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- PDB-8fmf: Structure of CBASS Cap5 from Pseudomonas syringae as an activated... -

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Basic information

Entry
Database: PDB / ID: 8fmf
TitleStructure of CBASS Cap5 from Pseudomonas syringae as an activated tetramer with the cyclic dinucleotide 3'2'-c-diAMP ligand (1 tetramer in the AU)
ComponentsSAVED domain-containing protein
KeywordsIMMUNE SYSTEM / cyclic dinucleotide / bacterial immunity / CBASS / Cap5 effector DNA endonuclease / viral defense
Function / homologyHNH endonuclease / SMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / HNH nuclease / dodecaethylene glycol monomethyl ether / : / HNH endonuclease
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRechkoblit, O. / Kreitler, D.F. / Aggarwal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM13170 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Activation of CBASS Cap5 endonuclease immune effector by cyclic nucleotides.
Authors: Rechkoblit, O. / Sciaky, D. / Kreitler, D.F. / Buku, A. / Kottur, J. / Aggarwal, A.K.
History
DepositionDec 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SAVED domain-containing protein
B: SAVED domain-containing protein
C: SAVED domain-containing protein
D: SAVED domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,53827
Polymers171,0774
Non-polymers4,46123
Water8,161453
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Mass photometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.536, 83.536, 401.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
SAVED domain-containing protein / CBASS Cap5


Mass: 42769.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2P0QGK5

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Non-polymers , 7 types, 476 molecules

#2: Chemical
ChemComp-Y4F / Cyclic (adenosine-(2'-5')-monophosphate-adenosine-(3'-5')-monophosphate


Mass: 658.412 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-RWB / dodecaethylene glycol monomethyl ether / PEG-MME fragment n=12;polyethylene glycol monomethyl ether fragment n=12;PEG 550 MME


Mass: 560.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H52O13
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris, pH 5.5-6.0, 0.2 M magnesium chloride, 19-20% PEG3350
PH range: 5.5-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.1→133.987 Å / Num. obs: 64199 / % possible obs: 94.8 % / Redundancy: 12 % / Biso Wilson estimate: 31.68 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.251 / Net I/σ(I): 8.8
Reflection shellResolution: 2.1→2.32 Å / Rmerge(I) obs: 1.961 / Num. unique obs: 3211 / CC1/2: 0.595

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→66.99 Å / SU ML: 0.2528 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7582
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2367 3210 5 %
Rwork0.1897 60965 -
obs0.1921 64175 66.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.57 Å2
Refinement stepCycle: LAST / Resolution: 2.1→66.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11124 0 280 453 11857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003211679
X-RAY DIFFRACTIONf_angle_d0.557415937
X-RAY DIFFRACTIONf_chiral_restr0.04181781
X-RAY DIFFRACTIONf_plane_restr0.00452089
X-RAY DIFFRACTIONf_dihedral_angle_d15.73344398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.393690.240864X-RAY DIFFRACTION1.79
2.14-2.170.323160.2652240X-RAY DIFFRACTION6.47
2.17-2.210.3104250.2498458X-RAY DIFFRACTION11.72
2.21-2.240.3609320.277663X-RAY DIFFRACTION17.14
2.24-2.280.2938320.2665814X-RAY DIFFRACTION20.62
2.28-2.330.3002580.2549946X-RAY DIFFRACTION24.16
2.33-2.380.3011590.25051135X-RAY DIFFRACTION29.21
2.38-2.430.3239670.25671350X-RAY DIFFRACTION34.43
2.43-2.480.3108790.25241664X-RAY DIFFRACTION42.57
2.48-2.550.32461230.24862401X-RAY DIFFRACTION60.94
2.55-2.610.30411630.25013323X-RAY DIFFRACTION84.08
2.61-2.690.28981850.24763762X-RAY DIFFRACTION94.65
2.69-2.780.28492150.24943908X-RAY DIFFRACTION99.3
2.78-2.880.27032330.23193888X-RAY DIFFRACTION100
2.88-2.990.26272300.22253929X-RAY DIFFRACTION100
2.99-3.130.24722290.19923922X-RAY DIFFRACTION100
3.13-3.290.24472120.18823972X-RAY DIFFRACTION100
3.29-3.50.26241830.17384033X-RAY DIFFRACTION100
3.5-3.770.22271710.16394017X-RAY DIFFRACTION99.98
3.77-4.150.20752060.14554045X-RAY DIFFRACTION99.95
4.15-4.750.17022270.13553997X-RAY DIFFRACTION99.95
4.75-5.980.22122350.17314123X-RAY DIFFRACTION99.98
5.98-66.990.21492210.20174311X-RAY DIFFRACTION99.5
Refinement TLS params.Method: refined / Origin x: -29.706 Å / Origin y: 46.86 Å / Origin z: 32.941 Å
111213212223313233
T0.16796853719 Å20.0252247308634 Å2-0.0284521462316 Å2-0.153618468144 Å20.0281431605744 Å2--0.218068743197 Å2
L0.639819977616 °20.174475838431 °2-0.297150267964 °2-0.464588733732 °20.0190861413997 °2--1.09420546014 °2
S0.0401586946195 Å °0.0700933988406 Å °0.0737117054566 Å °0.00199756661124 Å °9.87771793644E-5 Å °0.077873388597 Å °-0.0576678144251 Å °-0.161278711969 Å °-0.0368527231439 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )A14 - 382
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )A401 - 406
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )A407
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )A408 - 409
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )A501 - 644
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )B15 - 382
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )B401 - 402
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )B403
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )B404
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )B501 - 584
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )C15 - 382
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )C401 - 402
13X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )C403
14X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )C404 - 405
15X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )C501 - 621
16X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )D13 - 382
17X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )D401 - 402
18X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )D403
19X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )D404 - 405
20X-RAY DIFFRACTION1( CHAIN A AND ( RESID 14:382 OR RESID 401:406 OR RESID 407:407 OR RESID 408:409 OR RESID 501:644 ) ) OR ( CHAIN B AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:404 OR RESID 501:584 ) ) OR ( CHAIN C AND ( RESID 15:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:621 ) ) OR ( CHAIN D AND ( RESID 13:382 OR RESID 401:402 OR RESID 403:403 OR RESID 404:405 OR RESID 501:604 ) )D501 - 604

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