[English] 日本語
Yorodumi
- PDB-5ed2: Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ed2
TitleHuman Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from human GLI1 gene
Components
  • Double-stranded RNA-specific editase 1
  • RNA (5'-R(P*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')
  • RNA (5'-R(P*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')
KeywordsHYDROLASE/RNA / deaminase / human / HYDROLASE-RNA complex
Function / homology
Function and homology information


hypoglossal nerve morphogenesis / muscle tissue morphogenesis / facial nerve morphogenesis / spinal cord ventral commissure morphogenesis / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / adenosine to inosine editing / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity ...hypoglossal nerve morphogenesis / muscle tissue morphogenesis / facial nerve morphogenesis / spinal cord ventral commissure morphogenesis / C6 deamination of adenosine / Formation of editosomes by ADAR proteins / double-stranded RNA adenine deaminase / adenosine to inosine editing / tRNA-specific adenosine deaminase activity / double-stranded RNA adenosine deaminase activity / negative regulation of protein kinase activity by regulation of protein phosphorylation / base conversion or substitution editing / neuromuscular process controlling posture / neuromuscular synaptic transmission / innervation / motor behavior / motor neuron apoptotic process / positive regulation of viral genome replication / RNA processing / negative regulation of cell migration / multicellular organism growth / mRNA processing / double-stranded RNA binding / defense response to virus / regulation of cell cycle / negative regulation of cell population proliferation / innate immune response / mRNA binding / synapse / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
ADAR2, first double-stranded RNA binding domain / ADAR2, second double-stranded RNA binding domain / Adenosine deaminase/editase / Adenosine-deaminase (editase) domain / Adenosine to inosine editase domain profile. / tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase) / Cytokine IL1/FGF / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / RNA / RNA (> 10) / Double-stranded RNA-specific editase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMatthews, M.M. / Fisher, A.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM061115 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity.
Authors: Matthews, M.M. / Thomas, J.M. / Zheng, Y. / Tran, K. / Phelps, K.J. / Scott, A.I. / Havel, J. / Fisher, A.J. / Beal, P.A.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 14, 2020Group: Derived calculations / Structure summary / Category: chem_comp / struct_conn / struct_conn_type
Item: _chem_comp.pdbx_synonyms / _struct_conn.conn_type_id ..._chem_comp.pdbx_synonyms / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Double-stranded RNA-specific editase 1
B: RNA (5'-R(P*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')
C: RNA (5'-R(P*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')
D: Double-stranded RNA-specific editase 1
E: RNA (5'-R(P*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')
F: RNA (5'-R(P*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,96110
Polymers119,5116
Non-polymers1,4514
Water00
1
A: Double-stranded RNA-specific editase 1
B: RNA (5'-R(P*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')
C: RNA (5'-R(P*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4815
Polymers59,7553
Non-polymers7252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-87 kcal/mol
Surface area22530 Å2
MethodPISA
2
D: Double-stranded RNA-specific editase 1
E: RNA (5'-R(P*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')
F: RNA (5'-R(P*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4815
Polymers59,7553
Non-polymers7252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-87 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.130, 81.614, 256.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Double-stranded RNA-specific editase 1 / adenosine deaminase acting on RNA


Mass: 45004.398 Da / Num. of mol.: 2 / Fragment: A to I editase (UNP residues 327-729) / Mutation: E488Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADAR2, DRADA2, RED1 / Plasmid: pSc / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BCY123
References: UniProt: P78563, double-stranded RNA adenine deaminase
#2: RNA chain RNA (5'-R(P*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')


Mass: 7415.422 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: RNA chain RNA (5'-R(P*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3')


Mass: 7335.472 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 65.22 % / Description: diamond-shaped prism
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES/NaOH, pH 6.5, 12% PEG20000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 35355 / % possible obs: 98.1 % / Redundancy: 5.19 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.27
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 5.13 % / Rmerge(I) obs: 1.351 / Mean I/σ(I) obs: 1.16 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZY7

