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- PDB-3tws: Crystal structure of ARC4 from human Tankyrase 2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3tws
TitleCrystal structure of ARC4 from human Tankyrase 2 in complex with peptide from human TERF1 (chimeric peptide)
Components
  • Tankyrase-2
  • human TERF1
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 / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / 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 / nucleus / metal ion binding / cytoplasm / cytosol
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: 1.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tankyrase-2
B: Tankyrase-2
C: Tankyrase-2
D: Tankyrase-2
E: human TERF1
F: human TERF1
G: human TERF1
H: human TERF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,53638
Polymers78,5018
Non-polymers3,03530
Water8,809489
1
A: Tankyrase-2
E: human TERF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3408
Polymers19,6252
Non-polymers7156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-2
F: human TERF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,53412
Polymers19,6252
Non-polymers90910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tankyrase-2
G: human TERF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5009
Polymers19,6252
Non-polymers8757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tankyrase-2
H: human TERF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1629
Polymers19,6252
Non-polymers5367
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.910, 104.969, 129.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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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 TERF1


Mass: 1773.994 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: solid-state synthesized peptide / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 519 molecules

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


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.51 %
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

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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: 1.7→50 Å / Num. all: 93277 / Num. obs: 93277 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.8 / Redundancy: 5.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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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: 1.7→33.286 Å / SU ML: 0.47 / σ(F): 0.52 / Phase error: 18.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 4671 5.04 %Random
Rwork0.1789 ---
obs0.1805 92767 99.53 %-
all-92767 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.103 Å2 / ksol: 0.398 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8167 Å20 Å20 Å2
2--0.3166 Å2-0 Å2
3---0.5001 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5164 0 166 489 5819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065517
X-RAY DIFFRACTIONf_angle_d0.9817420
X-RAY DIFFRACTIONf_dihedral_angle_d13.9882054
X-RAY DIFFRACTIONf_chiral_restr0.068812
X-RAY DIFFRACTIONf_plane_restr0.005974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.35451430.30112943X-RAY DIFFRACTION100
1.7193-1.73950.30971710.28422867X-RAY DIFFRACTION100
1.7395-1.76080.27421510.27612891X-RAY DIFFRACTION100
1.7608-1.7830.3091820.26072901X-RAY DIFFRACTION100
1.783-1.80650.30461310.24362932X-RAY DIFFRACTION100
1.8065-1.83120.2851630.22682900X-RAY DIFFRACTION100
1.8312-1.85740.24961550.21722894X-RAY DIFFRACTION100
1.8574-1.88510.20821580.19582931X-RAY DIFFRACTION100
1.8851-1.91460.21291650.18642872X-RAY DIFFRACTION100
1.9146-1.9460.20221630.17782917X-RAY DIFFRACTION100
1.946-1.97950.21411610.16822913X-RAY DIFFRACTION100
1.9795-2.01550.19291530.16472928X-RAY DIFFRACTION100
2.0155-2.05430.23261560.16032935X-RAY DIFFRACTION100
2.0543-2.09620.22191430.16552897X-RAY DIFFRACTION100
2.0962-2.14180.19951500.16442962X-RAY DIFFRACTION100
2.1418-2.19160.2111650.16622898X-RAY DIFFRACTION100
