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- PDB-9l8c: Structure of human TREX1-DNA complex -

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Basic information

Entry
Database: PDB / ID: 9l8c
TitleStructure of human TREX1-DNA complex
Components
  • DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
  • Three-prime repair exonuclease 1
KeywordsIMMUNE SYSTEM/DNA / nuclease / DNase / innate immunity / autoimmunity / cancer / IMMUNE SYSTEM-DNA complex
Function / homology
Function and homology information


Regulation by TREX1 / adenyl deoxyribonucleotide binding / MutSalpha complex binding / oligosaccharyltransferase complex / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / MutLalpha complex binding / 3'-5'-DNA exonuclease activity / IRF3-mediated induction of type I IFN / DNA catabolic process ...Regulation by TREX1 / adenyl deoxyribonucleotide binding / MutSalpha complex binding / oligosaccharyltransferase complex / exodeoxyribonuclease III / double-stranded DNA 3'-5' DNA exonuclease activity / MutLalpha complex binding / 3'-5'-DNA exonuclease activity / IRF3-mediated induction of type I IFN / DNA catabolic process / DNA binding, bending / WW domain binding / DNA metabolic process / negative regulation of cGAS/STING signaling pathway / nuclear replication fork / mismatch repair / 3'-5' exonuclease activity / negative regulation of innate immune response / protein-DNA complex / nuclear envelope / single-stranded DNA binding / double-stranded DNA binding / DNA recombination / DNA replication / DNA repair / endoplasmic reticulum membrane / magnesium ion binding / protein homodimerization activity / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Three-prime repair exonuclease 1/2 / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Three-prime repair exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsZhu, J. / Wang, L. / Lin, C. / Zhou, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270920 China
CitationJournal: Immunity / Year: 2026
Title: Distinct recognition pattern for double-stranded DNA allows TREX1 to maintain immune homeostasis
Authors: Zhu, J. / Wang, L. / Lin, C. / Zhou, W.
History
DepositionDec 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
C: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
D: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
E: Three-prime repair exonuclease 1
F: Three-prime repair exonuclease 1
G: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
H: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)131,1138
Polymers131,1138
Non-polymers00
Water4,828268
1
A: Three-prime repair exonuclease 1
B: Three-prime repair exonuclease 1
C: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
D: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)65,5574
Polymers65,5574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-13 kcal/mol
Surface area22590 Å2
MethodPISA
2
E: Three-prime repair exonuclease 1
F: Three-prime repair exonuclease 1
G: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')
H: DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)65,5574
Polymers65,5574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-12 kcal/mol
Surface area21420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.310, 92.787, 161.508
Angle α, β, γ (deg.)90.00, 91.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Three-prime repair exonuclease 1 / 3'-5' exonuclease TREX1 / Deoxyribonuclease III / DNase III


Mass: 26067.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TREX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NSU2, exodeoxyribonuclease III
#2: DNA chain
DNA (5'-D(P*GP*TP*TP*GP*GP*CP*CP*CP*TP*CP*TP*TP*TP*AP*GP*GP*GP*CP*CP*AP*TP*C)-3')


Mass: 6710.313 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.05 M Li2SO4, 22.5% PEG-3350, 0.1M Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.52→44.3 Å / Num. obs: 43791 / % possible obs: 99.08 % / Redundancy: 8.3 % / Biso Wilson estimate: 35.15 Å2 / CC1/2: 0.969 / Rpim(I) all: 0.077 / Net I/σ(I): 10.1
Reflection shellResolution: 2.52→2.59 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4177 / CC1/2: 0.761 / Rpim(I) all: 0.346 / % possible all: 94.35

