[English] 日本語
Yorodumi
- PDB-8e67: ETV6 H396Y variant bound to DNA containing the sequence GGAT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8.0E+67
TitleETV6 H396Y variant bound to DNA containing the sequence GGAT
Components
  • Complementary 15 bp strand
  • GGAT-containing 15 bp DNA
  • Transcription factor ETV6
KeywordsDNA BINDING PROTEIN/DNA / ETS / complex / winged-helix-turn-helix / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily ...Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Ets variant 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsScheu, K. / Chan, A.C. / Murphy, M.E. / McIntosh, L.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: to be published
Title: The functional role of histidine within the ETV6 ETS domain
Authors: Scheu, K. / Chan, A.C. / Murphy, M.E. / McIntosh, L.P.
History
DepositionAug 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: GGAT-containing 15 bp DNA
C: Complementary 15 bp strand
A: Transcription factor ETV6
D: GGAT-containing 15 bp DNA
E: Complementary 15 bp strand
F: Transcription factor ETV6
G: GGAT-containing 15 bp DNA
H: Complementary 15 bp strand
I: Transcription factor ETV6
J: GGAT-containing 15 bp DNA
K: Complementary 15 bp strand
L: Transcription factor ETV6


Theoretical massNumber of molelcules
Total (without water)86,06512
Polymers86,06512
Non-polymers00
Water57632
1
B: GGAT-containing 15 bp DNA
C: Complementary 15 bp strand
A: Transcription factor ETV6


  • defined by author&software
  • Evidence: surface plasmon resonance, Binding between the protein and DNA complex was confirmed through NMR, while affinity was determined through SPR. The dimerization of DNA was confirmed through gel filtration.
  • 21.5 kDa, 3 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)21,5163
Polymers21,5163
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-19 kcal/mol
Surface area9870 Å2
MethodPISA
2
D: GGAT-containing 15 bp DNA
E: Complementary 15 bp strand
F: Transcription factor ETV6


Theoretical massNumber of molelcules
Total (without water)21,5163
Polymers21,5163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-20 kcal/mol
Surface area10000 Å2
MethodPISA
3
G: GGAT-containing 15 bp DNA
H: Complementary 15 bp strand
I: Transcription factor ETV6


Theoretical massNumber of molelcules
Total (without water)21,5163
Polymers21,5163
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-19 kcal/mol
Surface area9560 Å2
MethodPISA
4
J: GGAT-containing 15 bp DNA
K: Complementary 15 bp strand
L: Transcription factor ETV6


Theoretical massNumber of molelcules
Total (without water)21,5163
Polymers21,5163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-20 kcal/mol
Surface area10160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.940, 74.350, 76.620
Angle α, β, γ (deg.)90.000, 98.020, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: DNA chain
GGAT-containing 15 bp DNA


Mass: 4683.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain
Complementary 15 bp strand


Mass: 4495.922 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein
Transcription factor ETV6


