[English] 日本語
Yorodumi
- PDB-3l27: Crystal structure of Zaire Ebola VP35 interferon inhibitory domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3l27
TitleCrystal structure of Zaire Ebola VP35 interferon inhibitory domain R312A mutant
ComponentsPolymerase cofactor VP35
KeywordsRNA BINDING PROTEIN / RNA BINDING DOMAIN / INTERFERON ANTIVIRAL EVASION / RNA REPLICATION / RNA-BINDING PROTEIN / TRANSCRIPTION / Host cytoplasm / Interferon antiviral system evasion / RNA-binding / Virion
Function / homology
Function and homology information


suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / molecular sequestering activity / positive regulation of protein sumoylation ...suppression by virus of host cytokine production / symbiont-mediated suppression of host defenses / symbiont-mediated suppression of host RNAi-mediated antiviral immune response / negative regulation of miRNA-mediated gene silencing / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / suppression by virus of host type I interferon production / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / molecular sequestering activity / positive regulation of protein sumoylation / : / viral transcription / viral genome replication / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / viral nucleocapsid / host cell cytoplasm / negative regulation of gene expression / RNA binding
Similarity search - Function
Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 ...Filoviridae VP35, C-terminal inhibitory domain, beta-sheet subdomain / Filoviridae VP35, C-terminal inhibitory domain, helical subdomain / Filoviruses VP35 interferon inhibitory domain, beta-sheet subdomain / Filoviridae VP35 protein / Filoviruses VP35 interferon inhibitory domain / Filoviruses VP35 interferon inhibitory domain, helical subdomain / Filoviridae VP35 / Filoviruses VP35 interferon inhibitory domain profile. / Seminal Fluid Protein PDC-109 (Domain B) / Helicase, Ruva Protein; domain 3 / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / PHOSPHATE ION / Polymerase cofactor VP35
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLeung, D.W. / Prins, K.C. / Borek, D.M. / Farahbakhsh, M. / Tufariello, J.M. / Ramanan, P. / Nix, J.C. / Helgeson, L.A. / Otwinowski, Z. / Honzatko, R.B. ...Leung, D.W. / Prins, K.C. / Borek, D.M. / Farahbakhsh, M. / Tufariello, J.M. / Ramanan, P. / Nix, J.C. / Helgeson, L.A. / Otwinowski, Z. / Honzatko, R.B. / Basler, C.F. / Amarasinghe, G.K.
Citation
#1: Journal: To be Published
Title: Preliminary X-ray studies of the Ebola VP35 IFN inhibitory domain mutants that display diminished dsRNA binding and immune suppression.
Authors: Leung, D.W. / Prins, K.C. / Borek, D.M. / Farahbakhsh, M. / Tufariello, J.M. / Ramanan, P. / Nix, J.C. / Helgeson, L.A. / Otwinowski, Z. / Honzatko, R.B. / Basler, C.F. / Amarasinghe, G.K.
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polymerase cofactor VP35
B: Polymerase cofactor VP35
C: Polymerase cofactor VP35
D: Polymerase cofactor VP35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,58732
Polymers56,4984
Non-polymers2,09028
Water5,927329
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.549, 81.549, 343.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Polymerase cofactor VP35


Mass: 14124.408 Da / Num. of mol.: 4 / Fragment: INTERFERON INHIBITORY DOMAIN / Mutation: R312A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: VP35 / Plasmid: MODIFIED PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL(21)DE3 / References: UniProt: Q05127

-
Non-polymers , 6 types, 357 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.92 Å3/Da / Density % sol: 57.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.15
Details: 1.85 M SODIUM PHOSPHATE, 0.15 M POTASSIUM PHOSPHATE, pH 4.15, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2009
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 50802 / Num. obs: 50802 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 27
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2481 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.3.0037refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FKE

