protein-lipid complex assembly / : / chylomicron assembly / negative regulation of plasma lipoprotein oxidation / positive regulation of triglyceride catabolic process / chylomicron remodeling / response to lipid hydroperoxide / protein metabolic process => GO:0019538 / response to stilbenoid / regulation of intestinal cholesterol absorption ...protein-lipid complex assembly / : / chylomicron assembly / negative regulation of plasma lipoprotein oxidation / positive regulation of triglyceride catabolic process / chylomicron remodeling / response to lipid hydroperoxide / protein metabolic process => GO:0019538 / response to stilbenoid / regulation of intestinal cholesterol absorption / Assembly of active LPL and LIPC lipase complexes / regulation of cholesterol transport / positive regulation of lipoprotein lipase activity / phosphatidylcholine metabolic process / very-low-density lipoprotein particle remodeling / Chylomicron remodeling / phosphatidylcholine-sterol O-acyltransferase activator activity / lipid transporter activity / Chylomicron assembly / lipoprotein metabolic process / positive regulation of fatty acid biosynthetic process / chylomicron / phosphatidylcholine binding / high-density lipoprotein particle remodeling / phospholipid efflux / very-low-density lipoprotein particle / reverse cholesterol transport / cholesterol transfer activity / high-density lipoprotein particle assembly / high-density lipoprotein particle / triglyceride homeostasis / lipid transport / retinoid metabolic process / cholesterol efflux / leukocyte cell-cell adhesion / cholesterol binding / cholesterol biosynthetic process / lipid homeostasis / antioxidant activity / positive regulation of lipid biosynthetic process / lipid catabolic process / Retinoid metabolism and transport / removal of superoxide radicals / cholesterol metabolic process / innate immune response in mucosa / cholesterol homeostasis / hydrogen peroxide catabolic process / phospholipid binding / collagen-containing extracellular matrix / early endosome / blood microparticle / copper ion binding / Amyloid fiber formation / endoplasmic reticulum lumen / lipid binding / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / cytosol Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2890 / Apolipoprotein / Apolipoprotein A/E / Apolipoprotein A1/A4/E domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2010
Radiation
Monochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing. Design parameters for this beamline are: Monochromator energy range 3.5 35 keV ...Monochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing. Design parameters for this beamline are: Monochromator energy range 3.5 35 keV monochromator energy resolution E/E < 2x10-4 over full energy range Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.9794947
