[English] 日本語
Yorodumi
- PDB-5kvd: Zika specific antibody, ZV-2, bound to ZIKA envelope DIII -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kvd
TitleZika specific antibody, ZV-2, bound to ZIKA envelope DIII
Components
  • (ZV-2 Antibody Fab ...) x 2
  • Zika Envelope DIII
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / ZIKA VIRUS / ENVELOPE DIII / VIRAL PROTEIN / antibody / IgG2c / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID. / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / molecular adaptor activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / centrosome / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus ...Immunoglobulin-like - #350 / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsZhao, H. / Nelson, C.A. / Fremont, D.H. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Cell / Year: 2016
Title: Structural Basis of Zika Virus-Specific Antibody Protection.
Authors: Zhao, H. / Fernandez, E. / Dowd, K.A. / Speer, S.D. / Platt, D.J. / Gorman, M.J. / Govero, J. / Nelson, C.A. / Pierson, T.C. / Diamond, M.S. / Fremont, D.H.
History
DepositionJul 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Zika Envelope DIII
L: ZV-2 Antibody Fab Light Chain
H: ZV-2 Antibody Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3457
Polymers60,0413
Non-polymers3034
Water12,430690
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.020, 113.440, 132.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules E

#1: Protein Zika Envelope DIII


Mass: 11935.734 Da / Num. of mol.: 1 / Fragment: UNP residues 589-697
Source method: isolated from a genetically manipulated source
Details: refolded / Source: (gene. exp.) Zika virus / Strain: French Polynesia H/PF/2013 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: A0A024B7W1, UniProt: A0A0X8GJ44*PLUS

-
Antibody , 2 types, 2 molecules LH

#2: Antibody ZV-2 Antibody Fab Light Chain


Mass: 24081.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: HYBRIDOMA MONOCLONAL ANTIBODY / Source: (natural) Mus musculus (house mouse) / Strain: C57BL/6, Irf3 knockout
#3: Antibody ZV-2 Antibody Fab Heavy Chain


Mass: 24023.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Plasmid details: HYBRIDOMA MONOCLONAL ANTIBODY / Variant: Irf3 knockout / Strain: C57BL/6, Irf3 knockout

-
Non-polymers , 4 types, 694 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH6.5, 0.6 M NaCl and 20.6% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00004 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.65→33.65 Å / Num. obs: 71401 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 20.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.76
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.65-1.690.9892.040.711100
1.69-1.740.8012.590.767199.9
1.74-1.790.593.440.8541100
1.79-1.840.4574.180.9051100
1.84-1.910.4754.080.925194.4
1.91-1.970.2716.570.971194.2
1.97-2.050.2018.980.979199.9
2.05-2.130.1611.950.985199.8
2.13-2.220.12814.280.992199.2
2.22-2.330.10816.470.992197
2.33-2.460.08220.770.9961100
2.46-2.610.06526.390.9971100
2.61-2.790.05330.850.9981100
2.79-3.010.04137.510.9991100
3.01-3.30.03344.210.9991100
3.3-3.690.03245.840.999199.9
3.69-4.260.03148.130.999199.7
4.26-5.220.02460.690.999199.9
5.22-7.380.02261.190.9991100
7.380.02161.040.999194.6