Mass: 12337.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Etv6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9Q8J8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Protein in 50 mM NaCl, 20 mM HEPES, pH 7.5 at ~300 uM incubated 1:1 with 50 mM Sodium cacodylate, 25 mM Ammonium acetate, 10 mM MgCl2, 20% PEG-8000, pH 6.0
PH range: 6.0-7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.52127 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52127 Å / Relative weight: 1
ReflectionResolution: 2.3→48.2 Å / Num. obs: 58090 / % possible obs: 99.3 % / Redundancy: 3.287 % / Biso Wilson estimate: 50.32 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.074 / Χ2: 0.868 / Net I/σ(I): 10.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.423.2080.6831.6814271445544490.7480.82199.9
2.42-2.553.3360.4742.4913211396939600.8820.56399.8
2.55-2.693.2920.3183.6611187341233980.9290.37999.6
2.69-2.863.4520.2464.7211385330232980.9670.29199.9
2.86-3.043.3440.1576.929280278827750.9860.18799.5
3.04-3.253.1650.0879.927760247724520.9970.10599
3.25-3.53.3240.06214.517443226322390.9980.07498.9
3.5-3.783.0760.05217.025619185218270.9970.06498.7
3.78-4.123.3830.04721.225429162516050.9970.05698.8
4.12-4.513.3240.04123.414385133613190.9960.04998.7
4.51-53.2870.0423.813635112011060.9970.04798.8
5-48.23.2350.03525.5310165317831420.9980.04298.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MHG
Resolution: 2.3→48.2 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2667 2903 5 %
Rwork0.2113 55187 -
obs0.214 58090 93.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.81 Å2 / Biso mean: 67.4525 Å2 / Biso min: 23.59 Å2
Refinement stepCycle: final / Resolution: 2.3→48.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 2390 0 32 5655
Biso mean---50.48 -
Num. residues----493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.340.34571320.34592536266890
2.34-2.380.36341320.3222506263888
2.38-2.420.34051360.32572573270993
2.42-2.470.35551450.31672644278993
2.47-2.520.37751310.31332584271594
2.52-2.570.33511450.30892684282994
2.57-2.630.37641370.3012575271293
2.63-2.70.34591420.29982645278794
2.7-2.770.35121400.31272677281794
2.77-2.850.43531350.31492648278394
2.85-2.950.3961350.31062649278494
2.95-3.050.34871430.28342643278693
3.05-3.170.34971290.25332538266791
3.17-3.320.30451400.22562590273094
3.32-3.490.34531370.21132672280994
3.49-3.710.2241390.1972654279394
3.71-40.23061410.17842664280595
4-4.40.21111390.15582676281595
4.4-5.030.21621420.16272634277694
5.03-6.340.19251400.16062683282395
6.34-48.20.17891430.15722712285597
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)
12.12550.6714-2.22960.9591-0.52861.34610.5732-0.08470.79160.15310.41270.0556-0.18750.36360.39270.61550.1537-0.01540.5816-0.01990.781-21.0346-3.1688-32.2143
21.0229-0.0377-1.2250.8418-0.37141.18030.31670.18960.3983-0.0985-0.02340.1234-0.9518-0.2858-0.00770.5158-0.02030.10060.450.14210.5935-24.3114-3.1434-33.6333
30.223-0.1450.06430.0957-0.05240.0338-0.1660.80330.1395-0.26040.7907-0.46750.7006-0.26710.00040.62310.1670.10290.86880.08880.5603-19.5317-22.1941-44.1848
40.12410.0503-0.12010.0614-0.00940.13390.0890.6085-0.1906-0.6178-0.1577-0.11030.3029-0.46630.00010.5156-0.13470.01040.51760.02460.4211-20.1762-23.993-36.1522
50.0430.0942-0.05540.08930.04430.0228-0.46290.4959-0.7792-0.07190.1456-0.839-0.06310.607-0.00050.48340.013-0.0170.46250.08480.74-9.7608-27.6743-32.6394
60.0398-0-0.65410.38980.93712.9381-0.2779-0.0476-0.4902-0.14320.4343-0.44010.59041.03290.36210.5412-0.1152-0.09280.28410.24190.4662-18.3508-25.7154-25.3584
