, 0.978386), (-0.978386, -0.206785), (1)48.67626, 465.70369, 100.0461
95given(0.248031, -0.968752), (0.968752, 0.248031), (1)366.7202, -46.20074, 102.42815
96given(-0.288831, 0.95738), (-0.95738, -0.288831), (1)70.63889, 478.71254, 104.8102
97given(0.329114, -0.94429), (0.94429, 0.329114), (1)344.22638, -58.26788, 107.19225
98given(-0.368806, 0.929506), (-0.929506, -0.368806), (1)93.62353, 489.81633, 109.5743
99given(0.407837, -0.913055), (0.913055, 0.407837), (1)320.79215, -68.38839, 111.95635
100given(-0.446135, 0.894966), (-0.894966, -0.446135), (1)117.46531, 498.9354, 114.3384
101given(0.483634, -0.87527), (0.87527, 0.483634), (1)296.5856, -76.48967, 116.72045
102given(-0.520265, 0.854005), (-0.854005, -0.520265), (1)141.99321, 506.00435, 119.1025
103given(0.555962, -0.831208), (0.831208, 0.555962), (1)271.78036, -82.51361, 121.48455
104given(-0.590662, 0.806919), (-0.806919, -0.590662), (1)167.03129, 510.97247, 123.8666
105given(0.624302, -0.781183), (0.781183, 0.624302), (1)246.55436, -86.41699, 126.24865
106given(-0.656823, 0.754045), (-0.754045, -0.656823), (1)192.39996, 513.80412, 128.6307
107given(0.688165, -0.725555), (0.725555, 0.688165), (1)221.08853, -88.17184, 131.01275
108given(-0.718272, 0.695762), (-0.695762, -0.718272), (1)217.91725, 514.479, 133.3948
109given(0.747091, -0.664722), (0.664722, 0.747091), (1)195.56555, -87.76554, 135.77685
110given(-0.774569, 0.632489), (-0.632489, -0.774569), (1)243.40014, 512.99226, 138.1589
111given(0.800658, -0.599121), (0.599121, 0.800658), (1)170.16848, -85.20103, 140.54095
112given(-0.825311, 0.564679), (-0.564679, -0.825311), (1)268.66582, 509.35457, 142.923
113given(0.848483, -0.529223), (0.529223, 0.848483), (1)145.0795, -80.49669, 145.30505
114given(-0.870132, 0.492818), (-0.492818, -0.870132), (1)293.53309, 503.59202, 147.6871
115given(0.890221, -0.455529), (0.455529, 0.890221), (1)120.47857, -73.68626, 150.06915
116given(-0.908712, 0.417423), (-0.417423, -0.908712), (1)317.82355, 495.74595, 152.4512
117given(0.925574, -0.378568), (0.378568, 0.925574), (1)96.54214, -64.81861, 154.83325
118given(-0.940774, 0.339033), (-0.339033, -0.940774), (1)341.36299, 485.87263, 157.2153
119given(0.954287, -0.298891), (0.298891, 0.954287), (1)73.44192, -53.95733, 159.59735
120given(-0.966088, 0.258212), (-0.258212, -0.966088), (1)363.98256, 474.04288, 161.9794
121given(0.976156, -0.21707), (0.21707, 0.976156), (1)51.34359, -41.18034, 164.36145
122given(-0.984473, 0.175539), (-0.175539, -0.984473), (1)385.52001, 460.34156, 166.7435
123given(0.991023, -0.133692), (0.133692, 0.991023), (1)30.40567, -26.57927, 169.12555
124given(-0.995795, 0.091606), (-0.091606, -0.995795), (1)405.82084, 444.86694, 171.5076
125given(0.998781, -0.049355), (0.049355, 0.998781), (1)10.77833, -10.25887, 173.88965
126given(-0.999975, 0.007016), (-0.007016, -0.999975), (1)424.73946, 427.73003, 176.2717
127given(0.999376, 0.035336), (-0.035336, 0.999376), (1)-7.39762, 7.66381, 178.65375
128given(-0.996983, -0.077624), (0.077624, -0.996983), (1)442.14015, 409.05374, 181.0358
129given(0.992801, 0.119773), (-0.119773, 0.992801), (1)-23.99183, 27.0602, 183.41785
130given(-0.986839, -0.161707), (0.161707, -0.986839), (1)457.8981, 388.97204, 185.7999
131given(0.979106, 0.203351), (-0.203351, 0.979106), (1)-38.88526, 47.79118, 188.18195
132given(-0.969616, -0.244631), (0.244631, -0.969616), (1)471.90029, 367.62897, 190.564
133given(0.958387, 0.285471), (-0.285471, 0.958387), (1)-51.97108, 69.70805, 192.94605
134given(-0.945439, -0.325799), (0.325799, -0.945439), (1)484.04627, 345.17763, 195.3281
135given(0.930794, 0.365543), (-0.365543, 0.930794), (1)-63.15543, 92.65359, 197.71015
136given(-0.91448, -0.404631), (0.404631, -0.91448), (1)494.24892, 321.77905, 200.0922
137given(0.896525, 0.442993), (-0.442993, 0.896525), (1)-72.35808, 116.46323, 202.47425
138given(-0.876962, -0.48056), (0.48056, -0.876962), (1)502.43507, 297.60107, 204.8563
139given(0.855825, 0.517265), (-0.517265, 0.855825), (1)-79.51304, 140.96618, 207.23835
140given(-0.833153, -0.553043), (0.553043, -0.833153), (1)508.54599, 272.81711, 209.6204
141given(0.808986, 0.587828), (-0.587828, 0.808986), (1)-84.56896, 165.98667, 212.00245
142given(-0.783368, -0.621558), (0.621558, -0.783368), (1)512.53785, 247.60496, 214.3845
143given(0.756345, 0.654173), (-0.654173, 0.756345), (1)-87.48959, 191.34526, 216.76655
144given(-0.727964, -0.685615), (0.685615, -0.727964), (1)514.38202, 222.14545, 219.1486
145given(0.698278, 0.715827), (-0.715827, 0.698278), (1)-88.25399, 216.86002, 221.53065
146given(-0.667339, -0.744754), (0.744754, -0.667339), (1)514.06526, 196.62119, 223.9127
147given(0.635202, 0.772346), (-0.772346, 0.635202), (1)-86.85665, 242.34797, 226.29475
148given(-0.601927, -0.798551), (0.798551, -0.601927), (1)511.58986, 171.21529, 228.6768
149given(0.567571, 0.823325), (-0.823325, 0.567571), (1)-83.30762, 267.62626, 231.05885
150given(-0.532197, -0.846621), (0.846621, -0.532197), (1)506.97356, 146.10996, 233.4409
151given(0.495868, 0.868398), (-0.868398, 0.495868), (1)-77.63234, 292.51359, 235.82295
152given(-0.45865, -0.888617), (0.888617, -0.45865), (1)500.24949, 121.48529, 238.205
153given(0.420608, 0.907242), (-0.907242, 0.420608), (1)-69.87153, 316.83143, 240.58705
154given(-0.381813, -0.92424), (0.92424, -0.381813), (1)491.46586, 97.5179, 242.9691
155given(0.342332, 0.939579), (-0.939579, 0.342332), (1)-60.08085, 340.40536, 245.35115
156given(-0.302237, -0.953233), (0.953233, -0.302237), (1)480.68569, 74.37971, 247.7332
157given(0.2616, 0.965176), (-0.965176, 0.2616), (1)-48.33052, 363.06629, 250.11525
158given(-0.220493, -0.975389), (0.975389, -0.220493), (1)467.98629, 52.2367, 252.4973
159given(0.178991, 0.983851), (-0.983851, 0.178991), (1)-34.70484, 384.65167, 254.87935
160given(-0.137168, -0.990548), (0.990548, -0.137168), (1)453.45877, 31.24768, 257.2614
161given(0.095099, 0.995468), (-0.995468, 0.095099), (1)-19.30154, 405.00667, 259.64345
162given(-0.052859, -0.998602), (0.998602, -0.052859), (1)437.20732, 11.56322, 262.0255
163given(0.010524, 0.999945), (-0.999945, 0.010524), (1)-2.2311, 423.98528, 264.40755
164given(0.031829, -0.999493), (0.999493, 0.031829), (1)419.34852, -6.6755, 266.7896
165given(-0.074126, 0.997249), (-0.997249, -0.074126), (1)16.38403, 441.45138, 269.17165
166given(0.116289, -0.993215), (0.993215, 0.116289), (1)400.01046, -23.33765, 271.5537
167given(-0.158244, 0.9874), (-0.9874, -0.158244), (1)36.41032, 457.27969, 273.93575
168given(0.199915, -0.979813), (0.979813, 0.199915), (1)379.33185, -38.30372, 276.3178
169given(-0.241228, 0.970469), (-0.970469, -0.241228), (1)57.70414, 471.35666, 278.69985
170given(0.282107, -0.959383), (0.959383, 0.282107), (1)357.46103, -51.46634, 281.0819
171given(-0.32248, 0.946576), (-0.946576, -0.32248), (1)80.11274, 483.58133, 283.46395
172given(0.362275, -0.932071), (0.932071, 0.362275), (1)334.55486, -62.73112, 285.846

