MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / TRIF-mediated programmed cell death / Toll Like Receptor 4 (TLR4) Cascade / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / Heme signaling / Regulation of TLR by endogenous ligand / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex ...MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / TRIF-mediated programmed cell death / Toll Like Receptor 4 (TLR4) Cascade / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / Heme signaling / Regulation of TLR by endogenous ligand / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / lipopolysaccharide immune receptor activity / Toll-like receptor 4 binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / IKK complex recruitment mediated by RIP1 / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / innate immune response-activating signaling pathway / regulation of dendritic cell cytokine production / positive regulation of lymphocyte proliferation / detection of lipopolysaccharide / mast cell activation / intestinal epithelial structure maintenance / negative regulation of interleukin-23 production / lymphocyte proliferation / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / B cell proliferation involved in immune response / leukotriene metabolic process / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of interleukin-1 production / positive regulation of stress-activated MAPK cascade / positive regulation of lipopolysaccharide-mediated signaling pathway / macrophage activation / positive regulation of interleukin-13 production / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / response to fatty acid / activation of NF-kappaB-inducing kinase activity / regulation of tumor necrosis factor production / nucleotide-binding oligomerization domain containing 2 signaling pathway / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of MHC class II biosynthetic process / negative regulation of interleukin-17 production / positive regulation of platelet activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage activation / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of macrophage cytokine production / negative regulation of cold-induced thermogenesis / MyD88-dependent toll-like receptor signaling pathway / positive regulation of reactive oxygen species biosynthetic process / toll-like receptor 4 signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / B cell proliferation / positive regulation of nitric-oxide synthase biosynthetic process / cellular response to lipoteichoic acid / detection of temperature stimulus involved in sensory perception of pain / negative regulation of interleukin-6 production / phagocytic cup / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / positive regulation of interferon-alpha production / phosphatidylinositol 3-kinase binding / detection of mechanical stimulus involved in sensory perception of pain / phagocytosis / stress-activated MAPK cascade / positive regulation of chemokine production / positive regulation of B cell proliferation / JNK cascade / lipopolysaccharide-mediated signaling pathway / ruffle / nitric oxide biosynthetic process / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / activation of innate immune response / positive regulation of interferon-beta production / neurogenesis / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / response to bacterium / microglial cell activation / positive regulation of MAP kinase activity / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / cellular response to amyloid-beta Similarity search - Function
Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.88 / SU B: 27.394 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.947 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27743
2877
5 %
RANDOM
Rwork
0.23427
-
-
-
obs
0.23645
54275
96.51 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 55.119 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.76 Å2
-0 Å2
0 Å2
2-
-
-1.25 Å2
0 Å2
3-
-
-
3.01 Å2
Refinement step
Cycle: LAST / Resolution: 2.7→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11682
0
298
37
12017
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.02
12396
X-RAY DIFFRACTION
r_bond_other_d
0.007
0.02
42
X-RAY DIFFRACTION
r_angle_refined_deg
1.424
1.982
16788
X-RAY DIFFRACTION
r_angle_other_deg
0.742
3
72
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.306
5
1468
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.677
24.982
554
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.569
15
2096
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.476
15
36
X-RAY DIFFRACTION
r_chiral_restr
0.089
0.2
1949
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
9099
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
3
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.697→2.767 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.373
200
-
Rwork
0.32
3678
-
obs
-
-
95.12 %
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
0.165
0.1201
0.0366
0.225
0.0109
0.0154
0.0273
-0.044
-0.0171
0.0132
-0.0222
-0.0006
-0.0145
-0.0095
-0.0051
0.0857
-0.0069
0.0031
0.1255
0.0268
0.1097
14.7453
18.1942
29.5376
2
0.5577
0.1973
0.2494
0.4034
0.1127
0.2873
0.0631
-0.0363
0.0566
0.008
-0.1623
0.0792
-0.0268
-0.0104
0.0992
0.069
0.0131
0.0138
0.1045
-0.0584
0.1431
-1.2451
35.095
20.3753
3
0.0811
-0.0341
-0.0651
0.1196
-0.0125
0.0904
0.0222
-0.0187
-0.0048
-0.0898
-0.0292
0.0283
0.0038
-0.0081
0.007
0.1107
0.0275
-0.0133
0.1029
0.0201
0.1211
-7.2332
-4.428
-13.5706
4
0.4041
-0.1956
0.0984
0.2083
0.0714
0.74
0.0614
0.0314
-0.0033
-0.0141
-0.0775
-0.0326
0.1727
-0.0275
0.016
0.1817
0.0059
0.0203
0.0319
0.014
0.1101
9.2528
-20.9925
-4.8714
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
27 - 625
2
X-RAY DIFFRACTION
2
C
21 - 155
3
X-RAY DIFFRACTION
3
B
27 - 625
4
X-RAY DIFFRACTION
4
D
21 - 155
+
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