[English] 日本語
Yorodumi
- PDB-3twv: Crystal structure of ARC4 from human Tankyrase 2 in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3twv
TitleCrystal structure of ARC4 from human Tankyrase 2 in complex with peptide from human NUMA1 (chimeric peptide)
Components
  • Tankyrase-2
  • human NUMA1
KeywordsSIGNALING PROTEIN/PEPTIDE / ankyrin repeat / protein-protein interaction / substrate recruitment / poly(ADP-ribosyl)ation / SIGNALING PROTEIN-PEPTIDE complex
Function / homology
Function and homology information


XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...Ankyrin repeat / Ankyrin repeat-containing domain / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.301 Å
AuthorsGuettler, S. / Sicheri, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural basis and sequence rules for substrate recognition by tankyrase explain the basis for cherubism disease.
Authors: Guettler, S. / Larose, J. / Petsalaki, E. / Gish, G. / Scotter, A. / Pawson, T. / Rottapel, R. / Sicheri, F.
History
DepositionSep 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tankyrase-2
B: Tankyrase-2
C: Tankyrase-2
D: Tankyrase-2
E: human NUMA1
F: human NUMA1
G: human NUMA1
H: human NUMA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,03724
Polymers78,8818
Non-polymers2,15616
Water2,846158
1
A: Tankyrase-2
E: human NUMA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1874
Polymers19,7202
Non-polymers4662
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15450 Å2
ΔGint-80 kcal/mol
Surface area27170 Å2
MethodPISA
2
B: Tankyrase-2
F: human NUMA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9405
Polymers19,7202
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tankyrase-2
G: human NUMA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7778
Polymers19,7202
Non-polymers1,0576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tankyrase-2
H: human NUMA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1337
Polymers19,7202
Non-polymers4125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.219, 104.978, 129.555
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
Tankyrase-2 / / TANK2 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose ...TANK2 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 17851.180 Da / Num. of mol.: 4 / Fragment: UNP residues 488-649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP5B, TANK2, TNKL, TNKS2 / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Protein/peptide
human NUMA1


Mass: 1869.069 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: solid-state synthesized peptide / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 4 types, 174 molecules

