[English] 日本語
Yorodumi
- PDB-6c6y: Crystal structure of Middle-East Respiratory Syndrome (MERS) coro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c6y
TitleCrystal structure of Middle-East Respiratory Syndrome (MERS) coronavirus neutralizing antibody JC57-14 isolated from a vaccinated rhesus macaque in complex with MERS Receptor Binding Domain
Components
  • JC57-14 Heavy chain
  • JC57-14 Light chain
  • Spike glycoprotein
KeywordsIMMUNE SYSTEM / antibody / neutralizing / vaccine
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal ...ubp-family deubiquitinating enzyme fold - #30 / Spike protein, C-terminal core receptor binding subdomain / ubp-family deubiquitinating enzyme fold / Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Single Sheet / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesMacaca mulatta (Rhesus monkey)
Betacoronavirus England 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsJoyce, M.G. / Mascola, J.R. / Graham, B.S. / Kwong, P.D.
CitationJournal: J. Virol. / Year: 2018
Title: Importance of Neutralizing Monoclonal Antibodies Targeting Multiple Antigenic Sites on the Middle East Respiratory Syndrome Coronavirus Spike Glycoprotein To Avoid Neutralization Escape.
Authors: Wang, L. / Shi, W. / Chappell, J.D. / Joyce, M.G. / Zhang, Y. / Kanekiyo, M. / Becker, M.M. / van Doremalen, N. / Fischer, R. / Wang, N. / Corbett, K.S. / Choe, M. / Mason, R.D. / Van Galen, ...Authors: Wang, L. / Shi, W. / Chappell, J.D. / Joyce, M.G. / Zhang, Y. / Kanekiyo, M. / Becker, M.M. / van Doremalen, N. / Fischer, R. / Wang, N. / Corbett, K.S. / Choe, M. / Mason, R.D. / Van Galen, J.G. / Zhou, T. / Saunders, K.O. / Tatti, K.M. / Haynes, L.M. / Kwong, P.D. / Modjarrad, K. / Kong, W.P. / McLellan, J.S. / Denison, M.R. / Munster, V.J. / Mascola, J.R. / Graham, B.S.
History
DepositionJan 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 4, 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: JC57-14 Heavy chain
B: JC57-14 Light chain
H: JC57-14 Heavy chain
L: JC57-14 Light chain
R: Spike glycoprotein
S: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,3157
Polymers139,2196
Non-polymers961
Water00
1
A: JC57-14 Heavy chain
B: JC57-14 Light chain
S: Spike glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7064
Polymers69,6103
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: JC57-14 Heavy chain
L: JC57-14 Light chain
R: Spike glycoprotein


Theoretical massNumber of molelcules
Total (without water)69,6103
Polymers69,6103
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.580, 148.070, 259.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN B AND (RESID 2 THROUGH 104 OR RESID 107...
211(CHAIN L AND (RESID 2 THROUGH 104 OR RESID 107...

-
Components

#1: Antibody JC57-14 Heavy chain


Mass: 23074.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody JC57-14 Light chain


Mass: 23570.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein Spike glycoprotein / S glycoprotein / E2 / Peplomer protein


Mass: 22963.977 Da / Num. of mol.: 2 / Fragment: Receptor Binding Domain residues 381-588
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betacoronavirus England 1 / Gene: S, 3 / Production host: Homo sapiens (human) / References: UniProt: K9N5Q8
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 90 mM CHES pH 9.5, 18% PEG 8,000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 21926 / % possible obs: 91.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 9.96
Reflection shellResolution: 3.3→3.42 Å

