[English] 日本語
Yorodumi
- PDB-3e3o: Glycogen phosphorylase R state-IMP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e3o
TitleGlycogen phosphorylase R state-IMP complex
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / GLYCOGENOLYSIS / INHIBITION / TYPE 2 DIABETES / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / Pyridoxal phosphate
Function / homology
Function and homology information


SHG alpha-glucan phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / glycogen phosphorylase activity / glycogen phosphorylase / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Phosphorylase pyridoxal-phosphate attachment site / Glycogen/starch/alpha-glucan phosphorylase / Glycosyl transferase, family 35 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsLeonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Glycogen phosphorylase revisited: extending the resolution of the R- and T-state structures of the free enzyme and in complex with allosteric activators.
Authors: Leonidas, D.D. / Zographos, S.E. / Tsitsanou, K.E. / Skamnaki, V.T. / Stravodimos, G. / Kyriakis, E.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 15, 2021Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycogen phosphorylase, muscle form
B: Glycogen phosphorylase, muscle form
C: Glycogen phosphorylase, muscle form
D: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,23916
Polymers390,0774
Non-polymers2,16112
Water2,090116
1
A: Glycogen phosphorylase, muscle form
B: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1198
Polymers195,0392
Non-polymers1,0816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-81 kcal/mol
Surface area60850 Å2
MethodPISA
2
C: Glycogen phosphorylase, muscle form
D: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,1198
Polymers195,0392
Non-polymers1,0816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-81 kcal/mol
Surface area60420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.680, 188.448, 87.853
Angle α, β, γ (deg.)90.00, 109.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Glycogen phosphorylase, muscle form / / Myophosphorylase / Glycogen phosphorylase b


Mass: 97519.320 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLESkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 7.5
Details: 1.1-1.3M ammonium sulfate, 10mM beta-glycerophosphate buffer pH 7.5, 0.5mM EDTA, MICRODIALYSIS, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8063 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 25, 2006
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8063 Å / Relative weight: 1
ReflectionResolution: 2.6→99 Å / Num. all: 111241 / Num. obs: 105631 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 65.109 Å2 / Rsym value: 0.061 / Net I/σ(I): 7.07
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.62 / Num. unique all: 5388 / Rsym value: 0.441 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2abb
Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 31.917 / SU ML: 0.312 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26703 5573 5 %RANDOM
Rwork0.20073 ---
obs0.20405 105631 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.071 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å2-0.37 Å2
2--0.15 Å20 Å2
3---1.8 Å2
Refine analyzeLuzzati sigma a obs: 0.312 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26382 0 132 116 26630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02227096