#3: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol


Mass: 370.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O9
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES-NaOH pH 6.0, 2% (v/v) PEG 400, 2.5 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2010
RadiationMonochromator: Si (220), Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 37961 / Num. obs: 37961 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.6 / Redundancy: 4.9 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 11.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
REFMACrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.301→35.477 Å / SU ML: 0.66 / σ(F): 0.42 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2446 1864 4.94 %
Rwork0.1868 --
obs0.1896 37765 98.36 %
all-37765 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.5 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5708 Å20 Å20 Å2
2--0.2552 Å2-0 Å2
3---0.3155 Å2
Refinement stepCycle: LAST / Resolution: 2.301→35.477 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5190 0 108 158 5456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075377
X-RAY DIFFRACTIONf_angle_d1.0477246
X-RAY DIFFRACTIONf_dihedral_angle_d15.5592003
X-RAY DIFFRACTIONf_chiral_restr0.072800
X-RAY DIFFRACTIONf_plane_restr0.005947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.36340.34031310.24382540X-RAY DIFFRACTION92
2.3634-2.43290.26991480.21622745X-RAY DIFFRACTION99
2.4329-2.51150.25081570.19942724X-RAY DIFFRACTION99
2.5115-2.60120.27281380.18342774X-RAY DIFFRACTION99
2.6012-2.70530.24011590.18882751X-RAY DIFFRACTION99
2.7053-2.82840.29011460.19842742X-RAY DIFFRACTION99
2.8284-2.97740.26311410.19632750X-RAY DIFFRACTION99
2.9774-3.16390.23281390.18552723X-RAY DIFFRACTION98
3.1639-3.4080.22641300.18032774X-RAY DIFFRACTION98
3.408-3.75060.23221480.16722754X-RAY DIFFRACTION99
3.7506-4.29250.22851400.16292796X-RAY DIFFRACTION99
4.2925-5.4050.19331370.16452854X-RAY DIFFRACTION99
5.405-35.48110.27111500.21832974X-RAY DIFFRACTION99
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)
16.6209-1.56782.44016.4857-1.6256.5827-0.2116-0.0330.3486-0.65770.14370.5521-0.3816-0.51430.0830.2782-0.0004-0.120.25890.07330.3048-25.7872-12.45857.6141
27.7784-0.0723-5.342.31270.02383.67540.2662-0.1123-0.2023-0.22180.09520.2822-0.5755-0.1215-0.36780.2252-0.0402-0.00760.17850.01590.2321-19.2159-7.181113.2831
31.48420.82350.76483.672-0.53883.2882-0.02870.0126-0.0195-0.025-0.00790.154-0.0023-0.07380.02840.0458-0.01780.02580.1653-0.00990.1076-16.0509-19.754819.025
43.90132.19421.75786.0055-0.8264.05-0.1331-0.034-0.1433-0.1886-0.0161-0.00991.1710.00260.12080.34810.00250.01620.1770.04980.1055-12.4696-32.722324.808
56.2121-1.6206-4.53267.17641.0593.35180.163-0.41450.46631.19210.0473-0.29840.29120.1164-0.2610.379-0.0686-0.02030.3446-0.06910.2044-10.5463-27.396135.2116
60.594-0.4548-0.20030.76540.54310.43340.048-0.1311-0.29950.09210.28330.35960.6235-0.4114-0.26670.7818-0.0886-0.04640.26530.1460.262-14.1885-39.689332.1099
72.24622.25591.56563.98792.51293.4834-0.32430.09710.03390.60430.4968-1.0394-0.33350.5304-0.11520.2607-0.0384-0.08580.2661-0.07150.2582-46.311-17.165648.4521
86.0382-2.33942.11939.6516-1.4726.35860.23260.03950.50410.3956-0.25280.2207-0.3721-0.3062-0.00220.2711-0.01740.0280.1153-0.10340.2725-52.526-16.607344.0319
92.4404-1.3706-2.09685.1107-0.45985.3566-0.00490.05880.291-0.0150.1182-0.0026-0.33020.0743-0.00270.147-0.0425-0.04110.1141-00.1746-47.2886-22.826637.7988
100.95060.0409-1.46615.76680.11234.2756-0.1619-0.15310.1605-0.0560.09180.24880.1347-0.3023-0.01980.1332-0.0544-0.04630.22280.04610.1078-49.5242-31.671732.9061
114.9225-0.6163-2.84745.09360.30644.3942-0.33910.83320.6219-0.40070.2206-0.0633-0.08570.28130.09640.2432-0.0927-0.03230.2950.0720.17-39.1006-27.418925.2601
124.64170.1349-1.34241.9196-0.04982.3547-0.17620.22430.1993-0.34480.2124-0.12970.04550.0659-0.01030.1626-0.0628-0.00060.18290.02610.112-40.716-36.920224.9114
138.70124.2305-2.42542.7819-2.11441.8823-0.4588-0.1554-1.0715-0.41140.0775-0.44570.50120.51520.33060.3280.01080.10940.2462-0.01260.1804-36.5548-45.732425.5363
142.1977-0.2717-2.65492.98410.9113.91450.0783-0.1854-0.3208-0.5954-0.2863-1.1620.19090.6370.40720.43890.04160.29030.28840.18290.47937.542712.42058.4073
156.13112.2845-3.03064.30822.78658.25020.41120.37810.7723-0.84880.16470.1937-0.5953-0.2832-0.47910.59770.00780.10340.23090.10890.3561-1.850116.64815.5384
