[English] 日本語
Yorodumi
- PDB-7pje: Inhibiting parasite proliferation using a rationally designed ant... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pje
TitleInhibiting parasite proliferation using a rationally designed anti-tubulin agent
Components
  • Darpin D1
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / Tubulin / Microtubules / Protozoa / Apicomplexa
Function / homology
Function and homology information


microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha chain / Tubulin beta chain
Similarity search - Component
Biological speciessynthetic construct (others)
Tetrahymena thermophila (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSharma, A. / Gaillard, N. / Ehrhard, V.A. / Steinmetz, M.O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Novartis FreeNovation Switzerland
CitationJournal: Embo Mol Med / Year: 2021
Title: Inhibiting parasite proliferation using a rationally designed anti-tubulin agent.
Authors: Gaillard, N. / Sharma, A. / Abbaali, I. / Liu, T. / Shilliday, F. / Cook, A.D. / Ehrhard, V. / Bangera, M. / Roberts, A.J. / Moores, C.A. / Morrissette, N. / Steinmetz, M.O.
History
DepositionAug 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 3, 2021Group: Atomic model / Data collection / Database references
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / pdbx_data_processing_status / pdbx_database_proc
Item: _atom_site_anisotrop.id / _citation.page_first ..._atom_site_anisotrop.id / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.1Nov 17, 2021Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume
Revision 2.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin alpha chain
B: Tubulin beta chain
F: Darpin D1
C: Tubulin alpha chain
D: Tubulin beta chain
E: Darpin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,55013
Polymers231,3856
Non-polymers2,1667
Water18,9701053
1
A: Tubulin alpha chain
B: Tubulin beta chain
F: Darpin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7877
Polymers115,6923
Non-polymers1,0954
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-49 kcal/mol
Surface area35660 Å2
MethodPISA
2
C: Tubulin alpha chain
D: Tubulin beta chain
E: Darpin D1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7636
Polymers115,6923
Non-polymers1,0713
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-40 kcal/mol
Surface area35690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.130, 183.920, 118.323
Angle α, β, γ (deg.)90.000, 92.440, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 3 types, 6 molecules ACBDFE

#1: Protein Tubulin alpha chain / Alpha-tubulin


Mass: 49639.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: P41351
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49617.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: P41352
#3: Protein Darpin D1


Mass: 16435.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 3 types, 1060 molecules

#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1053 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M sodium sulfate, 10% DMSO and 18 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→46.83 Å / Num. obs: 219447 / % possible obs: 98.37 % / Redundancy: 5.9 % / Biso Wilson estimate: 30.28 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07281 / Rpim(I) all: 0.03267 / Rrim(I) all: 0.08004 / Net I/σ(I): 12.84
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 6 % / Rmerge(I) obs: 1.177 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 20372 / CC1/2: 0.796 / CC star: 0.942 / Rpim(I) all: 0.5162 / % possible all: 91.63

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DRX

4drx


Resolution: 1.75→46.83 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 10963 5 %
Rwork0.1815 208337 -
obs0.1831 219300 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 271.08 Å2 / Biso mean: 49.6015 Å2 / Biso min: 20.54 Å2
Refinement stepCycle: final / Resolution: 1.75→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15067 0 169 1053 16289
Biso mean--35.27 48.28 -
Num. residues----1946
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.37142890.3625494578378
1.77-1.790.35793680.34116983735198
1.79-1.810.34213600.31846851721198
1.81-1.840.31953640.30346914727899
1.84-1.860.32843700.27817018738899
1.86-1.890.29963630.27156893725699
1.89-1.910.30543670.26166960732798
1.91-1.940.28033690.25446985735499
1.94-1.970.28153630.24226880724399
1.97-20.2863700.23817034740499
2-2.040.26673640.22096908727299
2.04-2.080.24543670.2097010737799
2.08-2.120.23863660.20396952731899
2.12-2.160.22693670.19327007737499
2.16-2.210.23223650.18856936730199
2.21-2.260.22613710.18747051742299
2.26-2.310.21953660.17956951731799
2.31-2.380.21243720.18327068744099
2.38-2.450.22523660.1826934730099
2.45-2.520.22523690.18847025739499
2.52-2.610.25133720.19087053742599
2.61-2.720.21993680.182269877355100
2.72-2.840.22353690.18270137382100
2.84-2.990.21273710.189470407411100
2.99-3.180.22193720.184970697441100
3.18-3.430.1973710.172270527423100
3.43-3.770.18763720.160770637435100
3.77-4.320.17693690.14267035740499
4.32-5.440.15983710.13657029740099
5.44-46.830.20673720.183271427514100
Refinement TLS params.