1
2
0.9796317
1
3
0.9494888
1
Reflection
Resolution: 2.39→18.86 Å / Num. obs: 31511 / % possible obs: 99.9 % / Biso Wilson estimate: 74.37 Å2
-
Processing
Software
Name
Version
Classification
Blu-Ice
datacollection
CRANK
phasing
BUSTER
2.8.0
refinement
XDS
datareduction
XDS
datascaling
Refinement
Method to determine structure: MAD / Resolution: 2.4→18.86 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9325 / Cross valid method: THROUGHOUT / σ(F): 0
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2291
1583
5.09 %
RANDOM
Rwork
0.2002
-
-
-
obs
0.2016
31126
99.1 %
-
Displacement parameters
Biso mean: 95.78 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-4.3438 Å2
0 Å2
0 Å2
2-
-
-4.3438 Å2
0 Å2
3-
-
-
8.6877 Å2
Refine analyze
Luzzati coordinate error obs: 0.565 Å
Refinement step
Cycle: LAST / Resolution: 2.4→18.86 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3906
0
10
22
3938
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
3992
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.12
5363
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1561
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
157
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
560
HARMONIC
5
X-RAY DIFFRACTION
t_it
3992
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.47
X-RAY DIFFRACTION
t_other_torsion
20.25
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
506
SEMIHARMONIC
5
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
5126
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.4→2.48 Å / Total num. of bins used: 16
Rfactor
Num. reflection
% reflection
Rfree
0.2414
131
4.74 %
Rwork
0.23
2634
-
all
0.2306
2765
-
obs
-
-
99.1 %
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
3.6036
-1.1422
-1.1394
-2.5201
2.4767
0.4157
0.0441
-0.3644
0.0027
0.3828
0.1137
0.0064
0.0423
-0.1485
-0.1578
0.0948
-0.2761
0.1682
0.1412
-0.0592
-0.1956
4.2133
75.0675
-60.3926
2
1.9298
0.3733
-1.4831
19.0415
0.7767
0
0.1449
0.2585
0.0492
-1.7735
-0.3778
0.0982
0.035
-0.4581
0.233
0.2069
-0.2339
-0.034
-0.0785
-0.0169
-0.4499
6.8474
60.0783
-77.981
3
3.8314
5.0336
0.2128
6.688
-1.3057
0.2478
0.2645
-0.4312
-0.3043
0.2566
-0.557
-0.1643
0.8769
-0.5082
0.2925
0.3448
-0.4806
0.1602
0.0295
-0.0565
-0.1986
0.9549
29.4412
-58.5373
4
4.862
6.3444
-2.2113
7.704
-3.8465
2.3671
-0.4927
0.1136
-0.5752
-0.1342
-0.0477
-0.7602
-0.5062
0.4379
0.5405
0.4773
-0.4107
0.1095
-0.1014
0.0046
-0.185
-8.9773
6.1706
-35.9207
5
6.7058
1.2674
-6.0926
6.735
-5.8335
1.6588
-0.0592
-0.1968
-0.0089
0.0472
-0.1092
-0.3228
0.139
0.7346
0.1684
0.1741
-0.1333
0.001
-0.3176
0.0034
-0.3212
-24.2404
-11.6116
-13.1957
6
3.9565
3.0202
-1.7682
3.5138
-2.1924
0
-0.0885
-0.3871
-0.3901
0.0658
0.1119
0.2721
0.3688
0.2458
-0.0233
0.2302
0.0718
0.1161
-0.0915
0.1442