1zy7


Resolution: 2.95→39.565 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1742 4.94 %Random selection
Rwork0.1879 ---
obs0.1889 35272 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→39.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6038 1950 74 0 8062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078420
X-RAY DIFFRACTIONf_angle_d0.88511838
X-RAY DIFFRACTIONf_dihedral_angle_d15.223432
X-RAY DIFFRACTIONf_chiral_restr0.0341396
X-RAY DIFFRACTIONf_plane_restr0.0041166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.03680.41691410.34112757X-RAY DIFFRACTION98
3.0368-3.13480.31461260.29972702X-RAY DIFFRACTION96
3.1348-3.24680.33461270.28522789X-RAY DIFFRACTION99
3.2468-3.37670.29641270.25172798X-RAY DIFFRACTION100
3.3767-3.53030.28561720.2292768X-RAY DIFFRACTION100
3.5303-3.71630.20691380.20662809X-RAY DIFFRACTION99
3.7163-3.94890.18891330.1992745X-RAY DIFFRACTION96
3.9489-4.25350.21221410.17212792X-RAY DIFFRACTION99
4.2535-4.6810.17811720.15272804X-RAY DIFFRACTION99
4.681-5.35690.17711430.15792774X-RAY DIFFRACTION97
5.3569-6.74370.20011770.16912828X-RAY DIFFRACTION99
6.7437-39.56850.15291450.15062964X-RAY DIFFRACTION97
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)
11.99162.01748.69382.00468.2755.80640.94040.8025-1.33350.06590.0873-1.01910.8719-0.6658-0.2821.41920.0706-0.08051.0732-0.00750.964536.200138.0965103.0173
24.8832-0.01820.64865.6509-0.63826.564-0.13890.59880.5735-0.2390.0034-0.7968-0.80021.60280.12210.4622-0.0780.16080.93330.15630.670335.52837.351980.8116
33.6729-0.85320.5914.7452-0.88464.0416-0.0844-0.0493-0.46460.1572-0.1297-0.83060.48241.45540.18360.5060.21180.14651.24860.20420.702140.157725.024687.1031
43.25132.04070.06766.81754.90237.55611.04650.02591.91780.92741.24651.9337-0.0866-1.637-1.0140.96960.34950.1261.09880.11151.381614.126544.7994.956
56.6589-0.1869-3.18912.8014-2.65457.68950.0095-0.32370.06310.30810.45911.0595-0.5167-0.5412-0.51180.49220.09990.14020.92510.36160.860610.560331.494184.9009
61.37351.35572.87151.33242.83615.87970.66420.4849-1.02980.0164-0.7912.15010.7036-1.3773-0.00821.0667-0.2919-0.03231.10140.16691.073710.653819.254172.7057
76.0687-0.74120.37994.4857-1.96235.51980.12150.2909-0.6524-0.6814-0.1408-0.06280.85011.0245-0.00040.51430.20660.12630.7220.04660.548629.83222.982880.5096
84.6815-2.50464.31822.04-0.6554.29711.26321.17030.81410.28760.86392.1674-0.7399-0.8668-1.34390.7306-0.08280.31291.34960.65411.3034-2.743128.45591.6182
94.5105-0.3555-3.03144.99894.46135.53830.03481.80411.5791-0.47230.64861.17331.06810.1057-0.23480.9802-0.02110.05151.950.99821.528-7.031337.065179.7293
104.741-0.9303-1.11370.50591.00353.02250.3970.3840.2212-0.25990.75871.6049-1.4424-0.7033-0.89560.78580.25890.42221.11320.83011.378511.27342.497376.6541
112.894.7876-1.03189.2512-4.25384.86250.35270.67981.5926-0.4526-0.01222.1547-0.67861.1972-0.51711.2334-0.10980.10981.59190.66441.260914.915648.813660.1307
124.33740.03181.38622.04583.24547.8702-1.48310.90760.9257-1.25592.0633-0.1978-1.78290.0401-0.45071.3338-0.13380.40270.91750.18591.202126.077960.936262.3497
134.3905-1.7165-2.49665.2918-5.79612.0383-1.23370.25880.0828-1.50961.82570.52530.1323-1.1481-0.491.4076-0.39670.58821.39520.43251.281229.107252.200464.5188
146.66345.36251.95334.57871.38164.5301-0.3658-0.25260.44740.13960.95892.1876-1.0093-0.2816-0.5080.95730.05190.27481.21290.53241.435613.869554.377968.1667
152.1244-0.8814-0.20924.8992-4.47647.7570.24281.09461.0179-0.3551.13941.996-0.7698-1.5286-1.39330.72060.09780.13211.27270.57081.18966.747837.649972.8657
160.4236-0.83481.25711.5836-2.41563.33650.0003-0.27931.7323-0.04910.37971.13450.4347-1.8297-0.27170.73780.30840.40231.39030.4671.731-3.538540.865288.1494
176.6822.7528-1.66861.2162-1.14024.5561.01170.5181.06351.02270.0640.8359-0.3059-0.4579-0.3780.748-0.07980.2091.97370.82981.5593-12.332328.045690.2637
181.9897-9.22937.27847.2298-5.68784.46740.5305-0.7024-1.768-0.64550.62611.7908-0.2037-0.7849-0.83541.05140.0372-0.12931.19350.08570.86717.950627.847939.1417
194.51560.17521.29995.0016-1.51414.07980.3181-0.0683-0.3179-0.2901-0.1418-0.45160.34790.2859-0.13340.7245-0.04710.09750.4417-0.21670.563716.06426.825316.3815