70.15690.0590.17810.70270.11550.2961.26491.26320.13190.68780.4143-1.80310.62090.96210.56210.0516-0.34940.45840.21870.63140.0505-11.38-16.0894-36.5083
84.1545-0.07971.39570.16410.43051.8248-0.612-0.1871.4873-0.3709-0.3919-0.44-0.6508-0.6761-0.38560.5041-0.05310.08050.47310.40150.4354-12.5382-10.0341-41.2739
90.1270.19530.22310.16620.34680.3207-0.0502-0.09080.08750.0192-0.01390.2902-0.4142-0.0425-00.3770.02810.02710.26060.0640.4648-24.4453-12.2913-29.9252
100.0985-0.0049-0.11480.04890.0110.0630.6-0.24540.6911-0.2876-0.0889-0.4601-0.651-0.16360.00270.589-0.06440.06850.39930.15020.5785-19.808-16.9975-18.2262
113.2838-0.5020.36920.0825-0.11680.127-0.4462-0.9745-0.4218-0.41670.02690.7878-0.2685-0.71910.01380.4842-0.1872-0.05920.43510.12160.6108-28.8448-23.3248-31.2169
120.8321.15-1.02941.637-0.93450.7628-0.1636-0.24810.0668-0.03850.2916-0.2822-0.34990.0216-00.57470.109-0.01970.5864-0.14480.5629.6949-3.6754-31.5026
130.31060.3469-0.56551.1158-0.70150.4063-0.2431-0.31830.36010.080.1703-0.1143-0.89590.03130.00010.63120.0453-0.06110.3701-0.03790.51286.4377-3.201-32.708
141.4444-1.4421-0.00991.5354-0.72151.04830.30321.1699-0.3243-1.24620.2170.75680.8802-0.33010.10030.49220.03470.04550.51650.02680.308113.1213-22.4561-40.0481
150.02440.0019-0.00970.1325-0.16460.5472-0.4199-0.8955-0.60370.21930.1097-0.19860.33240.7139-0.03020.42720.16990.11750.60470.10460.681223.2511-25.3294-33.0659
160.9079-0.5341-0.0120.3367-0.39160.46510.038-0.2538-0.11140.0412-0.1931-0.39790.43380.7096-0.00150.33430.00880.0340.32570.08680.38916.9757-21.3791-30.1815
170.0437-0.0098-0.00830.080.01870.05720.10810.34691.4135-0.49760.1709-1.1658-0.71560.72330.00180.5592-0.10690.04070.4680.05050.589818.1009-7.7259-40.7381
180.221-0.3214-0.09440.4916-0.63740.3114-0.2381-0.3060.45890.21390.2247-0.0597-0.0290.06250.00010.34670.04290.02290.344-0.04470.39558.0403-14.0354-27.4032
190.4893-0.0045-0.06730.4059-0.14640.279-0.0437-0.462-0.6240.1251-0.00030.1482-0.0997-0.49780.00440.3579-0.02950.03830.3243-0.07440.54952.6402-24.4268-33.4369
201.7492-0.8788-2.42391.00310.95022.0019-0.1860.4747-0.7814-0.31810.12910.1890.52670.75740.00020.87680.031-0.10220.79080.18240.8162-3.0673-42.7507-5.6122
211.1709-0.6656-0.84840.08950.39230.81140.1579-0.1803-1.0521-0.2035-0.25470.11910.4006-0.0384-0.00410.62060.0119-0.02530.62580.06430.7248-3.1414-43.9683-3.6432
220.0669-0.17270.20810.4752-0.60650.54430.0549-0.26610.07640.39550.6197-0.4851-0.07510.66741.51620.5736-0.1157-0.22471.22860.25790.61786.456-24.7332-1.3439
230.4786-0.3585-0.31150.04040.26690.1562-0.0089-0.50930.3273-0.62010.1834-0.3881-0.26470.22970.00080.5033-0.09980.06270.5329-0.01010.4149-0.114-20.3171-8.7017
240.2282-0.29920.1910.089-0.25490.19490.77540.83030.0822-0.3142-0.34660.2937-0.7287-0.36430.00950.61990.08060.0610.39310.03240.4427-9.8814-19.3572-11.2411
250.2364-0.7250.10080.9554-0.72650.3610.1455-0.1989-0.54980.2659-0.3486-0.1350.10440.3097-0.00040.39840.0068-0.00280.4220.02950.4713-0.6908-33.4102-9.803
260.15530.2894-0.21230.4097-0.12020.45420.1670.0497-0.34450.48620.45570.32170.2965-1.116-0.00440.5928-0.12270.01520.71010.16590.594-14.3104-28.5785-8.0362
270.04810.099-0.1094-0.0182-0.16590.1455-0.2399-0.45140.35990.26460.3130.0878-0.3322-0.46270.00030.7204-0.0086-0.04460.5393-0.06440.4714-9.5989-23.16921.0256
281.66730.3993-1.33260.6929-0.13630.93710.0936-0.3452-0.50770.11540.0287-0.33090.5837-0.01770.00010.65620.0335-0.12720.63260.12610.5926-36.5289-45.2197-8.4704