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

IDL11 (°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)
10.49550.1209-0.02381.4823-2.21974.09330.0216-0.4046-0.14360.4145-0.05320.16640.268-0.65510.2030.3454-0.04680.03880.52050.00330.38968.6696-21.806676.8876
22.469-0.0746-0.21070.87810.14172.09380.1038-0.2548-0.06850.135-0.0990.23990.0436-0.57320.05490.25610.0030.03050.4141-0.050.30126.0279-16.63169.2132
31.76360.42160.55711.5481-0.47552.50530.08-0.227-0.13620.0285-0.02240.0590.20750.0191-0.12670.30460.0190.02170.3723-0.02310.274323.4964-19.123979.1446
40.8540.20430.51680.2950.72682.6876-0.0324-0.19370.06150.07410.0227-0.0524-0.10740.2627-0.02110.29040.03050.03260.3204-0.06210.33227.049-11.356674.9699
51.5528-0.26570.18821.7999-0.53421.2433-0.0283-0.3667-0.40470.3504-0.00390.250.1774-0.2104-0.01140.2145-0.06710.01440.31340.03480.38285.1588-39.878841.8224
62.04770.1019-0.55381.1622-0.11631.76560.01440.3008-0.1358-0.1024-0.02990.19170.1357-0.4793-0.03690.25360.015-0.03560.3671-0.02850.3266.0057-27.611127.314
71.53360.56030.68121.4599-0.68771.21510.04810.018-0.2989-0.0889-0.0525-0.05780.2447-0.0135-0.03980.17380.0084-0.01780.19790.01060.297520.5477-34.395536.4988
81.3599-0.26210.25851.4553-0.08220.87780.1345-0.1505-0.38920.1065-0.0653-0.26820.1760.3048-0.01110.2969-0.0128-0.01420.35590.0090.432429.9255-32.403543.2619
90.7398-0.04850.33290.83880.54721.31690.0416-0.057-0.12840.0883-0.0053-0.0574-0.13420.13470.05670.1905-0.00330.01160.3005-0.00310.314327.6658-26.332236.688
100.8889-0.6131-0.34961.03680.19470.9549-0.01730.19810.0136-0.36990.02740.1274-0.6029-0.0642-0.21950.3663-0.01680.01210.30080.03280.295721.2178-14.057621.7283
110.6408-0.0708-0.01720.3051-0.16490.2082-0.05920.18510.9491-0.2881-0.09970.2829-1.06690.01530.25570.51380.0519-0.04650.6257-0.04590.487114.5152-18.9524-9.4791
120.44570.45310.32162.25981.90511.6493-0.20530.0717-0.4589-0.6948-0.30010.7213-0.1504-0.55320.02510.6348-0.0261-0.08610.597-0.06030.533113.5605-26.9113-14.9553
131.25820.0721-0.2040.5798-0.64711.2489-0.00210.1364-0.055-0.1488-0.005-0.0544-0.0650.27360.03320.38770.00660.04280.3792-0.0360.261128.3836-23.652-2.4733
141.111-0.48720.31560.22420.14684.61-0.1575-0.0982-0.27740.0155-0.1129-0.46670.13910.28010.12490.4130.16220.0250.5822-0.0580.485338.264-32.68974.9629
152.9712-0.4072-1.09241.3367-0.21060.93960.01330.59120.168-0.3004-0.09640.06510.0246-0.6412-0.21030.26580.0563-0.0070.44740.0150.28313.135823.1897-20.3163
160.33540.0067-0.06090.01520.03890.180.04240.5228-0.0624-0.1609-0.16760.0539-0.1386-0.5985-0.1680.39080.1419-0.06350.8350.07360.43645.146426.3042-29.7617
170.5534-0.0872-0.53340.2442-0.43741.21840.0774-0.0067-0.03010.0941-0.04420.01970.0007-0.49240.0020.2431-0.0006-0.00320.4558-0.08920.295610.914916.7533-8.8725