206.2523.4306-1.2528.304-3.22062.96750.7454-0.9623-0.37850.9968-0.6439-0.09170.04230.0021-0.07390.8004-0.13930.0170.7374-0.11690.36727.559725.686125.7286
213.27720.479-1.02639.86846.11564.42080.2223-0.57280.8937-0.17120.4579-0.2792-0.6380.5339-0.55180.93910.01740.23630.65-0.24060.77058.823551.18815.9095
228.58180.6119-0.38848.0171-1.28913.294-0.67721.20891.4396-0.89410.73750.5098-1.184-0.2255-0.31281.36430.069-0.20911.1770.10441.1226-1.667644.1055-0.3008
233.42880.3687-0.62055.197-0.67673.73870.3083-0.45060.29140.2875-0.0477-0.2540.09380.0047-0.20980.6249-0.160.05630.4771-0.16520.48428.541934.164420.4748
243.55940.9758-0.26996.91360.38442.8740.05360.446-0.2407-0.5911-0.03031.26170.6727-0.6680.0190.7284-0.2004-0.11440.692-0.13140.6884-4.57126.678811.6505
257.4618-0.5029-5.25782.0361-1.8564.22070.9701-1.34372.5021-1.46590.9528-0.4146-1.13621.0386-1.1811.31750.11740.45960.9665-0.50181.32525.49565.351321.9383
263.84231.6431-0.7126.8796-1.65357.4515-0.13440.81250.5059-1.8453-0.2245-1.6335-0.3628-1.2530.59392.16220.26450.84431.1799-0.11341.559713.654468.63189.6242
270.4120.86620.8915.73580.57715.85270.60670.02721.512-0.42980.0859-0.8775-0.59110.6948-0.73070.9659-0.01960.49830.6728-0.25511.290820.474950.33328.6455
287.0807-2.34911.14122.8339-2.71682.72330.19860.82251.8413-0.8424-0.1327-1.18490.97340.54520.03741.77020.35820.6331.3033-0.20961.237726.569444.6222-7.5367
298.63032.35262.92152.65635.16092.04962.22612.29030.21750.4501-1.3631-0.36240.35790.4406-0.7771.18820.30220.34791.0379-0.31351.361939.475534.8277-4.4612
303.98140.5828-3.52014.44944.26398.46770.34461.4204-0.0053-0.1225-0.5508-0.3321-1.0485-0.8902-0.04291.0460.2130.82430.9997-1.01751.808731.120232.0599-1.7423
312.1104-7.3005-0.32897.0517-0.26371.24170.0691-0.18632.5837-0.25280.0029-2.8897-0.3703-0.1844-0.03971.31350.09160.55910.7377-0.03391.6128.784949.3104-0.6474
325.4927-2.2537-0.93345.27832.72995.92590.9741-0.10891.7093-0.4881-0.1554-0.03811.12860.7012-0.58141.05870.04960.31920.5976-0.10050.862312.535554.08977.5836
330.01330.0591-0.05770.17210.0026-0.0021.4185-1.26522.8273-0.7719-0.3328-1.6963-2.1961-0.3714-0.76551.5596-0.09530.71370.6828-0.48651.996917.881766.406518.286
343.4957-3.14532.10114.110.79846.9278-0.5099-1.52862.0387-1.05090.4427-1.4512-0.1369-0.45440.31992.03890.33870.78930.993-0.14631.67064.326674.589919.5826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 316:321)
2X-RAY DIFFRACTION2(chain A and resid 322:393)
3X-RAY DIFFRACTION3(chain A and resid 394:457)
4X-RAY DIFFRACTION4(chain A and resid 458:466)
5X-RAY DIFFRACTION5(chain A and resid 467:492)
6X-RAY DIFFRACTION6(chain A and resid 493:501)
7X-RAY DIFFRACTION7(chain A and resid 502:700)
8X-RAY DIFFRACTION8(chain B and resid 1:4)
9X-RAY DIFFRACTION9(chain B and resid 5:8)
10X-RAY DIFFRACTION10(chain B and resid 9:15)
11X-RAY DIFFRACTION11(chain B and resid 16:19)
12X-RAY DIFFRACTION12(chain B and resid 20:23)
13X-RAY DIFFRACTION13(chain C and resid 1:4)
14X-RAY DIFFRACTION14(chain C and resid 5:8)
15X-RAY DIFFRACTION15(chain C and resid 9:14)
16X-RAY DIFFRACTION16(chain C and resid 15:19)
17X-RAY DIFFRACTION17(chain C and resid 20:23)
18X-RAY DIFFRACTION18(chain D and resid 316:320)
19X-RAY DIFFRACTION19(chain D and resid 321:405)
20X-RAY DIFFRACTION20(chain D and resid 406:468)
21X-RAY DIFFRACTION21(chain D and resid 469:493)
22X-RAY DIFFRACTION22(chain D and resid 494:509)
23X-RAY DIFFRACTION23(chain D and resid 510:616)
24X-RAY DIFFRACTION24(chain D and resid 617:700)
25X-RAY DIFFRACTION25(chain E and resid 1:4)
26X-RAY DIFFRACTION26(chain E and resid 5:8)
27X-RAY DIFFRACTION27(chain E and resid 9:15)
28X-RAY DIFFRACTION28(chain E and resid 16:19)
29X-RAY DIFFRACTION29(chain E and resid 20:23)
30X-RAY DIFFRACTION30(chain F and resid 1:4)
31X-RAY DIFFRACTION31(chain F and resid 5:10)
32X-RAY DIFFRACTION32(chain F and resid 11:14)
33X-RAY DIFFRACTION33(chain F and resid 15:19)
34X-RAY DIFFRACTION34(chain F and resid 20:23)

+
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