163.8824-0.993-0.04165.32394.92165.650.02380.04460.0503-0.3088-0.10970.0632-0.1812-0.0034-0.00330.4690.04920.20360.1739-0.04830.18742.95674.58314.4561
173.40130.2917-1.66552.14370.35845.45610.03660.08350.2207-0.24060.106-0.57010.08330.4872-0.13360.18410.0090.08680.16870.02830.27683.27376.643715.9889
181.29272.20031.64897.41965.05897.90110.23320.04650.0049-1.1115-0.41610.4373-0.5715-0.91220.20180.35820.02250.02010.2840.04210.2171-8.50379.42598.8001
192.4037-0.2083-0.70653.15270.16773.3163-0.06640.0576-0.2568-0.2061-0.1757-0.21920.03110.14710.22190.1826-0.02080.07990.13660.02980.1901-1.45460.299418.4707
200.9044-1.6728-2.04694.65815.06116.5270.14020.12260.3044-0.1396-0.2741.178-0.1234-0.76560.24570.16960.04160.02860.2240.0370.3068-12.95814.623118.7329
217.5036-1.3763.16891.93341.13063.0788-0.2958-0.2065-0.404-0.13610.1138-0.00560.03810.1750.20460.21210.02270.13590.17570.00580.244-2.7193-6.921221.5436
220.95071.86681.33915.4710.69464.5703-0.3974-0.0915-0.14130.16630.01420.0634-0.2937-0.32180.3020.16910.05190.06380.1714-0.0220.1572-10.1995-0.618429.1975
235.49-2.13371.39981.9413-0.09250.5404-0.30370.2674-0.66520.15040.1104-0.22050.29650.3135-0.01360.1930.11790.15490.28340.06330.4139-3.5144-12.13130.4989
244.2777-1.7126-2.70554.00420.00572.0614-0.6649-0.9098-0.27771.04560.34510.05390.50880.4855-0.17250.47270.21370.1850.28390.01750.1864-8.842-3.506239.0944
254.87020.15283.73582.9175-1.83776.4406-0.00960.31280.2227-0.6431-0.32210.0616-0.04010.37110.0070.47010.0143-0.21850.1620.02550.1677-27.6725-32.0972-8.5938
266.95972.2216-0.50114.98130.62186.2009-0.2869-0.62120.39720.14930.0963-0.1697-0.40830.24220.09620.24250.0087-0.16060.153-0.05960.2397-30.6541-41.7088-9.1356
271.665-0.11190.60132.99830.32252.6781-0.0048-0.05020.0193-0.0991-0.00970.21010.10170.0358-0.01540.1176-0.0045-0.07510.16120.02080.1467-22.398-43.89112.0269
283.0837-0.06640.62614.05010.06793.6387-0.1222-0.121-0.15160.52510.3461-0.38760.1708-0.0311-0.20880.19860.0568-0.0920.19110.03340.1817-13.616-50.969212.088
290.95480.08842.3362.29112.08317.9157-0.22860.1450.32080.6770.1485-0.758-0.17340.93610.12810.37010.0875-0.29060.3369-0.03780.4117-5.7196-49.69717.3368
302.82481.90172.7623.88221.24514.49590.0874-0.4074-0.0710.3329-0.36130.57560.1654-0.86460.26390.0419-0.04560.00470.28330.00620.2961-26.0482-25.751521.7914
319.10172.3218-2.51328.2995-1.41836.71540.1613-0.6440.02070.2509-0.215-0.72440.09151.1450.13560.15810.0345-0.02050.2463-0.03210.197-40.5386-33.287441.3445
326.3829-5.1424-0.43868.49170.03282.9014-0.5362-0.47320.47240.32690.7005-0.88110.39350.2274-0.13710.25930.02520.02970.2627-0.10950.25133.97446.440825.7533
331.46011.00020.20358.43524.07373.46990.15110.0624-0.1273-0.0558-0.1312-0.4763-0.35070.4714-0.06280.2847-0.0319-0.09860.36460.02530.1715-12.1399-37.85351.7078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 490:511)
2X-RAY DIFFRACTION2chain 'A' and (resseq 512:521)
3X-RAY DIFFRACTION3chain 'A' and (resseq 522:594)
4X-RAY DIFFRACTION4chain 'A' and (resseq 595:613)
5X-RAY DIFFRACTION5chain 'A' and (resseq 614:628)
6X-RAY DIFFRACTION6chain 'A' and (resseq 629:644)
7X-RAY DIFFRACTION7chain 'B' and (resseq 488:502)
8X-RAY DIFFRACTION8chain 'B' and (resseq 503:521)
9X-RAY DIFFRACTION9chain 'B' and (resseq 522:561)
10X-RAY DIFFRACTION10chain 'B' and (resseq 562:581)
11X-RAY DIFFRACTION11chain 'B' and (resseq 582:594)
12X-RAY DIFFRACTION12chain 'B' and (resseq 595:627)
13X-RAY DIFFRACTION13chain 'B' and (resseq 628:644)
14X-RAY DIFFRACTION14chain 'C' and (resseq 488:502)
15X-RAY DIFFRACTION15chain 'C' and (resseq 503:511)
16X-RAY DIFFRACTION16chain 'C' and (resseq 512:521)
17X-RAY DIFFRACTION17chain 'C' and (resseq 522:538)
18X-RAY DIFFRACTION18chain 'C' and (resseq 539:548)
19X-RAY DIFFRACTION19chain 'C' and (resseq 549:571)
20X-RAY DIFFRACTION20chain 'C' and (resseq 572:580)
21X-RAY DIFFRACTION21chain 'C' and (resseq 581:594)
22X-RAY DIFFRACTION22chain 'C' and (resseq 595:614)
23X-RAY DIFFRACTION23chain 'C' and (resseq 615:627)
24X-RAY DIFFRACTION24chain 'C' and (resseq 628:644)
25X-RAY DIFFRACTION25chain 'D' and (resseq 489:511)
26X-RAY DIFFRACTION26chain 'D' and (resseq 512:521)
27X-RAY DIFFRACTION27chain 'D' and (resseq 522:594)
28X-RAY DIFFRACTION28chain 'D' and (resseq 595:627)
29X-RAY DIFFRACTION29chain 'D' and (resseq 628:644)
30X-RAY DIFFRACTION30chain 'E'
31X-RAY DIFFRACTION31chain 'F'
32X-RAY DIFFRACTION32chain 'G'
33X-RAY DIFFRACTION33chain 'H'

+
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