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementResolution: 1.65→33.65 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.13
RfactorNum. reflection% reflection
Rfree0.2212 3558 4.99 %
Rwork0.19 --
obs0.1916 71267 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.48 Å2 / Biso mean: 31.6917 Å2 / Biso min: 10.57 Å2
Refinement stepCycle: final / Resolution: 1.65→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4200 0 18 690 4908
Biso mean--34.31 38.55 -
Num. residues----550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044391
X-RAY DIFFRACTIONf_angle_d0.7525998
X-RAY DIFFRACTIONf_chiral_restr0.049676
X-RAY DIFFRACTIONf_plane_restr0.005757
X-RAY DIFFRACTIONf_dihedral_angle_d12.962652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.67260.30511500.28142600X-RAY DIFFRACTION97
1.6726-1.69650.2681320.27192752X-RAY DIFFRACTION100
1.6965-1.72180.29721580.26232656X-RAY DIFFRACTION100
1.7218-1.74870.26641280.25182709X-RAY DIFFRACTION100
1.7487-1.77740.28561250.24132731X-RAY DIFFRACTION100
1.7774-1.8080.27371520.23542665X-RAY DIFFRACTION100
1.808-1.84090.2551790.22552692X-RAY DIFFRACTION100
1.8409-1.87630.24531370.24612696X-RAY DIFFRACTION100
1.8763-1.91460.3641160.34412414X-RAY DIFFRACTION90
1.9146-1.95630.4111500.34492513X-RAY DIFFRACTION92
1.9563-2.00180.27661330.21512667X-RAY DIFFRACTION100
2.0018-2.05180.25321360.21252765X-RAY DIFFRACTION100
2.0518-2.10730.23181140.19432720X-RAY DIFFRACTION100
2.1073-2.16930.21581330.19132751X-RAY DIFFRACTION100
2.1693-2.23930.22531300.21012634X-RAY DIFFRACTION98
2.2393-2.31930.25861390.24932660X-RAY DIFFRACTION97
2.3193-2.41220.23871420.19622759X-RAY DIFFRACTION100
2.4122-2.52190.21081430.19362722X-RAY DIFFRACTION100
2.5219-2.65490.22141550.19222741X-RAY DIFFRACTION100
2.6549-2.82110.22991610.18682749X-RAY DIFFRACTION100
2.8211-3.03890.1971360.18092763X-RAY DIFFRACTION100
3.0389-3.34450.18881670.16752755X-RAY DIFFRACTION100
3.3445-3.82810.18941490.15062798X-RAY DIFFRACTION100
3.8281-4.82130.17741450.13612844X-RAY DIFFRACTION100
4.8213-33.650.18921480.15782953X-RAY DIFFRACTION99
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)
10.00570.00560.0031-0.0009-0.0013-0.0034-0.07080.00050.0851-0.0656-0.04550.27330.0440.059800.57170.02080.05810.42680.00310.5446-13.191747.279-1.4946
2-0.0134-0.0377-0.01430.0214-0.01190.00360.00410.13330.2605-0.02220.05890.0648-0.22020.1642-0.00010.1815-0.01970.01070.16770.04120.1741-4.66549.0748-14.5086
30.00740.0085-0.0067-0.0009-0.0203-0.020.13870.18160.03740.0368-0.09840.0832-0.0056-0.002-00.14140.02280.01670.22790.04860.1933-17.871937.4797-23.6234
40.0683-0.0781-0.02670.1292-0.01270.01930.04730.10690.10360.1337-0.0277-0.0365-0.1115-0.063300.1829-0.00910.00060.16360.03190.172-5.929744.7912-13.0706
50.0143-0.0203-0.00490.05450.01950.0240.26610.12710.3641-0.07180.08930.0538-0.0772-0.09470.02730.26170.04460.07950.21930.11620.3732-17.077256.4565-21.7574
60.1388-0.03540.03230.01190.01690.04310.086-0.39980.26480.1620.12490.1552-0.1225-0.01420.05940.17290.01870.08750.20750.0020.2894-20.522849.4104-15.0548
70.029-0.0249-0.00120.0991-0.06250.04380.07880.07380.08870.0876-0.0578-0.00130.04110.0337-00.1527-0.0090.00430.18350.03860.1501-6.712841.0592-11.572
80.0113-0.0219-0.01330.07090.04680.0234-0.05810.19630.19890.12450.11080.1305-0.2525-0.15580.01370.1320.03510.01350.28050.10540.2444-20.156649.0778-23.9978
9-0.00010.0019-0.00320.0040.00520.0034-0.0148-0.03130.13980.16920.0111-0.1171-0.11940.0003-00.5213-0.0631-0.00350.21990.05880.3828-5.313156.0178-18.1614
100.10570.0920.04860.0879-0.00380.012-0.06310.34170.01370.1070.15-0.1242-0.1007-0.10210.00580.1796-0.00970.00220.30660.1130.2222-19.655846.6233-27.6042
110.0709-0.02970.10530.1839-0.00480.06660.16640.2092-0.3295-0.2477-0.28460.12120.1223-0.12170.00380.32630.0527-0.00090.3011-0.0540.2059-10.326812.1336-33.504