290.5897-0.7224-0.36510.79991.49430.52420.3463-0.3524-0.5716-0.07320.136-0.0520.5613-0.25570.00260.7379-0.1238-0.18450.78790.2680.5419-36.3096-45.544-4.8065
300.7046-2.1669-0.67919.5079-1.52833.6043-0.4321-1.05990.31030.29850.3638-1.1656-0.69040.42350.06980.4631-0.0346-0.07580.66850.03020.3271-30.876-25.4907-3.285
310.02170.0218-0.00090.0523-0.06640.0527-0.122-0.42110.2750.4540.18990.40410.2948-0.298-0.00020.7481-0.2625-0.0290.62650.04280.5884-28.4002-19.6448-14.0694
320.24180.04720.0747-0.11320.00110.1381-0.0020.34870.51290.0002-0.18060.24150.1775-0.4158-0.00370.525-0.07790.03940.49970.09310.4855-40.1654-21.3689-11.758
330.23220.48870.01810.677-0.72181.08650.0457-0.4431-0.2231-0.0546-0.0584-0.1730.64320.46060.06680.4497-0.0379-0.04830.61690.15980.4113-33.1684-35.2974-8.5022
340.0665-0.10850.09150.0824-0.14630.07590.0111-0.3164-1.0627-1.34890.19050.820.0199-0.7438-0.00010.522-0.08-0.10650.44750.09490.5821-46.0468-29.0525-16.5814
350.2053-0.06210.33290.3526-0.47210.56440.352-0.23180.44650.41410.17570.55720.299-0.93840.17150.5956-0.03830.15130.6828-0.07770.4792-41.0533-25.29050.0424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 15 )B1 - 15
2X-RAY DIFFRACTION2chain 'C' and (resid 1 through 15 )C1 - 15
3X-RAY DIFFRACTION3chain 'A' and (resid 331 through 336 )A331 - 336
4X-RAY DIFFRACTION4chain 'A' and (resid 337 through 346 )A337 - 346
5X-RAY DIFFRACTION5chain 'A' and (resid 347 through 353 )A347 - 353
6X-RAY DIFFRACTION6chain 'A' and (resid 354 through 368 )A354 - 368
7X-RAY DIFFRACTION7chain 'A' and (resid 369 through 379 )A369 - 379
8X-RAY DIFFRACTION8chain 'A' and (resid 380 through 386 )A380 - 386
9X-RAY DIFFRACTION9chain 'A' and (resid 387 through 405 )A387 - 405
10X-RAY DIFFRACTION10chain 'A' and (resid 406 through 411 )A406 - 411
11X-RAY DIFFRACTION11chain 'A' and (resid 412 through 423 )A412 - 423
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 15 )D1 - 15
13X-RAY DIFFRACTION13chain 'E' and (resid 1 through 15 )E1 - 15
14X-RAY DIFFRACTION14chain 'F' and (resid 330 through 346 )F330 - 346
15X-RAY DIFFRACTION15chain 'F' and (resid 347 through 353 )F347 - 353
16X-RAY DIFFRACTION16chain 'F' and (resid 354 through 379 )F354 - 379
17X-RAY DIFFRACTION17chain 'F' and (resid 380 through 386 )F380 - 386
18X-RAY DIFFRACTION18chain 'F' and (resid 387 through 411 )F387 - 411
19X-RAY DIFFRACTION19chain 'F' and (resid 412 through 426 )F412 - 426
20X-RAY DIFFRACTION20chain 'G' and (resid 3 through 15 )G3 - 15
21X-RAY DIFFRACTION21chain 'H' and (resid 1 through 14 )H1 - 14
22X-RAY DIFFRACTION22chain 'I' and (resid 331 through 336 )I331 - 336
23X-RAY DIFFRACTION23chain 'I' and (resid 337 through 353 )I337 - 353
24X-RAY DIFFRACTION24chain 'I' and (resid 354 through 368 )I354 - 368
25X-RAY DIFFRACTION25chain 'I' and (resid 369 through 399 )I369 - 399
26X-RAY DIFFRACTION26chain 'I' and (resid 400 through 411 )I400 - 411
27X-RAY DIFFRACTION27chain 'I' and (resid 412 through 424 )I412 - 424
28X-RAY DIFFRACTION28chain 'J' and (resid 1 through 15 )J1 - 15
29X-RAY DIFFRACTION29chain 'K' and (resid 1 through 15 )K1 - 15
30X-RAY DIFFRACTION30chain 'L' and (resid 333 through 346 )L333 - 346
31X-RAY DIFFRACTION31chain 'L' and (resid 347 through 353 )L347 - 353
32X-RAY DIFFRACTION32chain 'L' and (resid 354 through 368 )L354 - 368
33X-RAY DIFFRACTION33chain 'L' and (resid 369 through 405 )L369 - 405
34X-RAY DIFFRACTION34chain 'L' and (resid 406 through 411 )L406 - 411
35X-RAY DIFFRACTION35chain 'L' and (resid 412 through 424 )L412 - 424

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more