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZPT

4zpt


Resolution: 3.32→42.44 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.62
RfactorNum. reflection% reflection
Rfree0.267 971 5.09 %
Rwork0.232 --
obs0.234 19078 80.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 87.41 Å2
Refinement stepCycle: LAST / Resolution: 3.32→42.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9698 0 5 0 9703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029948
X-RAY DIFFRACTIONf_angle_d0.57713576
X-RAY DIFFRACTIONf_dihedral_angle_d14.1865974
X-RAY DIFFRACTIONf_chiral_restr0.0421553
X-RAY DIFFRACTIONf_plane_restr0.0051727
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11B1839X-RAY DIFFRACTIONPOSITIONAL
12L1839X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3169-3.49170.37250.2995424X-RAY DIFFRACTION13
3.4917-3.71040.3136930.30071705X-RAY DIFFRACTION54
3.7104-3.99670.31431630.26513045X-RAY DIFFRACTION96
3.9967-4.39850.26941700.23143175X-RAY DIFFRACTION100
4.3985-5.03410.2421720.19623223X-RAY DIFFRACTION100
5.0341-6.3390.27611660.23553215X-RAY DIFFRACTION100
6.339-42.44630.2381820.22213320X-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)
11.8884-0.51580.87621.78360.33760.6098-0.08440.09581.1563-0.16050.24430.3511-0.8001-0.91160.32320.95690.455-0.28550.85160.1411.007852.94223.6772212.7812
21.8495-0.49790.5541.7355-0.07510.8389-0.14520.08010.5485-0.338-0.01220.5497-0.1742-0.13710.09770.51810.3419-0.24291.06070.11180.779250.3548213.7911207.6672
31.14830.028-0.38810.24270.39660.8326-0.02950.11810.7194-0.05370.12580.2657-0.3492-0.48280.26150.75240.5772-0.19961.03840.09370.89350.3352219.9837214.9068
41.97281.7158-0.56781.5075-0.33421.82120.3162-0.35390.10830.42810.055-0.07060.0070.31360.15220.76780.29060.00130.539-0.20230.619560.059208.0626255.3165
51.8054-1.12760.52160.9431-0.53520.33540.04590.16720.3126-0.0381-0.13870.0675-0.357-0.3334-0.54931.03360.520.00220.8512-0.20580.713857.5292216.4454244.3632
61.0735-0.4203-0.58011.19170.5910.71450.2070.13570.1586-0.1107-0.0808-0.0935-0.2315-0.26830.77620.59960.4155-0.08450.7138-0.2940.57961.0329214.0484246.3771
71.8105-1.1453-1.02132.34130.71230.73690.24780.32280.1915-0.1941-0.23850.0632-0.3461-0.31680.04961.18780.476-0.01290.8974-0.34150.79255.6681222.3238250.0221
81.1051-0.3524-0.02731.1535-0.17841.6017-0.05380.0234-0.0042-0.09950.06130.21590.0973-0.2203-0.29680.28030.1075-0.18090.32290.14650.400167.1736198.7712216.2195
91.06360.7746-1.07521.5269-1.07392.3313-0.3706-0.01740.3235-0.12740.16730.09560.0724-0.2507-0.1880.32060.1838-0.10790.45250.03630.514568.8416205.1577208.1631
108.3749-0.02414.74052.5294-0.43196.3891-0.03710.09790.6652-0.04880.0213-0.232-0.3854-0.04980.09510.33130.0779-0.16190.3256-0.0690.412471.431206.5494217.183
110.67030.2627-0.47591.5778-0.99210.78180.07870.40210.0178-0.13450.23430.4050.3598-0.41430.07170.3670.0976-0.04060.37960.00420.267964.4884202.3805219.0933
126.0084-1.3707-1.86112.1576-0.23135.2543-0.1423-0.71420.39260.90130.00231.3875-0.8047-0.849-0.22670.87830.26310.1470.8954-0.30321.081355.2084205.2406250.7586
