[English] 日本語
Yorodumi
- PDB-5e6o: Crystal structure of C. elegans LGG-2 bound to an AIM/LIR motif -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e6o
TitleCrystal structure of C. elegans LGG-2 bound to an AIM/LIR motif
Components
  • Protein lgg-2
  • TRP-GLU-GLU-LEU
KeywordsPROTEIN BINDING/PEPTIDE / ubiquitin-like protein / Atg8 protein family / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


PINK1-PRKN Mediated Mitophagy / KEAP1-NFE2L2 pathway / Receptor Mediated Mitophagy / Macroautophagy / cellular response to toxic substance / xenophagy / plasma membrane repair / cellular response to nitrogen starvation / positive regulation of autophagosome maturation / autophagosome maturation ...PINK1-PRKN Mediated Mitophagy / KEAP1-NFE2L2 pathway / Receptor Mediated Mitophagy / Macroautophagy / cellular response to toxic substance / xenophagy / plasma membrane repair / cellular response to nitrogen starvation / positive regulation of autophagosome maturation / autophagosome maturation / autophagosome membrane / autophagosome assembly / autophagosome / macroautophagy / cytoplasmic vesicle / microtubule binding / defense response to Gram-positive bacterium / ubiquitin protein ligase binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesCaenorhabditis elegans (invertebrata)
Scheffersomyces stipitis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsQi, X. / Ren, J.Q. / Wu, F. / Zhang, H. / Feng, W.
CitationJournal: Mol.Cell / Year: 2015
Title: Structural Basis of the Differential Function of the Two C. elegans Atg8 Homologs, LGG-1 and LGG-2, in Autophagy
Authors: Wu, F. / Watanabe, Y. / Guo, X.Y. / Qi, X. / Wang, P. / Zhao, H.Y. / Wang, Z. / Fujioka, Y. / Zhang, H. / Ren, J.Q. / Fang, T.C. / Shen, Y.X. / Feng, W. / Hu, J.J. / Noda, N.N. / Zhang, H.
History
DepositionOct 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein lgg-2
B: Protein lgg-2
C: Protein lgg-2
D: Protein lgg-2
E: TRP-GLU-GLU-LEU
F: TRP-GLU-GLU-LEU
G: TRP-GLU-GLU-LEU
H: TRP-GLU-GLU-LEU


Theoretical massNumber of molelcules
Total (without water)57,6988
Polymers57,6988
Non-polymers00
Water8,467470
1
A: Protein lgg-2
H: TRP-GLU-GLU-LEU


Theoretical massNumber of molelcules
Total (without water)14,4242
Polymers14,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-4 kcal/mol
Surface area7320 Å2
MethodPISA
2
B: Protein lgg-2
E: TRP-GLU-GLU-LEU


Theoretical massNumber of molelcules
Total (without water)14,4242
Polymers14,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-4 kcal/mol
Surface area7260 Å2
MethodPISA
3
C: Protein lgg-2
G: TRP-GLU-GLU-LEU


Theoretical massNumber of molelcules
Total (without water)14,4242
Polymers14,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-5 kcal/mol
Surface area7270 Å2
MethodPISA
4
D: Protein lgg-2
F: TRP-GLU-GLU-LEU


Theoretical massNumber of molelcules
Total (without water)14,4242
Polymers14,4242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-5 kcal/mol
Surface area7220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.933, 62.351, 67.599
Angle α, β, γ (deg.)90.000, 109.540, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Protein lgg-2


Mass: 13848.853 Da / Num. of mol.: 4 / Fragment: UNP residues 17-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lgg-2, ZK593.6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q23536
#2: Protein/peptide
TRP-GLU-GLU-LEU