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5127refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7TQQ
Resolution: 2.52→44.3 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 1999 4.56 %
Rwork0.196 --
obs0.1976 43791 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.36 Å2
Refinement stepCycle: LAST / Resolution: 2.52→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 1265 0 268 8067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048117
X-RAY DIFFRACTIONf_angle_d0.68711311
X-RAY DIFFRACTIONf_dihedral_angle_d20.0433063
X-RAY DIFFRACTIONf_chiral_restr0.041294
X-RAY DIFFRACTIONf_plane_restr0.0061248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.590.29961300.22662777X-RAY DIFFRACTION93
2.59-2.660.27731430.22242965X-RAY DIFFRACTION99
2.66-2.730.31271420.23152979X-RAY DIFFRACTION99
2.73-2.820.3041430.22752959X-RAY DIFFRACTION99
2.82-2.920.27721530.23672997X-RAY DIFFRACTION99
2.92-3.040.30071340.21872977X-RAY DIFFRACTION100
3.04-3.180.24541390.20673023X-RAY DIFFRACTION100
3.18-3.350.24671430.20482973X-RAY DIFFRACTION100
3.35-3.550.261420.20213005X-RAY DIFFRACTION100
3.55-3.830.22581480.18652994X-RAY DIFFRACTION100
3.83-4.210.17651450.16713017X-RAY DIFFRACTION100
4.21-4.820.18041460.15883036X-RAY DIFFRACTION100
4.82-6.070.18771440.18473044X-RAY DIFFRACTION100
6.07-44.30.22021470.20243046X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.20720.01180.09260.0516-0.15420.32330.0488-0.19280.11350.6802-0.1874-0.1319-0.18280.1888-0.01390.454-0.06170.02350.29370.00550.35867.831624.6478-55.1443
20.01580.0330.08850.2845-0.0330.3013-0.0484-0.6172-0.08490.43810.2022-0.085-0.3024-0.0260.18520.39840.08240.03960.421-0.03720.3304-4.989137.4826-58.8212
30.1651-0.4081-0.09260.6992-0.03891.01080.0109-0.07580.0736-0.0562-0.16250.03930.11890.0907-0.01940.2554-0.0126-0.0120.31310.01250.35958.68514.8841-64.3997
40.3380.1049-0.46891.01660.34280.6151-0.0011-0.3201-0.07690.1653-0.0826-0.0609-0.0260.1858-0.03970.3542-0.0467-0.04670.4943-0.02660.316912.556324.2491-50.9479
50.0047-0.0517-0.00150.2943-0.14170.059-0.2449-1.56610.42811.00620.26470.4498-0.46620.43080.02210.59160.05030.06110.6404-0.10210.4304-6.426325.47-42.9373
60.1005-0.08860.19340.25080.11040.9716-0.0847-0.59160.07610.3669-0.13280.88280.8659-0.45590.03060.4551-0.03880.06240.3923-0.080.4157-4.715324.0407-54.7776
71.17710.33230.26560.9839-0.79920.94-0.5579-1.15030.9290.57860.40590.223-0.2916-0.10170.13280.9356-0.04860.08210.503-0.20010.46953.698737.1571-44.4618
80.15570.0635-0.01650.3995-0.29540.19340.1952-0.54150.2051.416-0.1925-0.16850.09380.36490.03830.506-0.0606-0.13660.6943-0.02040.431918.268620.2268-47.7882
90.17210.2428-0.25360.2302-0.2140.67820.0383-0.048-0.2413-0.2792-0.11370.20670.20710.09380.09450.1834-0.01730.02040.259-0.02340.29752.010230.4239-82.7199
100.7820.25430.07441.0661-0.63621.10910.0911-0.15790.35990.0154-0.73280.1941-0.30320.5518-0.958-0.0167-0.08120.08280.1787-0.02380.20520.439220.2161-76.4754
110.5167-0.55160.82613.1771-0.0421.5106-0.6519-0.3574-0.7541-0.06030.01431.660.5361-0.7555-0.31080.4226-0.12530.20450.4323-0.11950.675-11.197112.017-70.2528