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要素

#1: タンパク質・ペプチド ...
Amyloid-beta protein 40 / Abeta40 / Beta-APP40


分子量: 4334.867 Da / 分子数: 172 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P05067
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: らせん対称体再構成法

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試料調製

構成要素名称: V'-shaped short pitch amyloid fiber (40) of Tottori (D7N) mutant
タイプ: COMPLEX / Entity ID: all / 由来: NATURAL
由来(天然)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

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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）: 1200 nm / 最小 デフォーカス（公称値）: 800 nm / Cs: 0.021 mm
撮影電子線照射量: 50 e/Å2
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)

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解析

CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
らせん対称回転角度/サブユニット: 177.573 ° / 軸方向距離/サブユニット: 2.38205 Å / らせん対称軸の対称性: C1
3次元再構成解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 40424 / 対称性のタイプ: HELICAL
拘束条件
Refine-IDタイプDev ideal数Weight
ELECTRON MICROSCOPYs_bond_nonh_d0.0035276920.0118
ELECTRON MICROSCOPYs_angle_nonh_deg0.8486369801.7374
ELECTRON MICROSCOPYs_dihedral_angle_1_deg6.326737845
ELECTRON MICROSCOPYs_dihedral_angle_2_deg0.13951725
ELECTRON MICROSCOPYs_dihedral_angle_3_deg10.3724825610
ELECTRON MICROSCOPYs_dihedral_angle_6_deg11.9248172010
ELECTRON MICROSCOPYs_chiral_restr0.02844720.1283
ELECTRON MICROSCOPYs_planes0.002371520.02
ELECTRON MICROSCOPYs_nbd0.1909372870.2
ELECTRON MICROSCOPYs_nbtor0.2096508620.2
ELECTRON MICROSCOPYs_hbond_nbd0.02875120.2

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る