Mass: 575.610 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Scheffersomyces stipitis (fungus)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 1.79 Å3/Da / Density % sol: 31.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1.5M sodium citrate tribasic dihydrate / PH range: 5.9 - 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.8→47.07 Å / Num. obs: 36467 / % possible obs: 99 % / Redundancy: 6.8 % / Net I/σ(I): 18.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 4.1 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data collection
HKL-3000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.058 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 1816 4.99 %
Rwork0.1774 34552 -
obs0.1806 36368 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.89 Å2 / Biso mean: 24.1879 Å2 / Biso min: 8.29 Å2
Refinement stepCycle: final / Resolution: 1.8→47.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3979 0 0 470 4449
Biso mean---34.95 -
Num. residues----477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084076
X-RAY DIFFRACTIONf_angle_d1.1435489
X-RAY DIFFRACTIONf_chiral_restr0.066574
X-RAY DIFFRACTIONf_plane_restr0.006729
X-RAY DIFFRACTIONf_dihedral_angle_d15.541612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7979-1.84650.33051500.2352617276799
1.8465-1.90090.28331310.213426562787100
1.9009-1.96220.25711390.204426212760100
1.9622-2.03240.26281420.196526542796100
2.0324-2.11370.25741360.191326482784100
2.1137-2.20990.23091070.186126822789100
2.2099-2.32650.24551490.180426562805100
2.3265-2.47220.21951300.179526642794100
2.4722-2.66310.26031470.191926812828100
2.6631-2.9310.26231480.187426452793100
2.931-3.35510.2241350.168526732808100
3.3551-4.22660.24581460.142526862832100
4.2266-47.07420.19761560.16772669282598
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)
18.9453-2.9264-2.26497.4682-0.61847.38520.27970.2332-0.6003-0.56740.19950.33060.3429-0.1088-0.46620.1646-0.0084-0.03150.10930.00220.1824-12.1297-16.7356-22.186
29.42783.91863.30314.35382.49823.9840.2052-0.35-0.04490.4233-0.1709-0.13730.2063-0.1771-0.07890.24650.03720.01240.18930.00090.1261-6.4137-7.6171-14.4697
31.92160.461.33931.25010.87774.9003-0.0245-0.1146-0.19670.15490.2318-0.4061-0.17120.3745-0.21730.1382-0.0003-0.00260.2128-0.03560.16-0.7563-6.3713-24.3236
43.18290.73210.3582.88770.64083.13020.1602-0.0297-0.24010.3970.0406-0.09250.39930.0501-0.17340.13120.0451-0.03650.1586-0.00310.1539-3.361-11.9261-32.9337
53.4979-1.0213-1.76575.41393.54152.8479-0.06650.0482-0.0841-0.20810.2081-0.3139-0.18170.2051-0.110.1263-0.01160.04080.17470.0230.15251.731-7.1385-38.3901
62.0041-0.0171-0.40792.37740.84391.67330.03690.03760.1201-0.0196-0.067-0.177-0.05190.119-0.00290.1317-0.0114-0.00790.11810.03090.1226-6.3155-3.5102-37.0276
71.557-0.62551.25240.9413-0.54432.4702-0.0651-0.024-0.02960.04650.00290.0227-0.0871-0.02340.02770.0952-0.0210.01560.09330.01440.1262-11.1571-7.3453-32.8257
84.21431.0767-1.96872.96381.98653.52490.0457-0.293-0.5343-0.13720.07380.00331.1473-0.0336-0.140.2555-0.02450.00240.17830.04050.2542-37.029-16.1243-21.3963
93.28763.63732.28324.20981.87173.12930.3745-0.29440.05230.2354-0.15770.12910.1062-0.0085-0.21930.17370.02210.00760.19940.00340.1613-29.9023-7.2671-14.1828
101.8171-0.69790.42361.43411.18484.0310.0286-0.2365-0.01660.125-0.2302-0.04220.18830.01790.15470.0886-0.004-0.00160.09190.01770.1062-26.6004-7.4101-25.6554
112.8723-1.8693-0.18313.07430.68412.58490.2262-0.066-0.48820.0935-0.0093-0.05460.7513-0.5177-0.24580.2149-0.05920.01870.1724-0.02210.2648-32.1134-18.5831-35.7085
122.38141.6433-0.98536.3194-3.07332.91280.1552-0.25830.16690.1674-0.0985-0.0584-0.21640.2428-0.06990.12960.00110.01430.186-0.06560.1586-22.2394-3.5896-27.5721
