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

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Basic information

Entry
Database: PDB / ID: 9m5r
TitleES-type (short pitch) amyloid fibril (40) of Tottori (D7N) mutant
ComponentsAmyloid-beta protein 40
KeywordsPROTEIN FIBRIL / Amyloid
Function / homology
Function and homology information


amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport ...amyloid-beta complex / growth cone lamellipodium / cellular response to norepinephrine stimulus / collateral sprouting in absence of injury / growth cone filopodium / microglia development / hippocampal neuron apoptotic process / regulation of Wnt signaling pathway / Formyl peptide receptors bind formyl peptides and many other ligands / axo-dendritic transport / axon midline choice point recognition / regulation of synapse structure or activity / astrocyte activation involved in immune response / NMDA selective glutamate receptor signaling pathway / regulation of spontaneous synaptic transmission / mating behavior / growth factor receptor binding / peptidase activator activity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / positive regulation of amyloid fibril formation / Golgi-associated vesicle / PTB domain binding / astrocyte projection / neuron remodeling / Lysosome Vesicle Biogenesis / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / dendrite development / regulation of multicellular organism growth / nuclear envelope lumen / TRAF6 mediated NF-kB activation / positive regulation of protein metabolic process / signaling receptor activator activity / negative regulation of long-term synaptic potentiation / transition metal ion binding / Advanced glycosylation endproduct receptor signaling / The NLRP3 inflammasome / modulation of excitatory postsynaptic potential / intracellular copper ion homeostasis / Notch signaling pathway / main axon / ECM proteoglycans / response to insulin-like growth factor stimulus / positive regulation of T cell migration / regulation of presynapse assembly / neuronal dense core vesicle / swimming behavior / adult locomotory behavior / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / positive regulation of calcium-mediated signaling / extracellular matrix organization / positive regulation of mitotic cell cycle / axonogenesis / cellular response to manganese ion / neuron projection maintenance / clathrin-coated pit / astrocyte activation / regulation of neuron apoptotic process / Mitochondrial protein degradation / positive regulation of glycolytic process / ionotropic glutamate receptor signaling pathway / platelet alpha granule lumen / learning / response to interleukin-1 / cellular response to cAMP / cellular response to copper ion / endosome lumen / trans-Golgi network membrane / locomotory behavior / positive regulation of interleukin-1 beta production / dendritic shaft / central nervous system development / positive regulation of long-term synaptic potentiation / protein serine/threonine kinase binding / Post-translational protein phosphorylation / regulation of long-term neuronal synaptic plasticity / serine-type endopeptidase inhibitor activity / microglial cell activation / cellular response to nerve growth factor stimulus / visual learning / positive regulation of non-canonical NF-kappaB signal transduction / TAK1-dependent IKK and NF-kappa-B activation / synapse organization / positive regulation of interleukin-6 production / recycling endosome / positive regulation of JNK cascade / response to lead ion / Golgi lumen / cognition / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / endocytosis / neuron projection development / positive regulation of inflammatory response / calcium ion transport / positive regulation of tumor necrosis factor production / regulation of translation / regulation of gene expression / Platelet degranulation / heparin binding
Similarity search - Function
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, heparin-binding / Amyloid A4 N-terminal heparin-binding / Amyloidogenic glycoprotein, amyloid-beta peptide superfamily / Beta-amyloid peptide (beta-APP) / Amyloidogenic glycoprotein, amyloid-beta peptide ...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, heparin-binding / Amyloid A4 N-terminal heparin-binding / 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, E2 domain / E2 domain superfamily / Amyloidogenic glycoprotein, heparin-binding domain superfamily / 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
Similarity search - Domain/homology
Amyloid-beta precursor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBurton-Smith, R.N. / Murata, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP24ama121005 Japan
CitationJournal: ACS Chem Neurosci / Year: 2025
Title: Microgravity-Assisted Exploration of the Conformational Space of Amyloid β Affected by Tottori-Type Familial Mutation D7N.
Authors: 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 /
Abstract: 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.
History
DepositionMar 6, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)745,597172
Polymers745,597172
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
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
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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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Components

#1: Protein/peptide ...
Amyloid-beta protein 40 / Abeta40 / Beta-APP40


Mass: 4334.867 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05067
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: V'-shaped short pitch amyloid fiber (40) of Tottori (D7N) mutant
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 800 nm / Cs: 0.021 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 177.573 ° / Axial rise/subunit: 2.38205 Å / Axial symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40424 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
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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