-0.0671
-39.8169
-28.3689
10.508
7
4.2815
4.9772
-4.6616
4.3201
-2.8115
7.4033
-0.4461
0.2993
-0.3375
0.0899
-0.087
0.2183
0.6391
-0.1445
0.5331
0.2868
-0.0151
0.1745
-0.1048
0.0442
-0.0083
-48.2854
-30.8632
6.0568
8
2.1867
1.4088
-1.5314
0.8978
-1.2156
3.287
-0.0733
0.2093
0.2925
-0.2751
0.3371
0.496
-0.0145
-0.5297
-0.2638
0.2219
-0.0558
-0.0007
-0.2736
0.0251
-0.2718
-31.9468
-7.0414
-16.5118
9
2.7623
0.2165
-1.3399
-0.3609
4.8368
4.3852
-0.2853
0.4877
0.2987
-0.213
0.4963
-0.0705
-0.4227
-0.0864
-0.211
0.4455
-0.2218
-0.0707
-0.281
0.0592
-0.1999
-22.499
6.9895
-23.1395
10
3.7412
5.2052
-3.8142
4.7634
-5.1686
3.7273
0.3691
-0.1812
0.6009
0.2853
0.0379
0.8801
-0.6845
-0.0925
-0.407
0.5474
0.0553
0.208
-0.2356
0.0352
-0.0947
-43.5931
-12.1597
4.3945
11
-1.933
1.116
5.5758
1.933
-2.606
0
0.0079
0.0995
0.2149
-0.0285
-0.0831
0.1979
-0.274
0.1011
0.0753
0.3184
-0.071
0.1481
0.3047
0.0097
-0.1382
-67.3033
-25.4769
1.8447
12
19.2377
9.9373
-5.2291
5.2007
-3.1737
1.6647
0.6193
-0.8752
-0.196
0.4366
-0.5953
-0.0754
-0.3938
0.3668
-0.024
0.0855
0.0932
0.093
-0.2796
0.0488
-0.3294
-48.0071
-25.7163
17.1267
13
5.8823
3.7904
-2.6183
2.416
-2.7189
8.971
-0.0558
-0.2902
-0.1069
-0.2313
0.0335
-0.2335
-1.3774
0.5072
0.0223
0.4495
-0.1574
0.006
-0.2014
0.0227
-0.2965
-24.1991
-5.3766
-4.1314
14
5.2215
5.8517
0.7081
5.0175
-0.415
0
0.1073
-0.5638
-0.3718
0.2561
-0.8774
-0.7478
-0.6575
1.0173
0.7701
0.3946
-0.3476
0.0445
-0.257
0.0735
-0.3015
-6.0831
9.8445
-26.2233
15
-1.8744
2.4255
-1.0885
10.0182
1.2363
0
0.2978
-0.142
-0.2014
0.0412
-0.2789
-1.0029
0.241
0.3392
-0.0189
0.3879
-0.7196
-0.0761
0.1658
0.1518
-0.3481
4.3297
28.0145
-43.6805
16
0.3636
0.534
-0.8855
16.2842
-6.3976
4.8853
0.137
-0.0613
-0.0543
-0.3375
-0.4326
-0.8404
-0.0465
0.1265
0.2955
-0.1605
-0.3067
0.0754
-0.3205
-0.0374
-0.4607
12.8182
53.2137
-68.9824
17
0.5919
1.9958
0.5716
5.7179
-3.0807
4.8247
0.3134
-0.0562
0.2291
0.9248
-0.174
0.3744
0.4103
-0.7994
-0.1394
0.31
-0.3776
0.1923
-0.1061
-0.1016
-0.2938
5.2863
52.4844
-58.178
18
-1.5523
1.6113
1.0033
4.2395
-0.7589
18.1608
-0.4157
0.7062
-0.1302
0.0509
0.6452
0.1931
-0.232
-0.4585
-0.2295
0.4112
-0.6532
0.1256
0.1203
0.0032
-0.318
-9.7741
23.0982
-38.314
19
-0.3325
1.4094
0.5807
4.7414
0.0725
0.1011
-0.1554
0.0156
0.7271
-0.1556
0.5185
1.3475
-0.1582
-0.8917
-0.3631
-0.0878
-0.3862
-0.0094
-0.0616
0.04
-0.1848
-3.5405
44.7587
-62.6734
20
5.4145
-2.1201
4.4003
-4.2529
-0.3798
0
0.1495
0.1313
-0.0215
-0.4291
-0.1623
0.7553
-0.1468
-0.1533
0.0128
0.1897
-0.2177
-0.4157
-0.2692
0.0674
0.074
0.171
66.1794
-77.0273
21
3.6036
-1.1422
-1.1394
-2.5201
2.4767
0.4157
0.0441
-0.3644
0.0027
0.3828
0.1137
0.0064
0.0423
-0.1485
-0.1578
0.0948
-0.2761
0.1682
0.1412
-0.0592
-0.1956
4.2133
75.0675
-60.3926
22
1.9298
0.3733
-1.4831
19.0415
0.7767
0
0.1449
0.2585