132.65010.5408-1.70746.9413.43054.24380.179-0.0497-0.10670.1819-0.0090.06030.1792-0.1229-0.12780.0724-0.0075-0.00630.07920.01330.065-22.3201-7.1836-37.8033
143.0786-3.5969-3.71926.87073.75376.32430.07620.15830.4851-0.1262-0.0101-0.5095-0.0674-0.1284-0.15940.1018-0.0241-0.01340.13040.00140.1973-27.8141-11.146-43.394
156.45771.8936-2.86023.3408-0.87481.427-0.14620.7176-0.5424-0.4420.00110.38970.162-1.24580.08030.2908-0.133-0.07030.4434-0.00760.3187-32.3710.2661-36.2885
169.11341.8385-1.91962.22430.24192.58780.07270.08590.2833-0.2284-0.0540.12910.1444-0.12-0.03290.1692-0.0360.00660.08250.02480.1889-30.51473.0586-27.7431
172.5894-3.82933.16486.5079-5.72955.18620.27790.24050.0380.2066-0.0820.3106-0.1104-0.1629-0.28430.12730.01820.00350.1356-0.0170.1976-35.3118-3.547-21.0171
181.6828-1.24230.25971.9685-1.563.360.18820.1668-0.1916-0.1908-0.02750.0527-0.11570.1361-0.17290.1399-0.01250.00210.1413-0.01050.1795-36.4199-9.2529-38.7935
196.43410.19124.27889.5526-3.49654.3015-0.22430.29520.25850.1039-0.07130.0944-1.09010.10940.30620.2839-0.0029-0.04040.1649-0.00850.1591-15.367710.7672-53.5346
209.58074.3321-0.04683.72690.14351.40360.2004-0.3533-0.01140.108-0.21230.0203-0.0385-0.03160.04480.16010.00960.00190.11630.02720.0823-20.45371.8964-46.4626
212.0812.3634-2.99533.5371-3.91285.9617-0.0851-0.07570.0265-0.06910.03180.16080.0982-0.11430.00550.1082-0.0028-0.00190.1815-0.00780.1406-26.22911.354-56.279
225.024-0.2783-0.09085.9577-1.25667.103-0.15640.07520.24180.19490.0327-0.1021-0.33920.16850.08850.120.0192-0.02670.13440.01240.1721-19.99713.5935-67.3867
232.39350.9171-0.06745.51862.4673.05250.2011-0.3852-0.1474-0.1957-0.148-0.08070.1969-0.5758-0.04120.1767-0.0142-0.03260.26540.07350.1445-29.5661-1.8378-60.2805
245.8778-0.79850.50012.6556-2.19084.11810.32230.025-0.2534-0.1794-0.03480.46470.0228-0.4201-0.2250.1323-0.016-0.00730.27010.01720.1488-29.49362.4512-70.2334
257.5475-4.46833.51456.001-3.86725.67450.04220.10070.0627-0.090.13150.4341-0.0032-0.2181-0.15020.1189-0.0192-0.00970.14270.02640.1537-24.10657.2405-75.4889
269.81927.8077-0.64166.1452-0.60010.6274-0.24970.1624-0.7042-0.43890.2473-0.49090.28020.058-0.00030.26660.00790.00360.2116-0.01410.1928-18.1662-5.497-68.6041
272.25070.1781.28023.344-2.46013.62730.03070.4718-0.1787-0.57640.1891-0.06650.4735-0.0055-0.14660.2643-0.02350.01850.1152-0.04360.2347-20.8895-8.1543-60.8934
280.395-0.14461.05981.8915-2.6325.40280.0056-0.0215-0.0397-0.0358-0.0113-0.02530.13300.03220.11660.0050.00730.1442-0.00030.1406-16.68052.3032-63.2923
296.04-0.56663.83153.883-3.53985.1789-0.4108-0.08020.57160.38430.06610.2421-0.9868-0.11080.3380.25780.0107-0.04940.1705-0.02480.25889.842811.0512-53.6798
309.76132.9366-2.4012.4931-0.81011.5677-0.0158-0.98190.2425-0.0957-0.06040.1064-0.11510.02040.03910.2190.0394-0.02290.1981-0.01330.14563.33461.942-46.2768
312.2113-1.1579-0.5090.6814-0.33333.4057-0.23110.0676-0.1473-0.01790.0406-0.08620.0926-0.10840.19990.1229-0.0204-0.00590.12890.01290.1033-0.5851.3565-57.6271
323.8237-0.8607-0.93533.6228-0.68785.5195-0.03850.21530.4241-0.1868-0.0369-0.2933-0.18680.25830.05730.1974-0.0044-0.00960.17060.04790.2394.992813.6017-67.4759
333.80452.57120.62397.96172.64213.49750.14820.00160.09060.2151-0.08140.35540.4548-0.3877-0.08590.2158-0.0170.01930.21740.03920.1398-4.588-1.7666-60.1538
344.9856-1.29291.81252.24260.26823.25190.29160.52330.0724-0.1039-0.3380.02280.2365-0.2020.04990.1308-0.00760.00160.23620.01050.153-4.31152.9871-70.156
358.6346-5.98784.71476.119-4.36673.18760.31620.4048-0.0071-0.50030.03950.27990.3533-0.0113-0.32430.2154-0.0378-0.0130.23070.04840.18951.24476.8146-75.8775
366.21491.7004-1.85460.6233-0.66370.6795-0.16740.7818-0.6147-0.69580.1279-0.31090.51660.24020.03250.41380.0396-0.00970.3295-0.02270.15846.9944-5.4298-68.4176