3fke


Resolution: 1.95→40.79 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 5.909 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22893 2348 5.1 %RANDOM
Rwork0.17619 ---
all0.17884 50802 --
obs0.17884 43621 90.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.607 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.02 Å20 Å2
2---0.05 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 114 329 4260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224188
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9845694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1345527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26323.757173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50915704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.3171528
X-RAY DIFFRACTIONr_chiral_restr0.0990.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023152
X-RAY DIFFRACTIONr_nbd_refined0.2170.22032
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22872
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2284
X-RAY DIFFRACTIONr_metal_ion_refined0.2120.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.2107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.232
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2220.24
X-RAY DIFFRACTIONr_mcbond_it0.7541.52594
X-RAY DIFFRACTIONr_mcangle_it1.27324236
X-RAY DIFFRACTIONr_scbond_it2.41231598
X-RAY DIFFRACTIONr_scangle_it3.8684.51458
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 81 -
Rwork0.181 1301 -
obs--38.06 %
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)
110.3847-8.41325.13577.6334-4.563611.4216-0.0859-0.48240.3890.2883-0.15390.2441-0.7011-0.27250.23990.10670.0071-0.0318-0.0027-0.0640.109311.376-10.27821.321
21.88880.8082-0.69411.4011-0.31854.4871-0.07-0.12610.0702-0.04290.1218-0.0832-0.29950.069-0.05180.1315-0.0063-0.00020.0316-0.00630.04721.072-15.39121
313.14193.0808-2.03129.1165-2.49665.1762-0.03470.69950.7792-0.32990.11420.1709-0.4453-0.4594-0.07950.14260.0542-0.06270.06640.02120.03489.267-11.5911.835
45.1015-0.15221.20340.73010.08411.0215-0.0134-0.2221-0.1084-0.15810.0338-0.11370.14210.0012-0.02040.11030.0006-0.03520.09080.0130.051311.353-25.06520.454
54.0374-2.87682.05752.8477-1.2797.7862-0.00770.3059-0.251-0.58730.15420.0130.01570.0322-0.14650.1458-0.0112-0.04550.0334-0.00520.04914.986-21.94511.157
617.92127.51164.13437.3471-0.46936.24310.28760.15560.75690.0498-0.5638-0.0647-0.29760.15760.27620.16010.00350.0894-0.03060.04890.089929.403-10.5049.83
76.01551.8713-3.063716.81114.078922.48410.1718-1.0304-0.2002-0.30660.0955-0.9544-1.07291.8988-0.26730.0326-0.16930.02140.2053-0.02230.009934.915-14.91321.104
85.3956-1.5466-0.97812.2558-2.4584.71420.19750.41790.0755-0.3327-0.0568-0.11890.27020.0926-0.14070.1768-0.00850.04920.0307-0.0051-0.007629.106-18.9016.971
912.584210.5074-2.340323.4327-3.65317.0044-0.15710.16510.3498-0.53590.0769-0.9771-0.51990.7330.08020.1166-0.09340.05150.08190.02650.105535.97-12.310.302
106.3072.95683.38954.31681.70517.7502-0.0785-0.1636-0.18160.1469-0.0150.28840.1056-0.32270.09350.1017-0.0007-0.01270.07190.01540.0619-7.453-39.59822.015
111.47680.11030.18823.72630.4572.78520.0165-0.0487-0.037-0.1439-0.07220.25490.0339-0.36980.05580.0762-0.0007-0.05070.09680.01690.0331-6.713-35.75415.216
122.4248-0.44080.2614.04390.54951.3008-0.04840.00740.25890.09690.0934-0.1644-0.0120.0838-0.0450.13630.0134-0.0290.08190.01230.04995.01-40.92219.239
135.90110.7439-0.23612.4574-1.47264.3430.14830.56240.0769-0.35030.0079-0.2307-0.02750.0919-0.15610.14840.0151-0.02840.06870.0070.03651.411-37.1139.501
1420.014-10.8392-12.62810.906910.838119.0688-0.2379-0.9111-0.2159-0.58490.23230.4611-0.24630.54710.00560.0937-0.005-0.11330.05150.0482-0.0081-8.023-25.697.884
1517.3533-7.68934.52274.54981.808513.9-0.7806-0.74550.55650.59330.33430.3925-0.9073-0.82520.44630.24490.0858-0.01680.0508-0.0350.1045-6.925-17.06721.477
160.8079-1.38330.39663.06741.74448.5971-0.1849-0.04450.0974-0.28550.1249-0.0405-0.33990.4370.06010.2073-0.0158-0.0820.0537-0.0150.0315-0.629-19.2157.1
176.7885-1.40973.10585.96450.96773.56180.05210.17570.1817-0.40320.005-0.1810.01770.2123-0.05710.18110.0143-0.04560.06240.032-0.0046-0.537-25.6998.675