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9636680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.27953220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78123.4641374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.193154739
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.98715241
X-RAY DIFFRACTIONr_chiral_restr0.0980.23958
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220669
X-RAY DIFFRACTIONr_nbd_refined0.2170.212352
X-RAY DIFFRACTIONr_nbtor_refined0.310.218056
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2868
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.25
X-RAY DIFFRACTIONr_mcbond_it0.4621.516482
X-RAY DIFFRACTIONr_mcangle_it0.827226009
X-RAY DIFFRACTIONr_scbond_it1.089312003
X-RAY DIFFRACTIONr_scangle_it1.8114.510671
LS refinement shellResolution: 2.597→2.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 414 -
Rwork0.27 7369 -
obs--94.5 %
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)
10.90070.7011-2.10910.5458-1.64184.93890.12750.5962-0.3502-0.4008-0.2017-0.36260.581-0.41360.07420.15330.0822-0.1191-0.1223-0.34530.972956.6782-28.310350.75
21.7050.3248-0.48041.97332.17244.74-0.00880.0885-0.69090.0899-0.0124-0.16250.08220.12430.02120.07890.0084-0.03880.0455-0.10480.435750.325-13.484451.5494
31.44880.7836-0.61620.8504-0.26471.913-0.07440.2713-0.42260.05430.0221-0.1088-0.0667-0.21640.05230.10360.00370.00360.1503-0.20370.336846.7341-8.808137.3986
44.2128-3.78033.14384.0972-3.45962.9245-0.4265-0.12860.43690.50450.0948-0.6013-0.2985-0.12590.33170.1881-0.0109-0.09630.1681-0.12690.221148.05711.761840.8085
53.2261-0.54151.2655-0.45671.3945-0.0960.1811-0.4949-0.0885-0.1154-0.2270.01460.18870.21140.15710.01160.00220.1242-0.16710.289866.8811-5.183733.0949
66.75912.5105-1.0727.7741.87553.49790.4015-0.15870.10650.4405-0.2246-0.3645-0.45830.4182-0.17690.2321-0.0258-0.02630.096-0.08640.077269.338511.21435.8738
73.1251.1251-1.28241.342-0.74291.7192-0.24270.4164-0.9448-0.0889-0.0914-0.23530.15880.00710.33410.0945-0.03620.08160.2268-0.30210.357968.2561-8.961922.0731
81.61930.7303-0.11921.24990.24313.1424-0.17291.0277-0.2466-0.18080.0184-0.02-0.3146-0.19230.15450.0421-0.02510.04650.5271-0.31560.094665.2192.11468.9271
94.07751.015-2.63170.9531-0.94632.9214-0.23581.2319-0.44-0.3070.2632-0.0828-0.0166-0.3916-0.02750.0154-0.13360.02480.5561-0.3840.085145.8677-4.971613.4151
104.20980.48-0.56245.64381.6723.15460.05950.0302-0.43520.39310.11150.15850.0466-0.1731-0.1710.0742-0.05570.00550.2124-0.05480.164823.7751-7.401833.2811
112.31540.3650.50761.709-0.00291.1391-0.09880.37790.2320.04090.15150.0797-0.0645-0.0078-0.05280.0726-0.03310.00160.2588-0.04190.114829.439612.221827.5764
122.12540.23110.27721.43570.27810.6204-0.22770.8335-0.0403-0.19150.26480.1669-0.0774-0.0091-0.03710.0428-0.1436-0.01550.4675-0.10220.016631.00537.593817.1774
136.7782-3.4549-2.2285.82462.16760.9945-0.0782-0.6235-1.50560.5502-0.2420.37340.1207-0.22040.32020.0879-0.0967-0.02860.08140.06820.427450.6274-19.000163.6907
142.7232-0.00010.53112.11780.97882.5110.10280.1032-0.7046-0.0026-0.0652-0.10390.00410.2228-0.03760.1582-0.0244-0.03370.0107-0.06940.432163.8773-16.41954.8411
151.58470.28890.09161.87831.02581.49520.1279-0.1101-0.56110.03080.0168-0.27470.19770.1139-0.14470.1540.004-0.04510.05910.06150.207268.5227-7.175368.8455
1638.39284.47724.77270.52210.55660.5933-0.34151.10270.3617-0.3850.05970.04970.32680.29760.28180.16620.0465-0.00050.28750.02220.106385.08830.350253.2358