0.0492
-1.7735
-0.3778
0.0982
0.035
-0.4581
0.233
0.2069
-0.2339
-0.034
-0.0785
-0.0169
-0.4499
6.8474
60.0783
-77.981
23
3.8314
5.0336
0.2128
6.688
-1.3057
0.2478
0.2645
-0.4312
-0.3043
0.2566
-0.557
-0.1643
0.8769
-0.5082
0.2925
0.3448
-0.4806
0.1602
0.0295
-0.0565
-0.1986
0.9549
29.4412
-58.5373
24
4.862
6.3444
-2.2113
7.704
-3.8465
2.3671
-0.4927
0.1136
-0.5752
-0.1342
-0.0477
-0.7602
-0.5062
0.4379
0.5405
0.4773
-0.4107
0.1095
-0.1014
0.0046
-0.185
-8.9773
6.1706
-35.9207
25
6.7058
1.2674
-6.0926
6.735
-5.8335
1.6588
-0.0592
-0.1968
-0.0089
0.0472
-0.1092
-0.3228
0.139
0.7346
0.1684
0.1741
-0.1333
0.001
-0.3176
0.0034
-0.3212
-24.2404
-11.6116
-13.1957
26
3.9565
3.0202
-1.7682
3.5138
-2.1924
0
-0.0885
-0.3871
-0.3901
0.0658
0.1119
0.2721
0.3688
0.2458
-0.0233
0.2302
0.0718
0.1161
-0.0915
0.1442
-0.0671
-39.8169
-28.3689
10.508
27
4.2815
4.9772
-4.6616
4.3201
-2.8115
7.4033
-0.4461
0.2993
-0.3375
0.0899
-0.087
0.2183
0.6391
-0.1445
0.5331
0.2868
-0.0151
0.1745
-0.1048
0.0442
-0.0083
-48.2854
-30.8632
6.0568
28
2.1867
1.4088
-1.5314
0.8978
-1.2156
3.287
-0.0733
0.2093
0.2925
-0.2751
0.3371
0.496
-0.0145
-0.5297
-0.2638
0.2219
-0.0558
-0.0007
-0.2736
0.0251
-0.2718
-31.9468
-7.0414
-16.5118
29
2.7623
0.2165
-1.3399
-0.3609
4.8368
4.3852
-0.2853
0.4877
0.2987
-0.213
0.4963
-0.0705
-0.4227
-0.0864
-0.211
0.4455
-0.2218
-0.0707
-0.281
0.0592
-0.1999
-22.499
6.9895
-23.1395
30
3.7412
5.2052
-3.8142
4.7634
-5.1686
3.7273
0.3691
-0.1812
0.6009
0.2853
0.0379
0.8801
-0.6845
-0.0925
-0.407
0.5474
0.0553
0.208
-0.2356
0.0352
-0.0947
-43.5931
-12.1597
4.3945
31
-1.933
1.116
5.5758
1.933
-2.606
0
0.0079
0.0995
0.2149
-0.0285
-0.0831
0.1979
-0.274
0.1011
0.0753
0.3184
-0.071
0.1481
0.3047
0.0097
-0.1382
-67.3033
-25.4769
1.8447
32
19.2377
9.9373
-5.2291
5.2007
-3.1737
1.6647
0.6193
-0.8752
-0.196
0.4366
-0.5953
-0.0754
-0.3938
0.3668
-0.024
0.0855
0.0932
0.093
-0.2796
0.0488
-0.3294
-48.0071
-25.7163
17.1267
33
5.8823
3.7904
-2.6183
2.416
-2.7189
8.971
-0.0558
-0.2902
-0.1069
-0.2313
0.0335
-0.2335
-1.3774
0.5072
0.0223
0.4495
-0.1574
0.006
-0.2014
0.0227
-0.2965
-24.1991
-5.3766
-4.1314
34
5.2215
5.8517
0.7081
5.0175
-0.415
0
0.1073
-0.5638
-0.3718
0.2561
-0.8774
-0.7478
-0.6575
1.0173
0.7701
0.3946
-0.3476
0.0445
-0.257
0.0735
-0.3015
-6.0831
9.8445
-26.2233
35
-1.8744
2.4255
-1.0885
10.0182
1.2363
0
0.2978
-0.142
-0.2014
0.0412
-0.2789
-1.0029
0.241
0.3392
-0.0189
0.3879
-0.7196
-0.0761
0.1658
0.1518
-0.3481
4.3297
28.0145
-43.6805
36
0.3636
0.534
-0.8855
16.2842
-6.3976
4.8853
0.137
-0.0613
-0.0543
-0.3375
-0.4326
-0.8404
-0.0465
0.1265
0.2955
-0.1605
-0.3067
0.0754
-0.3205
-0.0374
-0.4607
12.8182
53.2137
-68.9824
37
0.5919
1.9958
0.5716
5.7179
-3.0807
4.8247
0.3134
-0.0562
0.2291
0.9248
-0.174
0.3744
0.4103
-0.7994
-0.1394
0.31
-0.3776
0.1923
-0.1061