133.5015-1.8126-2.25751.6381-0.55645.77110.07340.272-0.1440.0028-0.20961.5359-0.5806-1.3454-0.10660.67150.1559-0.0210.7053-0.36621.152256.7021199.7928242.193
142.849-0.46353.51741.1769-0.34544.3896-0.6033-1.1189-0.46950.99890.19481.4614-0.1611-1.22330.84820.90880.2460.47420.7642-0.04271.548651.3591194.8134253.1185
155.6561-2.14310.99642.49941.90693.269-0.119-1.1186-0.11260.86140.23451.01790.3092-0.2980.19030.94050.04330.31920.3883-0.06810.715860.0717194.1605252.3175
163.6239-0.1218-0.45845.28580.32282.7492-0.17020.7932-0.0753-0.2122-0.24380.4238-0.0302-0.90670.04750.40920.22760.0770.5420.00210.340343.616163.7152251.3395
170.72610.7929-0.53721.1007-1.1061.3802-0.29360.6382-0.1198-0.11410.5890.0817-0.0751-0.93330.08760.31950.1287-0.01870.7624-0.08980.302847.6124165.8273238.0174
185.7649-0.01662.49314.4094-1.53193.1123-0.35640.8055-1.833-1.37970.50.28210.952-0.5893-0.16440.9648-0.29330.22460.9757-0.30411.427655.0652165.8093217.3051
193.0191-1.4073-1.60193.9061-0.38483.29860.27530.07340.37980.2001-0.2175-0.2499-0.5650.20080.10830.4754-0.0690.04330.27210.09520.377367.5022177.4697249.2402
202.68740.5437-0.08612.0603-0.88543.5110.42030.08290.00270.0048-0.4347-0.2902-0.34480.16050.33340.42440.02680.0380.17530.05240.248165.6398170.0343256.3356
210.97130.6819-0.0970.815-0.86343.8576-0.1144-0.03580.21570.1103-0.0237-0.11590.19320.59130.28060.45920.12410.04370.24970.01160.375865.6183172.4974246.4275
223.06910.73241.41090.17880.28161.6866-0.15380.4953-0.1197-0.3057-0.02610.60290.1953-0.4284-0.41570.7922-0.1696-0.42210.5573-0.11120.752354.6147178.0655210.2965
231.4950.92750.44291.10650.49312.09660.17920.0745-0.0074-0.3136-0.15890.6598-0.06350.1084-0.63550.5667-0.0591-0.21780.2794-0.12810.461757.4498178.548218.2436
242.6859-1.6325-0.63752.27380.65431.4228-0.3725-0.34140.02790.18880.21840.0925-0.2863-0.72690.1120.6046-0.0330.0550.5834-0.16590.18662.7241185.3065225.662
255.5753-1.8282-0.17255.3838-0.8583.7739-0.0402-0.13-0.91780.10580.10220.97480.1109-1.18020.16350.6346-0.17030.32680.7524-0.18690.612257.0194180.5891222.837
263.3141-1.3244-0.52412.18190.40932.83140.06110.43620.0509-0.7932-0.20641.0903-0.3935-0.86510.92510.7356-0.2135-0.36341.13020.00750.639755.5371189.4918213.4672
273.34220.744-1.11172.4031-0.04350.389-0.21311.0825-0.2061-1.0498-0.16740.40280.1186-0.2026-0.53510.78840.0616-0.0460.5719-0.03510.203264.5041187.0813214.0575
281.228-0.89660.94710.7606-0.37681.724-0.1298-0.19130.6877-0.0271-0.0835-0.4341-0.97030.6349-4.10611.0097-0.59860.27860.6896-0.33270.646261.4794182.7535282.9763
299.2786-0.5435-1.66430.2274-0.14240.5928-0.0734-0.09982.01770.18180.1374-0.5302-1.8970.97690.24481.8141-1.03030.05222.6995-0.29941.252473.1342180.7254294.615
302.17330.2384-0.37851.92721.19023.25410.1581-0.4684-0.04440.0654-0.1519-0.0217-0.00690.3728-0.18650.4509-0.14740.1030.21-0.11460.181857.7086165.8393278.5781
310.2382-0.26990.19922.61921.01320.83080.3395-0.01051.3369-1.0975-0.0251-1.384-1.53941.3162-0.49421.9149-0.09450.85052.3893-0.3922.535278.3067185.7749287.875