171.82420.40520.37972.863-0.66521.36370.01360.0461-0.06370.09810.06510.3488-0.1981-0.0588-0.07870.2316-0.01730.03810.15820.01370.089961.46499.417462.4305
182.8559-3.47991.39959.0025-4.591110.99970.19980.68480.4294-0.8472-0.5123-0.2804-0.19690.11850.31260.3543-0.1040.11440.17330.0235-0.002367.61916.354147.9021
191.63960.21130.51982.00730.15872.9133-0.0121-0.17670.09390.06950.07590.104-0.23620.061-0.06370.2584-0.00660.050.1658-0.00430.059866.653820.77173.4404
201.57130.37660.55692.16120.99511.20060.0004-0.31470.01660.0640.0654-0.2437-0.18840.1181-0.06590.2199-0.04730.06180.2446-0.00690.052979.596715.839381.8711
215.5593-0.8509-2.52144.7502-0.41775.18570.0481-0.2297-1.1356-0.20160.1523-0.30680.4399-0.0851-0.20030.099-0.068-0.1418-0.08110.13430.42187.1421-20.181977.8606
222.65840.68790.30581.1637-0.94232.56940.02510.0631-0.5410.016-0.1055-0.4364-0.10750.04960.08040.11290.0144-0.03840.04080.0060.264899.4562-4.958769.349
232.12980.5839-0.72832.3003-1.01822.00030.0745-0.2218-0.10420.3528-0.2818-0.6499-0.76150.35750.20730.2287-0.0862-0.26880.0470.12910.2165106.9976.631474.5089
242.7314-0.8173-0.41870.8228-0.1711.40320.0786-0.5559-0.53980.3222-0.0438-0.25890.13360.0676-0.03480.2229-0.0445-0.12650.10870.15320.267486.9648-7.204984.0467
250.9774-2.2286-4.74111.727314.763725.3489-0.57040.83690.7085-0.50280.25770.0343-0.92391.26260.3126-0.0478-0.1876-0.09720.46690.33960.3527103.392963.447618.223
261.5396-0.61770.21352.29750.01740.1709-0.01330.16860.47240.23770.05460.0804-0.17520.0858-0.04140.1447-0.08020.01840.12760.07940.1733101.565853.675234.0425
272.4109-1.08815.12530.4911-2.313110.89570.1605-0.32630.34250.5249-0.02310.2254-0.1636-1.158-0.13750.2527-0.05680.12740.306500.101790.215244.294950.076
281.54940.99990.29163.7783-0.35150.6678-0.03560.16170.1138-0.297-0.03580.1380.05360.00750.07140.1529-0.03430.03890.2880.05030.06697.880333.66126.5555
2919.94378.63774.87919.83873.03685.75680.04090.89760.39690.032-0.31391.23030.3953-0.36460.2730.0792-0.01630.11260.3042-0.02680.111681.619728.857933.1727
302.16440.10210.23792.86380.10551.141-0.0660.1032-0.07530.00270.0917-0.20630.14780.1115-0.02570.1163-0.0050.00780.2584-0.03040.0938107.620622.634230.3917
311.6142-0.4135-0.26644.10290.44021.0049-0.00150.0034-0.22770.43220.0239-0.52160.17480.2807-0.02240.14230.0039-0.0930.26830.03610.0982117.88324.656943.3806
322.0748-0.2874-1.24643.44221.19513.87780.07090.02360.73330.486-0.12950.0739-0.78120.18410.05860.3673-0.2785-0.12290.0041-0.00040.1486116.196460.975754.6754
332.17460.4417-0.05981.3703-0.48742.33530.2946-0.26870.10510.6809-0.2672-0.0118-0.32390.0992-0.02740.4333-0.2231-0.07740.0947-0.03230.0152107.693445.45565.0469
341.78422.7409-1.84244.5877-1.98243.80970.285-0.1833-0.02521.0033-0.291-0.75970.08160.47480.0060.4848-0.285-0.45030.20080.1141-0.0163117.06732.375373.3835
353.34470.6853-0.27793.4725-1.32771.33130.5598-0.7742-0.10790.8644-0.43-0.1534-0.08360.1352-0.12980.6066-0.3082-0.18560.1783-0.0399-0.1635107.706438.890574.1449
362.4340.9965-0.65152.86611.93622.82550.27820.02180.35320.2321-0.0992-0.5258-0.26030.3598-0.1790.1532-0.1212-0.0770.25110.04650.2313122.663648.082741.9754
373.7312-2.1503-3.04612.71288.062929.485-0.23370.28330.9779-0.1181-0.05010.267-1.1649-1.23750.28380.142-0.2244-0.0686-0.19920.2660.748190.067272.367922.7203
382.8260.0531-0.45190.07970.27871.1203-0.14030.40660.7569-0.02570.10570.0978-0.09760.170.03460.0991-0.0708-0.0240.10770.32850.414981.774959.28118.8691
391.15220.50610.14230.63490.47631.215-0.0020.5830.2895-0.11470.05470.11670.16740.235-0.05280.1031-0.0387-0.02460.23310.27020.280775.557348.965913.5883