120.02570.1685-0.15891.5217-0.72090.7308-0.01330.0543-0.03340.010.0104-0.1947-0.0630.0864-0.00060.21240.00040.01050.2247-0.0350.29044.595531.307-79.6328
130.57190.4933-0.56390.7529-0.48870.5701-0.27450.81950.0415-0.78930.37210.56120.4286-0.87160.00640.3595-0.0457-0.02640.43170.00880.4905-17.705626.5958-83.728
140.9841-0.8230.28082.2384-0.66671.273-0.08550.0184-0.2566-0.45840.10140.34620.0828-0.21690.5120.2169-00.00810.2301-0.05220.3365-4.660824.0602-82.9397
153.79491.74140.19232.2972-0.61670.55020.3385-1.39270.03061.7133-0.10220.66970.9291-0.28810.33741.27320.0387-0.02851.07520.15010.73625.166512.2597-33.3161
161.0066-0.7966-0.01631.0584-0.17910.05030.4062-0.47070.130.26470.3436-0.6110.44050.48430.79580.7266-0.0241-0.16380.5888-0.05280.2852.973311.4201-35.6451
170.77860.5491-0.09490.7638-0.57760.6723-0.25480.38320.760.20940.6619-0.10460.3399-0.80510.78480.3676-0.0969-0.05270.4404-0.20020.3222-7.256244.1596-92.2032
180.191-0.08190.38320.0213-0.13140.80160.63280.2163-0.4292-0.36680.29060.1018-0.12660.01261.28262.6445-0.8891-0.76181.4883-0.46921.1207-14.898733.876-102.3836
190.14160.3111-0.03440.59770.06050.2674-0.2892-0.00510.0174-0.50710.2680.1558-0.7366-0.081-0.00150.3147-0.0052-0.07060.4206-0.02230.3389-12.634338.5425-90.1145
200.76110.49690.07360.25960.07380.7563-0.13360.06560.0462-0.1612-0.03980.0346-0.1028-0.2144-0.4750.31580.02120.03570.3063-0.01190.2793-15.2846-14.5056-25.2044
210.412-0.3335-0.32710.20490.2821.0993-0.0416-0.156-0.1226-0.0404-0.1179-0.5273-0.00110.4885-0.01680.2501-0.0618-0.03090.32150.02510.3909-8.752-3.5121-16.6193
220.30550.288-0.52061.4477-0.12660.6636-0.05190.2292-0.0726-0.2218-0.00110.07140.1058-0.1065-0.00010.27950.009-0.02410.3199-0.00030.2211-18.5072-18.7034-24.991
230.25730.3556-0.17910.483-0.22460.10550.05860.5255-0.1909-0.79920.0436-0.78070.19020.61380.04240.41570.04470.0720.542-0.00180.33683.6609-12.9306-29.3291
240.6012-0.01450.12740.39310.06790.4205-0.3394-0.1196-0.0085-0.04520.1648-0.83360.03410.3806-0.04570.21970.01480.02960.40570.03220.3473-3.7224-14.4712-19.2527
250.3446-0.28170.18280.20210.11161.2007-0.36540.64120.2216-0.52870.23960.069-0.29470.1728-0.50460.4647-0.059-0.01410.46510.05250.2871-12.3298-8.2916-33.8027
260.2513-0.10010.23460.57380.39450.20520.0207-0.01240.11020.4751-0.0140.04330.0475-0.114-0.01050.30590.0030.00870.1815-0.00690.3079-21.7263-11.80390.0848
270.18490.29-0.07960.6343-0.51880.9961-0.4474-0.4003-0.52790.30760.392-0.52560.52470.3779-0.16010.38960.1777-0.0950.4937-0.00350.4088-6.503-24.4877-2.9635
280.824-0.1853-0.83351.66410.13241.503-0.4202-0.06720.0257-0.52530.6948-0.1796-0.18970.6294-0.66790.2933-0.0425-0.07610.23810.02870.4092-20.9483-0.9458-8.1264
290.3788-0.1547-0.32690.35690.12950.25510.02340.253-0.0286-0.09620.0516-0.4497-0.93030.7213-0.05690.352-0.0248-0.01860.29930.04510.455-14.74537.5728-6.5268
300.3471-0.5118-0.47560.58650.34890.6915-0.00110.0744-0.0428-0.0358-0.02260.1781-0.0064-0.153-0.00010.27980.0069-0.03290.33880.02160.3043-26.3039-10.3021-5.6428