180.2759-0.13-0.20330.1857-0.19870.4470.05060.104-0.2070.16610.1213-0.3455-0.12720.12400.3633-0.0427-0.01160.2899-0.06540.301230.515325.5639-12.3021
190.16190.03230.04150.1288-0.13930.17470.07430.41580.0604-0.17230.0278-0.12580.0178-0.1804-00.34180.03190.00060.42030.01710.350721.292818.4141-24.9322
200.2563-0.12650.20560.11280.2450.6483-0.01280.0549-0.0580.0183-0.0326-0.0667-0.08120.070900.2934-0.0362-0.00890.35-0.03990.307934.853118.1051-21.4048
210.15280.02610.12340.22070.22760.2250.11810.1828-0.05730.0967-0.06520.08-0.01190.27700.3229-0.0058-0.00330.4404-0.02790.310535.898416.2972-33.6077
22-0.03230.1738-0.01760.2415-0.21680.45870.12850.20070.01320.0194-0.1879-0.1616-0.08250.159-00.42550.0275-0.04530.4494-0.05820.355732.057818.008-28.9927
230.46460.16630.26910.28060.4430.67370.0035-0.0128-0.08980.1016-0.0242-0.0290.2330.1368-00.34790.00660.00070.2709-0.04790.308228.09658.2324-2.8945
240.27540.15710.12160.2553-0.18610.3766-0.10670.00020.1514-0.1099-0.10140.2185-0.329-0.4716-0.08450.5330.2372-0.13160.3991-0.09720.45097.524842.047615.2276
250.02770.0123-0.05490.2406-0.02680.1093-0.0896-0.18350.17010.0615-0.04620.194-0.3336-0.378-0.11440.60410.2775-0.03640.6056-0.20710.56983.07942.402729.5591
260.7180.37840.51340.91630.72120.64430.2245-0.3945-0.01110.2603-0.23930.38890.2208-1.0165-0.00130.26110.18480.03270.6773-0.17770.44240.510729.744133.4119
270.9340.1177-0.35091.009-0.02020.99190.0127-0.05160.03150.041-0.0370.0312-0.1799-0.2344-00.34090.0686-0.02820.2996-0.06710.281717.071429.674124.9716
280.65150.09170.62720.06940.02330.78110.12910.0916-0.1088-0.04540.0020.0587-0.10330.70970.00750.5377-0.09020.01520.3063-0.04390.383932.922440.206517.9388
290.073-0.0128-0.04860.02890.01310.02180.1575-0.03420.0096-0.1311-0.0303-0.1066-0.00540.0751-00.44670.0331-0.01230.3253-0.07380.322231.175631.836416.2933
300.2242-0.08160.09950.46510.32150.2354-0.0011-0.02480.0158-0.0404-0.044-0.07550.03220.2373-00.37730.0327-0.02620.3425-0.03080.310930.861828.973518.3901
310.33220.32090.27370.40640.20160.19730.0428-0.0901-0.09740.1505-0.11520.0750.3830.0195-00.46650.0164-0.00080.3981-0.04780.357721.07615.949836.6443
320.0868-0.0187-0.03890.1132-0.0640.02510.0450.20560.09210.56160.28770.5934-0.2557-0.18070.00010.43860.00290.03560.5538-0.01530.486211.977125.477669.1011
330.1908-0.0859-0.02550.1518-0.20210.36140.0352-0.11380.049-0.0152-0.0543-0.03180.12480.129100.47140.0204-0.03450.3694-0.04890.294123.307324.260564.1782
340.02350.0415-0.00930.03780.00240.0123-0.2945-0.05590.23580.245-0.2487-0.0964-0.1923-0.15700.4774-0.0186-0.04970.4719-0.0620.393929.721234.667961.95
350.09590.0799-0.07360.1868-0.01650.0834-0.0101-0.08910.0768-0.0607-0.0239-0.03150.27640.533900.43230.0425-0.0050.5699-0.05110.333.70724.272153.9355