2.1916-2.24640.20661590.17122900X-RAY DIFFRACTION100
2.2464-2.30710.20561510.15592959X-RAY DIFFRACTION100
2.3071-2.3750.17111530.15572931X-RAY DIFFRACTION100
2.375-2.45160.19171610.15462911X-RAY DIFFRACTION100
2.4516-2.53920.18671550.15752952X-RAY DIFFRACTION100
2.5392-2.64080.18351500.1612942X-RAY DIFFRACTION100
2.6408-2.7610.20621780.17122937X-RAY DIFFRACTION100
2.761-2.90640.22891480.182966X-RAY DIFFRACTION100
2.9064-3.08840.19121640.17592969X-RAY DIFFRACTION100
3.0884-3.32670.19451440.17642981X-RAY DIFFRACTION100
3.3267-3.66110.19561480.16572990X-RAY DIFFRACTION100
3.6611-4.190.19221480.1552994X-RAY DIFFRACTION99
4.19-5.27550.19711460.16783000X-RAY DIFFRACTION98
5.2755-33.29240.25711560.23413083X-RAY DIFFRACTION97
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)
14.7131-1.85711.08882.0533-1.09316.4868-0.1551-0.09870.3783-0.3415-0.06011.0265-0.8882-1.04250.06310.28430.1028-0.07730.32350.00840.3039-27.7336-11.727211.0643
23.58331.8015-0.19225.113-0.62985.9122-0.08780.18030.2394-0.70850.23840.3503-0.3164-0.13-0.09220.2375-0.0025-0.05180.17040.02470.1886-20.9083-10.52038.6522
32.61341.94430.40584.8215-0.48685.3367-0.14980.08950.0612-0.33530.12720.1649-0.1745-0.0681-0.00080.0869-0.0053-0.00720.14140.01010.104-19.7176-17.873913.7942
41.17110.21080.60373.760.62142.11410.0121-0.0612-0.00440.11020.0494-0.10790.02720.0301-0.06210.0984-0.00280.02020.1675-0.00410.1084-13.4347-21.447621.9548
54.55721.44951.40825.9692-0.2063.3025-0.0232-0.0692-0.2886-0.04860.0474-0.25150.7025-0.0145-0.03080.32060.029-0.01330.16130.0260.1276-11.4412-32.586124.6069
67.9307-1.5806-6.67673.49081.08198.0096-0.1221-1.00770.26080.72820.2968-0.22320.04430.5256-0.1020.36920.0158-0.06010.32180.01980.1741-10.933-27.581136.6424
73.1209-0.5398-0.18252.3021.76841.38320.239-0.3805-0.8670.32010.00240.15531.0527-0.0471-0.17720.8774-0.0096-0.06960.21250.16340.2504-12.6226-40.146632.2283
84.83581.24510.74644.91773.43745.5321-0.2447-0.08590.29620.42110.3278-0.6124-0.54460.4535-0.02570.2272-0.0316-0.06780.1915-0.01970.2295-45.6843-17.235848.3351
95.6507-2.1114-1.25782.3535-1.34098.1294-0.02910.12340.20080.15040.06350.0131-0.4178-0.2515-0.1370.1908-0.00990.00330.1214-0.06890.2247-51.9828-16.783243.6145
101.0269-1.1359-0.60743.35720.25093.03090.05350.02440.262-0.12780.0924-0.1167-0.2040.0771-0.06840.086-0.0309-0.00430.13180.00320.1505-46.3302-24.837436.5584
110.94661.8412-1.44256.6597-1.70666.012-0.17540.32630.015-0.2760.08080.49760.0646-0.7590.02150.1249-0.043-0.03890.25910.020.2067-54.0008-31.628530.8102
123.7630.884-1.60842.1291-0.28921.5863-0.09470.24870.1066-0.27350.1946-0.08210.0149-0.0634-0.09990.1715-0.04610.00430.16940.01260.1234-39.8925-34.398524.6759
137.77736.4762-3.58628.3136-1.8995.2502-0.4515-0.059-1.2466-0.26490.0331-1.09930.55340.2590.32770.2954-0.0050.12220.230.0050.3584-36.1427-46.036625.2483
142.9084-0.975-2.09241.49820.26876.34220.17350.04590.4093-0.49440.0173-1.0503-0.31960.699-0.22820.4315-0.0380.21760.25070.03150.44136.326513.15858.6231
152.24560.5282-0.79321.57240.26294.64990.21080.33840.2677-0.5613-0.1086-0.275-0.46170.0591-0.10160.45930.01060.16710.23590.03180.26780.413910.20285.0434
161.50870.0514-0.58043.1235-0.13684.55240.04570.11020.0225-0.3375-0.0102-0.2347-0.0440.1103-0.03260.17460.00270.07080.1319-0.00360.1837-1.52534.705115.5485
176.159-2.5898-2.95564.45055.26546.22610.0068-0.0119-0.1023-0.3723-0.12930.9303-0.238-0.19020.1220.1910.02010.00650.14590.03010.253-12.97824.114618.102
186.59-0.43792.31912.99360.53383.2549-0.09980.0985-0.1873-0.09180.0384-0.26190.28010.23080.04680.16650.02530.06640.13620.01010.1934-1.7198-7.872722.6476
191.68061.53091.42683.0880.77673.9005-0.1611-0.09560.06140.0851-0.01460.0739-0.08110.02010.17710.15370.03890.03720.14140.00010.1509-10.2892-0.816929.2533
204.80741.09461.46581.5413-0.17112.6624-0.0339-0.0681-0.54570.0174-0.085-0.31930.46860.2984-0.04880.20870.06540.03620.20640.0520.2357-3.6678-12.010830.6072
214.8884-2.1953-2.38033.4674-0.04041.6649-0.6939-1.0434-0.40930.80330.3687-0.06540.54540.51120.12840.45810.25190.17490.36440.05770.19-9.2747-3.845839.4017