402.70091.223-0.95512.1813-2.06093.62040.1441-0.12110.54880.32790.04440.1153-0.26550.0671-0.18850.1751-0.0037-0.00030.00520.0960.376869.85452.242635.4928
413.0099-1.2795-2.36227.4859-2.52543.6926-0.2667-0.0474-0.15210.1714-0.1493-0.110.59110.42320.41590.22590.01960.10180.04590.08990.215470.794736.820135.1228
421.67190.26140.60162.1903-0.62580.8791-0.03150.00410.6880.2795-0.00170.0243-0.1031-0.03360.03320.1134-0.00590.032-0.00280.11810.48657.823257.508337.2223
431.7590.1971-0.13140.8974-0.41281.4369-0.02380.30010.4788-0.00910.00240.1730.1046-0.22570.02150.083-0.0351-0.0060.07470.17840.422247.745150.640225.233
442.4524-0.1362-0.34773.50261.79672.125-0.44990.52490.2388-0.44150.37740.1476-0.10790.5590.07250.1506-0.0380.07050.45950.51820.230767.708957.8072-7.2134
452.4972-0.09820.41513.5216-0.06313.32030.04091.07160.0743-0.5719-0.0107-0.18540.3726-0.0038-0.03020.1646-0.0780.02330.57440.2145-0.132760.518734.2637-5.9525
460.11280.34620.17892.3983-1.05062.201-0.19071.11361.1647-0.15440.1379-0.10130.2208-0.15330.05280.0333-0.05690.01460.49110.4880.266658.103849.52232.06
471.2869-0.41620.19793.7735-1.19491.8586-0.00381.19830.1808-0.39920.26160.35760.3992-0.5134-0.2578-0.0257-0.2197-0.14040.73660.2636-0.04644.105135.31-3.9931
481.90970.41470.2221.25880.38961.6543-0.00960.95580.563-0.23790.0574-0.03610.1439-0.1524-0.0478-0.0017-0.038-0.04540.48530.45780.179655.013848.90231.0131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 257 - 25
2X-RAY DIFFRACTION2AA26 - 7626 - 76
3X-RAY DIFFRACTION3AA77 - 16177 - 161
4X-RAY DIFFRACTION4AA162 - 187162 - 187
5X-RAY DIFFRACTION5AA188 - 246188 - 246
6X-RAY DIFFRACTION6AA247 - 294247 - 294
7X-RAY DIFFRACTION7AA295 - 360295 - 360
8X-RAY DIFFRACTION8AA361 - 452361 - 452
9X-RAY DIFFRACTION9AA453 - 497453 - 497
10X-RAY DIFFRACTION10AA498 - 560498 - 560
11X-RAY DIFFRACTION11AA561 - 691561 - 691
12X-RAY DIFFRACTION12AA692 - 837692 - 837
13X-RAY DIFFRACTION13BB7 - 337 - 33
14X-RAY DIFFRACTION14BB34 - 6734 - 67
15X-RAY DIFFRACTION15BB68 - 16168 - 161
16X-RAY DIFFRACTION16BB162 - 184162 - 184
17X-RAY DIFFRACTION17BB185 - 246185 - 246
18X-RAY DIFFRACTION18BB247 - 281247 - 281
19X-RAY DIFFRACTION19BB287 - 418287 - 418
20X-RAY DIFFRACTION20BB419 - 498419 - 498
21X-RAY DIFFRACTION21BB499 - 559499 - 559
22X-RAY DIFFRACTION22BB560 - 694560 - 694
23X-RAY DIFFRACTION23BB695 - 773695 - 773
24X-RAY DIFFRACTION24BB774 - 837774 - 837
25X-RAY DIFFRACTION25CC9 - 289 - 28
26X-RAY DIFFRACTION26CC29 - 16329 - 163
27X-RAY DIFFRACTION27CC164 - 188164 - 188
28X-RAY DIFFRACTION28CC189 - 248189 - 248
29X-RAY DIFFRACTION29CC249 - 280249 - 280
30X-RAY DIFFRACTION30CC289 - 412289 - 412
31X-RAY DIFFRACTION31CC413 - 499413 - 499
32X-RAY DIFFRACTION32CC500 - 559500 - 559
33X-RAY DIFFRACTION33CC560 - 702560 - 702
34X-RAY DIFFRACTION34CC703 - 743703 - 743
35X-RAY DIFFRACTION35CC744 - 795744 - 795
36X-RAY DIFFRACTION36CC796 - 837796 - 837
37X-RAY DIFFRACTION37DD8 - 288 - 28
38X-RAY DIFFRACTION38DD29 - 10429 - 104
39X-RAY DIFFRACTION39DD105 - 188105 - 188
40X-RAY DIFFRACTION40DD189 - 243189 - 243
41X-RAY DIFFRACTION41DD244 - 294244 - 294
42X-RAY DIFFRACTION42DD295 - 376295 - 376
43X-RAY DIFFRACTION43DD377 - 505377 - 505
44X-RAY DIFFRACTION44DD506 - 559506 - 559
45X-RAY DIFFRACTION45DD560 - 646560 - 646
46X-RAY DIFFRACTION46DD647 - 701647 - 701
47X-RAY DIFFRACTION47DD702 - 751702 - 751
48X-RAY DIFFRACTION48DD752 - 837752 - 837

+
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