360.43410.217-0.23240.2386-0.29410.41620.35680.16780.5017-0.13010.14350.2798-0.41360.00330.0260.4199-0.1655-0.03980.61520.00420.404737.305434.790154.3488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )A2 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 197 )A29 - 197
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 300 )A198 - 300
4X-RAY DIFFRACTION4chain 'A' and (resid 301 through 436 )A301 - 436
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 64 )B1 - 64
6X-RAY DIFFRACTION6chain 'B' and (resid 65 through 199 )B65 - 199
7X-RAY DIFFRACTION7chain 'B' and (resid 200 through 259 )B200 - 259
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 338 )B260 - 338
9X-RAY DIFFRACTION9chain 'B' and (resid 339 through 401 )B339 - 401
10X-RAY DIFFRACTION10chain 'B' and (resid 402 through 440 )B402 - 440
11X-RAY DIFFRACTION11chain 'F' and (resid 13 through 24 )F13 - 24
12X-RAY DIFFRACTION12chain 'F' and (resid 25 through 36 )F25 - 36
13X-RAY DIFFRACTION13chain 'F' and (resid 37 through 125 )F37 - 125
14X-RAY DIFFRACTION14chain 'F' and (resid 126 through 138 )F126 - 138
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 28 )C1 - 28
16X-RAY DIFFRACTION16chain 'C' and (resid 29 through 64 )C29 - 64
17X-RAY DIFFRACTION17chain 'C' and (resid 65 through 197 )C65 - 197
18X-RAY DIFFRACTION18chain 'C' and (resid 198 through 223 )C198 - 223
19X-RAY DIFFRACTION19chain 'C' and (resid 224 through 259 )C224 - 259
20X-RAY DIFFRACTION20chain 'C' and (resid 260 through 311 )C260 - 311
21X-RAY DIFFRACTION21chain 'C' and (resid 312 through 337 )C312 - 337
22X-RAY DIFFRACTION22chain 'C' and (resid 338 through 372 )C338 - 372
23X-RAY DIFFRACTION23chain 'C' and (resid 373 through 436 )C373 - 436
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 64 )D1 - 64
25X-RAY DIFFRACTION25chain 'D' and (resid 65 through 88 )D65 - 88
26X-RAY DIFFRACTION26chain 'D' and (resid 89 through 126 )D89 - 126
27X-RAY DIFFRACTION27chain 'D' and (resid 127 through 268 )D127 - 268
28X-RAY DIFFRACTION28chain 'D' and (resid 269 through 300 )D269 - 300
29X-RAY DIFFRACTION29chain 'D' and (resid 301 through 324 )D301 - 324
30X-RAY DIFFRACTION30chain 'D' and (resid 325 through 401 )D325 - 401
31X-RAY DIFFRACTION31chain 'D' and (resid 402 through 440 )D402 - 440
32X-RAY DIFFRACTION32chain 'E' and (resid 13 through 35 )E13 - 35
33X-RAY DIFFRACTION33chain 'E' and (resid 36 through 92 )E36 - 92
34X-RAY DIFFRACTION34chain 'E' and (resid 93 through 101 )E93 - 101
35X-RAY DIFFRACTION35chain 'E' and (resid 102 through 125 )E102 - 125
36X-RAY DIFFRACTION36chain 'E' and (resid 126 through 137 )E126 - 137

+
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://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