120.18750.1187-0.05920.6765-0.03390.28430.17240.22010.086-0.2888-0.1697-0.0570.1191-0.00250.00150.18010.0574-0.01470.23810.00890.1149-11.148424.5591-27.478
130.1960.07420.03560.2092-0.03160.09850.19990.0964-0.1117-0.2605-0.2069-0.02120.0065-0.0592-0.00360.28990.0994-0.00180.2555-0.00410.1501-8.006718.7367-32.6461
14-0.01010.0785-0.11550.05520.0198-0.05870.060.1167-0.0208-0.0967-0.0408-0.034-0.0265-0.073900.14430.0188-0.02180.184-0.06310.1504-7.210110.3672-28.222
150.1297-0.20460.14230.09850.16680.39710.04770.0657-0.02440.0813-0.0623-0.03080.1944-0.0635-0.00280.2171-0.0126-0.02110.174-0.08240.21445.3199-15.7477-22.3261
160.1021-0.0520.050.04760.01750.1582-0.02910.0433-0.02590.2950.01670.0661-0.2639-0.0339-0.11570.25430.03180.02420.1953-0.10080.27844.1591-3.706-25.5686
170.06330.0371-0.07160.0077-0.06690.05660.16430.165-0.08250.22030.05350.20420.6459-0.31890.10630.5786-0.1252-0.02810.179-0.03820.27692.9586-22.0874-17.9717
180.07840.04560.01270.05240.03950.05240.30170.89170.11610.26290.1224-0.20550.2489-0.59760.16610.3356-0.1-0.1645-0.2034-0.30350.2127.1278-21.1162-29.5926
190.43650.0148-0.25220.14410.00140.11510.00120.0686-0.04460.0295-0.02790.01220.02220.046400.1238-0.0023-0.00890.0974-0.00620.1241-6.096421.4904-6.1864
200.44960.2171-0.11360.1204-0.12990.29970.12750.13540.0313-0.02830.0030.14630.1766-0.09650.16430.1752-0.0051-0.03630.1207-0.03590.0924-13.422415.6066-12.7178
210.1182-0.0087-0.08140.0211-0.01890.0550.0222-0.00570.05030.0446-0.0111-0.0530.0317-0.10190.00020.1513-0.02630.00980.1377-0.03670.1476-19.879819.145-5.8822
220.3701-0.20290.08690.1659-0.05440.2726-0.00490.0488-0.01650.022-0.02610.03870.0620.0321-00.15170.00060.00850.1195-0.00820.1452-7.793717.5439-7.369
230.00410.01060.01940.05520.00810.02380.18510.007-0.2525-0.0817-0.0625-0.1380.29120.0385-0.04780.41380.148-0.04910.2987-0.21320.377917.1892-17.6174-19.6317
240.0134-0.1611-0.01340.1868-0.18840.2367-0.12430.1153-0.02330.10890.1969-0.0697-0.04560.05490.02430.22570.0133-0.00260.2951-0.12320.289512.0328-5.0847-15.2045
250.0871-0.00920.07170.0933-0.11430.1529-0.1115-0.1172-0.13380.20430.213-0.0869-0.0540.4498-0.00420.29160.0792-0.0350.3676-0.16070.362121.3931-10.4811-12.8445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 298 through 302 )E298 - 302
2X-RAY DIFFRACTION2chain 'E' and (resid 303 through 311 )E303 - 311
3X-RAY DIFFRACTION3chain 'E' and (resid 312 through 322 )E312 - 322
4X-RAY DIFFRACTION4chain 'E' and (resid 323 through 339 )E323 - 339
5X-RAY DIFFRACTION5chain 'E' and (resid 340 through 348 )E340 - 348
6X-RAY DIFFRACTION6chain 'E' and (resid 349 through 358 )E349 - 358
7X-RAY DIFFRACTION7chain 'E' and (resid 359 through 375 )E359 - 375
8X-RAY DIFFRACTION8chain 'E' and (resid 376 through 386 )E376 - 386
9X-RAY DIFFRACTION9chain 'E' and (resid 387 through 392 )E387 - 392
10X-RAY DIFFRACTION10chain 'E' and (resid 393 through 402 )E393 - 402
11X-RAY DIFFRACTION11chain 'L' and (resid 1 through 25 )L1 - 25
12X-RAY DIFFRACTION12chain 'L' and (resid 26 through 61 )L26 - 61
13X-RAY DIFFRACTION13chain 'L' and (resid 62 through 90 )L62 - 90
14X-RAY DIFFRACTION14chain 'L' and (resid 91 through 113 )L91 - 113
15X-RAY DIFFRACTION15chain 'L' and (resid 114 through 155 )L114 - 155
16X-RAY DIFFRACTION16chain 'L' and (resid 156 through 174 )L156 - 174
17X-RAY DIFFRACTION17chain 'L' and (resid 175 through 197 )L175 - 197
18X-RAY DIFFRACTION18chain 'L' and (resid 198 through 214 )L198 - 214
19X-RAY DIFFRACTION19chain 'H' and (resid 2 through 39 )H2 - 39
20X-RAY DIFFRACTION20chain 'H' and (resid 40 through 52 )H40 - 52
21X-RAY DIFFRACTION21chain 'H' and (resid 53 through 66 )H53 - 66
22X-RAY DIFFRACTION22chain 'H' and (resid 67 through 119 )H67 - 119
23X-RAY DIFFRACTION23chain 'H' and (resid 120 through 136 )H120 - 136
24X-RAY DIFFRACTION24chain 'H' and (resid 137 through 194 )H137 - 194
25X-RAY DIFFRACTION25chain 'H' and (resid 195 through 230 )H195 - 230

+
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