1812.5143-1.43542.87265.6254-2.59937.1567-0.0904-0.14830.715-0.00290.11560.392-0.8669-0.5382-0.02520.26850.0561-0.09040.0047-0.02960.0796-7.573-16.39712.326
1915.9286-5.31756.315721.2678-9.168520.8546-0.21190.0559-0.6132-0.1379-0.1532-1.13740.77060.99560.36510.05130.02740.00340.050.00150.13573.181-39.732-18.078
202.15420.2976-0.92871.78431.00546.9719-0.02010.14590.0569-0.0521-0.1196-0.1753-0.22560.25540.13970.0912-0.0102-0.030.0750.0010.0473-3.576-29.476-19.891
217.38094.45380.83057.886-1.16426.47470.0149-0.4582-0.26470.462-0.2356-0.34320.13230.26660.22060.1140.0679-0.06790.07480.01790.0285-0.602-40.144-10.034
222.05490.51760.59035.57310.08270.3536-0.0443-0.0429-0.0126-0.25260.0616-0.0043-0.00150.0647-0.01730.1322-0.0205-0.02160.06780.00310.0401-12.959-38.762-19.497
230.8571-0.70910.93026.8288-5.840215.67740.0978-0.1041-0.21820.30550.06090.3889-0.0329-0.3201-0.15870.1159-0.0155-0.01410.07560.00060.0796-12.547-35.093-11.783
240.7968-0.121.43052.7441.38653.5097-0.10740.29160.04930.47840.2145-0.4939-0.19290.2034-0.10710.104-0.0178-0.07850.1278-0.00340.0771-0.936-24.319-6.759
255.9961-3.2995-4.11125.8082.985124.05180.13290.30980.1844-0.45070.0515-0.3031-1.1072-0.1887-0.18440.2048-0.0543-0.0551-0.03760.02920.0365-5.99-15.551-14.952
262.69892.32736.477215.30737.639715.8618-0.1907-0.1915-0.0430.98040.21220.45660.158-0.6073-0.02150.21090.0227-0.02140.07990.01020.0411-9.476-24.155-0.478
278.67571.86633.77527.6440.22695.9095-0.25970.01920.45510.178-0.0263-0.3655-0.6340.34890.2860.1866-0.0474-0.10120.02010.01970.0161-2.442-17.034-7.398
2813.9858-9.1139-8.94576.28497.257911.62270.0061-0.2888-0.41090.0882-0.0754-0.40060.5997-0.01890.06930.17320.01710.0694-0.02650.07940.133322.013-63.63716.778
294.3357-0.08182.05041.6874-1.08534.0415-0.1837-0.2042-0.1863-0.19980.15570.05420.1941-0.15690.0280.1387-0.02160.01430.02350.03040.044111.559-57.29319.473
305.0382.1042-2.04925.1160.28033.7835-0.24750.3625-0.5074-0.55610.1173-0.21810.34020.12070.13020.20630.01110.05890.0404-0.01690.053721.651-58.7719.35
313.51731.4855-0.73332.19490.32484.8607-0.1032-0.04940.021-0.23690.11530.0218-0.0320.026-0.01210.1215-0.00780.03720.02560.01090.041919.128-48.11114.239
328.72380.9269-0.29971.45890.00163.47750.1190.4121-0.5486-0.2911-0.00660.20690.2006-0.1776-0.11240.1992-0.0206-0.0466-0.0891-0.03870.03263.325-60.588.543
3318.8801-13.21512.667144.46430.314717.51090.2152-1.5022-0.28171.18460.35171.417-0.0924-1.3736-0.56690.0426-0.09450.01360.220.0962-0.0316-1.952-55.60521.252
3410.52850.30661.44890.42941.17853.27030.03531.11390.0958-0.41320.0972-0.011-0.34150.0337-0.13250.223-0.052-0.0280.08760.0533-0.01332.482-51.1734.786
354.97646.38690.636817.8741-1.36472.4425-0.10820.0804-0.3222-0.74680.26591.00580.4209-0.1324-0.15780.2191-0.0658-0.08760.00690.01380.1067-1.819-60.2877.891
367.17414.42315.184814.07594.75416.8494-0.0066-0.4247-0.0631-0.264-0.15030.51680.0554-0.43690.15680.1357-0.0397-0.04320.02750.0220.0353-2.092-55.3629.311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A218 - 228
2X-RAY DIFFRACTION2A229 - 248
3X-RAY DIFFRACTION3A249 - 260
4X-RAY DIFFRACTION4A261 - 274
5X-RAY DIFFRACTION5A275 - 287
6X-RAY DIFFRACTION6A288 - 300
7X-RAY DIFFRACTION7A301 - 310
8X-RAY DIFFRACTION8A311 - 328
9X-RAY DIFFRACTION9A329 - 340
10X-RAY DIFFRACTION10B218 - 233
11X-RAY DIFFRACTION11B234 - 260
12X-RAY DIFFRACTION12B261 - 276
13X-RAY DIFFRACTION13B277 - 287
14X-RAY DIFFRACTION14B288 - 297
15X-RAY DIFFRACTION15B298 - 310
16X-RAY DIFFRACTION16B311 - 319
17X-RAY DIFFRACTION17B320 - 327
18X-RAY DIFFRACTION18B328 - 340
19X-RAY DIFFRACTION19C218 - 226
20X-RAY DIFFRACTION20C227 - 245
21X-RAY DIFFRACTION21C246 - 261
22X-RAY DIFFRACTION22C262 - 274
23X-RAY DIFFRACTION23C275 - 283
24X-RAY DIFFRACTION24C284 - 303
25X-RAY DIFFRACTION25C304 - 314
26X-RAY DIFFRACTION26C315 - 322
27X-RAY DIFFRACTION27C323 - 340
28X-RAY DIFFRACTION28D218 - 227
29X-RAY DIFFRACTION29D228 - 245
30X-RAY DIFFRACTION30D246 - 263
31X-RAY DIFFRACTION31D264 - 285
32X-RAY DIFFRACTION32D286 - 304
33X-RAY DIFFRACTION33D305 - 309
34X-RAY DIFFRACTION34D310 - 323
35X-RAY DIFFRACTION35D324 - 332
36X-RAY DIFFRACTION36D333 - 340

+
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