310.1216-0.0070.01520.37410.07630.6019-0.0928-0.0949-0.29290.79490.20820.4988-0.1814-0.3535-0.1330.44870.00240.02220.29560.04630.4377-26.9955-9.95684.3904
322.94240.46510.06062.0365-1.69321.75560.4877-1.23830.23121.2356-0.3174-0.3707-0.0640.93810.72350.54450.16-0.43790.41980.2415-0.7256-6.7145-10.957412.4643
330.9201-1.67891.06453.075-1.57664.0043-0.0615-0.07570.21790.7985-0.4545-0.9718-0.10540.8078-0.45150.35480.0172-0.03320.2043-0.01270.2532-12.1536-16.1544.4704
340.38080.0733-0.73140.0122-0.10841.4010.40610.1160.39141.006-0.67250.41-0.31-0.6602-0.00820.4563-0.0508-0.0260.3866-0.0440.4269-31.9609-7.3736.8675
353.3708-0.5091.59514.8342.18173.1706-0.77431.6405-0.0862-1.52660.4151-1.08480.29581.1058-0.94820.58440.00370.29310.80540.0710.3614-3.0043-26.9981-38.2713
363.8213-0.3119-1.55623.0546-0.57222.3756-0.1655-1.09670.14251.77540.5919-0.1844-0.1731.11260.83910.68940.1317-0.00620.39840.05830.2406-18.7521.406116.9242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 114 )
4X-RAY DIFFRACTION4chain 'A' and (resid 115 through 163 )
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 187 )
6X-RAY DIFFRACTION6chain 'A' and (resid 188 through 209 )
7X-RAY DIFFRACTION7chain 'A' and (resid 210 through 222 )
8X-RAY DIFFRACTION8chain 'A' and (resid 223 through 234 )
9X-RAY DIFFRACTION9chain 'B' and (resid 8 through 30 )
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 45 )
11X-RAY DIFFRACTION11chain 'B' and (resid 46 through 64 )
12X-RAY DIFFRACTION12chain 'B' and (resid 65 through 165 )
13X-RAY DIFFRACTION13chain 'B' and (resid 166 through 187 )
14X-RAY DIFFRACTION14chain 'B' and (resid 188 through 234 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 10 )
16X-RAY DIFFRACTION16chain 'C' and (resid 15 through 22 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1 through 5 )
18X-RAY DIFFRACTION18chain 'D' and (resid 6 through 16 )
19X-RAY DIFFRACTION19chain 'D' and (resid 17 through 22 )
20X-RAY DIFFRACTION20chain 'E' and (resid 8 through 43 )
21X-RAY DIFFRACTION21chain 'E' and (resid 44 through 70 )
22X-RAY DIFFRACTION22chain 'E' and (resid 71 through 163 )
23X-RAY DIFFRACTION23chain 'E' and (resid 164 through 187 )
24X-RAY DIFFRACTION24chain 'E' and (resid 188 through 208 )
25X-RAY DIFFRACTION25chain 'E' and (resid 209 through 234 )
26X-RAY DIFFRACTION26chain 'F' and (resid 7 through 45 )
27X-RAY DIFFRACTION27chain 'F' and (resid 46 through 64 )
28X-RAY DIFFRACTION28chain 'F' and (resid 65 through 78 )
29X-RAY DIFFRACTION29chain 'F' and (resid 79 through 94 )
30X-RAY DIFFRACTION30chain 'F' and (resid 95 through 129 )
31X-RAY DIFFRACTION31chain 'F' and (resid 130 through 163 )
32X-RAY DIFFRACTION32chain 'F' and (resid 164 through 187 )
33X-RAY DIFFRACTION33chain 'F' and (resid 188 through 222 )
34X-RAY DIFFRACTION34chain 'F' and (resid 223 through 234 )
35X-RAY DIFFRACTION35chain 'G' and (resid 1 through 22 )
36X-RAY DIFFRACTION36chain 'H' and (resid 1 through 22 )

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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