-0.1016
-0.2938
5.2863
52.4844
-58.178
38
-1.5523
1.6113
1.0033
4.2395
-0.7589
18.1608
-0.4157
0.7062
-0.1302
0.0509
0.6452
0.1931
-0.232
-0.4585
-0.2295
0.4112
-0.6532
0.1256
0.1203
0.0032
-0.318
-9.7741
23.0982
-38.314
39
-0.3325
1.4094
0.5807
4.7414
0.0725
0.1011
-0.1554
0.0156
0.7271
-0.1556
0.5185
1.3475
-0.1582
-0.8917
-0.3631
-0.0878
-0.3862
-0.0094
-0.0616
0.04
-0.1848
-3.5405
44.7587
-62.6734
40
5.4145
-2.1201
4.4003
-4.2529
-0.3798
0
0.1495
0.1313
-0.0215
-0.4291
-0.1623
0.7553
-0.1468
-0.1533
0.0128
0.1897
-0.2177
-0.4157
-0.2692
0.0674
0.074
0.171
66.1794
-77.0273
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
{ A|94 - A|105 }
A
94 - 105
2
X-RAY DIFFRACTION
2
{ A|106 - A|138 }
A
106 - 138
3
X-RAY DIFFRACTION
3
{ A|139 - A|159 }
A
139 - 159
4
X-RAY DIFFRACTION
4
{ A|160 - A|184 }
A
160 - 184
5
X-RAY DIFFRACTION
5
{ A|185 - A|201 }
A
185 - 201
6
X-RAY DIFFRACTION
6
{ A|202 - A|227 }
A
202 - 227
7
X-RAY DIFFRACTION
7
{ A|228 - A|252 }
A
228 - 252
8
X-RAY DIFFRACTION
8
{ A|253 - A|276 }
A
253 - 276
9
X-RAY DIFFRACTION
9
{ A|277 - A|297 }
A
277 - 297
10
X-RAY DIFFRACTION
10
{ A|298 - A|332 }
A
298 - 332
11
X-RAY DIFFRACTION
11
{ B|92 - B|104 }
B
92 - 104
12
X-RAY DIFFRACTION
12
{ B|105 - B|140 }
B
105 - 140
13
X-RAY DIFFRACTION
13
{ B|141 - B|161 }
B
141 - 161
14
X-RAY DIFFRACTION
14
{ B|162 - B|182 }
B
162 - 182
15
X-RAY DIFFRACTION
15
{ B|183 - B|196 }
B
183 - 196
16
X-RAY DIFFRACTION
16
{ B|197 - B|231 }
B
197 - 231
17
X-RAY DIFFRACTION
17
{ B|232 - B|266 }
B
232 - 266
18
X-RAY DIFFRACTION
18
{ B|267 - B|298 }
B
267 - 298
19
X-RAY DIFFRACTION
19
{ B|299 - B|324 }
B
299 - 324
20
X-RAY DIFFRACTION
20
{ B|325 - B|332 }
B
325 - 332
21
X-RAY DIFFRACTION
21
{ A|94 - A|105 }
A
94 - 105
22
X-RAY DIFFRACTION
22
{ A|106 - A|138 }
A
106 - 138
23
X-RAY DIFFRACTION
23
{ A|139 - A|159 }
A
139 - 159
24
X-RAY DIFFRACTION
24
{ A|160 - A|184 }
A
160 - 184
25
X-RAY DIFFRACTION
25
{ A|185 - A|201 }
A
185 - 201
26
X-RAY DIFFRACTION
26
{ A|202 - A|227 }
A
202 - 227
27
X-RAY DIFFRACTION
27
{ A|228 - A|252 }
A
228 - 252
28
X-RAY DIFFRACTION
28
{ A|253 - A|276 }
A
253 - 276
29
X-RAY DIFFRACTION
29
{ A|277 - A|297 }
A
277 - 297
30
X-RAY DIFFRACTION
30
{ A|298 - A|332 }
A
298 - 332
31
X-RAY DIFFRACTION
31
{ B|92 - B|104 }
B
92 - 104
32
X-RAY DIFFRACTION
32
{ B|105 - B|140 }
B
105 - 140
33
X-RAY DIFFRACTION
33
{ B|141 - B|161 }
B
141 - 161
34
X-RAY DIFFRACTION
34
{ B|162 - B|182 }
B
162 - 182
35
X-RAY DIFFRACTION
35
{ B|183 - B|196 }
B
183 - 196
36
X-RAY DIFFRACTION
36
{ B|197 - B|231 }
B
197 - 231
37
X-RAY DIFFRACTION
37
{ B|232 - B|266 }
B
232 - 266
38
X-RAY DIFFRACTION
38
{ B|267 - B|298 }
B
267 - 298
39
X-RAY DIFFRACTION
39
{ B|299 - B|324 }
B
299 - 324
40
X-RAY DIFFRACTION
40
{ B|325 - B|332 }
B
325 - 332
+
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