379.06724.93542.6984.1864-0.13872.4846-0.08250.317-0.6955-0.31660.0371-0.26340.91980.22910.020.40570.0033-0.01220.1507-0.03380.20093.8476-8.2213-60.5729
380.8548-0.24290.80813.4076-2.82075.9512-0.05270.20580.0196-0.23150.0169-0.11190.27230.11640.06880.1323-0.00530.00770.19150.00610.16798.33852.3008-63.2734
395.3859-0.35762.01237.3064-0.460.85460.2202-0.0310.0375-0.039-0.243-0.43880.24520.19620.06940.17660.03120.0120.2569-0.05590.1529-21.0547-10.9928-24.7097
404.7388-1.93521.6371.8127-2.49924.02190.10420.3469-0.14720.05020.13220.2753-0.2837-0.3154-0.22620.2598-0.0122-0.02910.33940.04480.2281-6.01935.4308-56.7934
413.4271-1.7215-1.39564.2628-0.04313.86390.07810.01840.1910.30460.4882-0.3091-0.33780.0874-0.40150.52830.0692-0.00190.4193-0.00870.3823-30.86325.5002-56.6804
427.8933-0.5161-2.81673.7147-1.44221.77080.11271.001-0.5826-0.2331-0.3581-0.05720.68181.02760.24140.30560.1113-0.02510.5178-0.00360.25663.9384-10.3797-24.868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 22 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 34 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 47 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 48 through 69 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 80 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 81 through 112 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 113 through 130 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 15 through 22 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 36 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 37 through 47 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 48 through 60 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 61 through 69 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 70 through 80 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 81 through 93 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 94 through 104 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 105 through 112 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 113 through 118 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 119 through 130 )B0
19X-RAY DIFFRACTION19chain 'C' and (resid 15 through 22 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 23 through 34 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 35 through 47 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 48 through 60 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 61 through 69 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 70 through 80 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 81 through 93 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 94 through 104 )C0
27X-RAY DIFFRACTION27chain 'C' and (resid 105 through 112 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 113 through 128 )C0
29X-RAY DIFFRACTION29chain 'D' and (resid 15 through 22 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 23 through 36 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 37 through 47 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 48 through 60 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 61 through 69 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 70 through 81 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 82 through 93 )D0
36X-RAY DIFFRACTION36chain 'D' and (resid 94 through 104 )D0
37X-RAY DIFFRACTION37chain 'D' and (resid 105 through 112 )D0
38X-RAY DIFFRACTION38chain 'D' and (resid 113 through 128 )D0
39X-RAY DIFFRACTION39chain 'E' and (resid 1 through 4 )E0
40X-RAY DIFFRACTION40chain 'F' and (resid 1 through 4 )F0
41X-RAY DIFFRACTION41chain 'G' and (resid 1 through 4 )G0
42X-RAY DIFFRACTION42chain 'H' and (resid 1 through 4 )H0

+
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