PROTEIN FIBRIL / amyloid / out-of-register / fiber-forming / macrocycle
Function / homology
Function and homology information
plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex ...plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / intracellular distribution of mitochondria / axonal transport of mitochondrion / axon development / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / apolipoprotein binding / glial cell projection / negative regulation of mitochondrial membrane potential / protein polymerization / negative regulation of mitochondrial fission / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / Activation of AMPK downstream of NMDARs / supramolecular fiber organization / regulation of cellular response to heat / stress granule assembly / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / phosphatidylinositol binding / nuclear periphery / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / response to lead ion / synapse organization / microglial cell activation / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / memory / cytoplasmic ribonucleoprotein granule / cellular response to reactive oxygen species / SH3 domain binding / microtubule cytoskeleton organization / activation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development / microtubule cytoskeleton / cell-cell signaling / protein-macromolecule adaptor activity / actin binding / single-stranded DNA binding / cellular response to heat / protein-folding chaperone binding / cell body / growth cone / microtubule binding / double-stranded DNA binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / nuclear speck / neuron projection / membrane raft / axon / negative regulation of gene expression / neuronal cell body / DNA damage response / dendrite / protein kinase binding / enzyme binding / mitochondrion / DNA binding Similarity search - Function
: / Microtubule associated protein, tubulin-binding repeat / Microtubule-associated protein Tau / Tau and MAP protein, tubulin-binding repeat / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP proteins tubulin-binding repeat profile. Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.91609 Å / Relative weight: 1
Reflection
Resolution: 1.75→18.22 Å / % possible obs: 99 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.82 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.83
Reflection shell
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Diffraction-ID
% possible all
1.75-1.8
0.424
2.5
1
98.7
1.8-1.84
0.414
2.55
1
98.8
1.84-1.9
0.286
3.52
1
99.7
1.9-1.96
0.225
4.23
1
99.3
1.96-2.02
0.162
4.99
1
99.5
2.02-2.09
0.138
6.15
1
99.4
2.09-2.17
0.125
7.11
1
99.5
2.17-2.26
0.132
7.12
1
99.3
2.26-2.36
0.118
7.84
1
100
2.36-2.48
0.108
8.02
1
98.4
2.48-2.61
0.109
8.8
1
99.8
2.61-2.77
0.083
10.4
1
99.3
2.77-2.96
0.085
10.77
1
99.5
2.96-3.2
0.068
12.43
1
98.4
3.2-3.5
0.058
14.11
1
100
3.5-3.91
0.058
15.04
1
98.6
3.91-4.52
0.056
15.53
1
97.3
4.52-5.53
0.041
16.41
1
97.2
5.53-7.83
0.052
15.66
1
95
7.83
0.044
14.97
1
89.4
-
Processing
Software
Name
Version
Classification
NB
XSCALE
datascaling
REFMAC
refinement
PDB_EXTRACT
3.1
dataextraction
BUSTER
2.10.0
refinement
Refinement
Method to determine structure: SAD / Resolution: 1.75→18.22 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.9272 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.937 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1287 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2213
642
9.85 %
RANDOM
Rwork
0.1854
-
-
-
obs
0.1889
6519
99.86 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 19.05 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.8619 Å2
0 Å2
-3.8144 Å2
2-
-
1.8581 Å2
0 Å2
3-
-
-
1.0038 Å2
Refine analyze
Luzzati coordinate error obs: 0.18 Å
Refinement step
Cycle: LAST / Resolution: 1.75→18.22 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
512
0
51
28
591
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
579
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.29
703
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
163
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
6
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
55
HARMONIC
5
X-RAY DIFFRACTION
t_it
579
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
X-RAY DIFFRACTION
t_other_torsion
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
LS refinement shell
Resolution: 1.75→1.96 Å / Total num. of bins used: 5
Rfactor
Num. reflection
% reflection
Rfree
0.2276
182
9.9 %
Rwork
0.1539
1657
-
all
0.1611
1839
-
obs
-
-
99.86 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.0753
1.6271
1.2704
1.745
0.3163
1.8355
0.0447
0.0558
0.1607
0.147
-0.0087
0.1412
0.0567
-0.004
-0.036
0.011
0.013
0.0192
-0.0115
-0.0117
-0.0023
-19.8576
-27.2394
-1.3919
2
0.9242
-1.227
0.0446
7.2824
2.6351
1.7875
0.1101
-0.0107
0.0987
-0.1211
-0.1104
0.0506
-0.1906
-0.1136
0.0003
-0.05
0.0137
0.0318
-0.0595
-0.0119
-0.0751
-19.1998
-17.7555
-3.2241
3
1.7149
0.513
0.3475
3.6902
0.6135
2.1247
0.0978
-0.1482
0.1472
0.0222
-0.1152
-0.0704
-0.0021
0.2262
0.0175
-0.1457
-0.0107
0.0268
-0.1138
0.0154
-0.0906
1.9368
-16.6877
-16.4196
4
1.391
-0.1185
-0.1887
4.5354
0.2754
1.469
-0.0514
-0.2411
-0.007
-0.0603
-0.0392
-0.1422
0.2287
0.0704
0.0906
-0.0646
-0.0038
0.0284
-0.03
0.015
-0.0582
2.8193
-26.4748
-17.7993
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
0 - 13
2
X-RAY DIFFRACTION
2
B
0 - 13
3
X-RAY DIFFRACTION
3
C
0 - 13
4
X-RAY DIFFRACTION
4
D
0 - 13
+
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