325.37090.8456-1.58045.6959-3.63497.27740.0173-0.8575-1.1696-0.616-0.2389-0.25611.63680.0336-0.98730.8482-0.2047-0.33530.86420.39160.718462.5729190.994187.8065
331.91190.2552-3.25351.1117-1.4756.5446-0.4823-0.8295-1.1780.1411-0.2534-0.09320.91850.25930.93350.9772-0.4269-0.06740.80580.30940.674656.7306190.6627175.6239
340.04590.0060.01142.353-2.78913.32810.27061.7039-0.7679-1.59710.26930.76812.4729-0.20660.19181.84820.1718-0.02921.58740.28491.1772.1617185.1149172.9845
351.8984-0.57060.77430.9748-0.45021.6014-0.1639-0.04960.51670.22690.12950.0664-0.1195-0.81950.35940.4729-0.1206-0.17570.81450.32920.306463.5416208.4291185.0665
362.46380.891-1.38181.93130.54741.45651.8045-2.27031.14580.8674-1.09741.44981.137-1.0101-0.48422.1807-0.93960.20981.84390.55532.882774.593180.3227180.873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 38 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 39 THROUGH 62 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 63 THROUGH 118 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 119 THROUGH 133 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 134 THROUGH 156 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 157 THROUGH 199 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 200 THROUGH 213 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 1 THROUGH 18 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 19 THROUGH 75 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 76 THROUGH 90 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 91 THROUGH 113 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 114 THROUGH 139 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 140 THROUGH 186 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 187 THROUGH 197 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 198 THROUGH 214 )
16X-RAY DIFFRACTION16CHAIN 'H' AND (RESID 1 THROUGH 71 )
17X-RAY DIFFRACTION17CHAIN 'H' AND (RESID 72 THROUGH 142 )
18X-RAY DIFFRACTION18CHAIN 'H' AND (RESID 143 THROUGH 213 )
19X-RAY DIFFRACTION19CHAIN 'L' AND (RESID 1 THROUGH 18 )
20X-RAY DIFFRACTION20CHAIN 'L' AND (RESID 19 THROUGH 75 )
21X-RAY DIFFRACTION21CHAIN 'L' AND (RESID 76 THROUGH 113 )
22X-RAY DIFFRACTION22CHAIN 'L' AND (RESID 114 THROUGH 126 )
23X-RAY DIFFRACTION23CHAIN 'L' AND (RESID 127 THROUGH 139 )
24X-RAY DIFFRACTION24CHAIN 'L' AND (RESID 140 THROUGH 150 )
25X-RAY DIFFRACTION25CHAIN 'L' AND (RESID 151 THROUGH 186 )
26X-RAY DIFFRACTION26CHAIN 'L' AND (RESID 187 THROUGH 197 )
27X-RAY DIFFRACTION27CHAIN 'L' AND (RESID 198 THROUGH 214 )
28X-RAY DIFFRACTION28CHAIN 'R' AND (RESID 381 THROUGH 425 )
29X-RAY DIFFRACTION29CHAIN 'R' AND (RESID 426 THROUGH 439 )
30X-RAY DIFFRACTION30CHAIN 'R' AND (RESID 440 THROUGH 576 )
31X-RAY DIFFRACTION31CHAIN 'R' AND (RESID 577 THROUGH 588 )
32X-RAY DIFFRACTION32CHAIN 'S' AND (RESID 381 THROUGH 410 )
33X-RAY DIFFRACTION33CHAIN 'S' AND (RESID 411 THROUGH 426 )
34X-RAY DIFFRACTION34CHAIN 'S' AND (RESID 427 THROUGH 439 )
35X-RAY DIFFRACTION35CHAIN 'S' AND (RESID 440 THROUGH 576 )
36X-RAY DIFFRACTION36CHAIN 'S' AND (RESID 577 THROUGH 588 )

+
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