223.4390.38013.43272.94470.70534.3233-0.37390.16580.415-1.14140.0020.5303-0.8218-0.00480.19450.4499-0.0135-0.17430.1733-0.00240.2415-27.5121-31.8073-8.092
235.45613.89381.5393.5491.27855.2037-0.30710.0450.2921-0.10920.1033-0.0059-0.30.01410.19870.25010.0105-0.12930.1478-0.00790.2293-30.9442-41.8977-9.0553
244.69250.03362.30824.59331.97396.1653-0.00850.4246-0.2158-0.43810.09530.1146-0.04630.3033-0.07920.1798-0.0169-0.06090.19770.00170.1453-20.0227-39.8242-4.1364
258.36981.62625.93083.50790.38944.3838-0.0304-0.45450.4404-0.2227-0.30541.1210.0166-0.8020.24060.16270.0197-0.09080.2424-0.06110.3051-31.4979-36.1892.8325
263.6654-0.35781.47514.73470.28852.40340.21490.221-0.1917-0.2851-0.11250.00840.1560.1475-0.10770.1750.0191-0.04230.16230.00490.1223-20.3037-46.16311.3212
274.06081.13543.10617.60931.83212.9897-0.0367-0.5368-0.02670.2468-0.07080.5875-0.0024-0.24830.02050.1696-0.0038-0.0130.23050.02490.2044-25.6923-41.265811.1724
285.0543-1.12310.16964.88510.39183.44610.35350.2035-0.5176-0.0964-0.08310.00920.29080.2569-0.23510.22330.0136-0.10590.180.00490.2381-18.6968-53.47924.0935
293.6786-1.66810.37385.89620.12062.6797-0.0952-0.22040.02280.46060.2172-0.33-0.01780.2111-0.14560.20830.0267-0.07610.16860.00940.2037-14.131-46.388513.745
304.4358-2.3899-0.82816.31170.67634.02130.10880.2692-0.4430.15420.0656-0.26120.55840.0975-0.17130.29460.05-0.13980.2213-0.010.3106-12.762-57.81589.9845
310.4365-0.67850.90313.25582.15857.72390.0175-0.01990.16430.65160.5038-1.0715-0.07930.91540.57740.3440.1423-0.40890.3079-0.0740.418-5.5274-49.989517.2382
322.2386-0.4431-0.57093.7553-1.60162.4326-0.0438-0.6643-0.09710.3937-0.02330.4878-0.1755-0.11970.10220.099-0.0340.05140.29640.01770.222-25.767-25.643323.5487
337.4633-2.1193-1.63694.21320.22322.57280.05810.0461-0.1286-0.06140.0815-0.48890.3440.371-0.04230.1769-0.0085-0.04720.2095-0.04030.1716-39.0698-33.398540.6576
344.4579-4.6764-2.20354.93822.37585.0506-0.3459-0.40910.06320.31590.3924-0.44050.03260.2356-0.09920.14620.0110.00610.2095-0.04450.30661.54599.21125.4896
351.17410.41750.16933.20144.98857.96730.04990.1236-0.14890.16450.3317-0.27790.18950.6312-0.5010.2111-0.0086-0.04190.3356-0.02760.2206-12.1635-37.73911.8672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 490:502)
2X-RAY DIFFRACTION2chain 'A' and (resseq 503:521)
3X-RAY DIFFRACTION3chain 'A' and (resseq 522:547)
4X-RAY DIFFRACTION4chain 'A' and (resseq 548:594)
5X-RAY DIFFRACTION5chain 'A' and (resseq 595:614)
6X-RAY DIFFRACTION6chain 'A' and (resseq 615:628)
7X-RAY DIFFRACTION7chain 'A' and (resseq 629:646)
8X-RAY DIFFRACTION8chain 'B' and (resseq 488:502)
9X-RAY DIFFRACTION9chain 'B' and (resseq 503:521)
10X-RAY DIFFRACTION10chain 'B' and (resseq 522:571)
11X-RAY DIFFRACTION11chain 'B' and (resseq 572:581)
12X-RAY DIFFRACTION12chain 'B' and (resseq 582:627)
13X-RAY DIFFRACTION13chain 'B' and (resseq 628:644)
14X-RAY DIFFRACTION14chain 'C' and (resseq 490:502)
15X-RAY DIFFRACTION15chain 'C' and (resseq 503:521)
16X-RAY DIFFRACTION16chain 'C' and (resseq 522:571)
17X-RAY DIFFRACTION17chain 'C' and (resseq 572:581)
18X-RAY DIFFRACTION18chain 'C' and (resseq 582:594)
19X-RAY DIFFRACTION19chain 'C' and (resseq 595:614)
20X-RAY DIFFRACTION20chain 'C' and (resseq 615:628)
21X-RAY DIFFRACTION21chain 'C' and (resseq 629:645)
22X-RAY DIFFRACTION22chain 'D' and (resseq 490:511)
23X-RAY DIFFRACTION23chain 'D' and (resseq 512:521)
24X-RAY DIFFRACTION24chain 'D' and (resseq 522:538)
25X-RAY DIFFRACTION25chain 'D' and (resseq 539:548)
26X-RAY DIFFRACTION26chain 'D' and (resseq 549:571)
27X-RAY DIFFRACTION27chain 'D' and (resseq 572:580)
28X-RAY DIFFRACTION28chain 'D' and (resseq 581:594)
29X-RAY DIFFRACTION29chain 'D' and (resseq 595:613)
30X-RAY DIFFRACTION30chain 'D' and (resseq 614:627)
31X-RAY DIFFRACTION31chain 'D' and (resseq 628:644)
32X-RAY DIFFRACTION32chain 'E'
33X-RAY DIFFRACTION33chain 'F'
34X-RAY DIFFRACTION34chain 'G'
35X-RAY DIFFRACTION35chain 'H'

+
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