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- PDB-8ams: Complex of human TRIM2 RING domain, UBCH5C, and Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 8ams
TitleComplex of human TRIM2 RING domain, UBCH5C, and Ubiquitin
Components
  • Polyubiquitin-C
  • Tripartite motif-containing protein 2
  • Ubiquitin-conjugating enzyme E2 D3
KeywordsANTIVIRAL PROTEIN / E3 ligase / zinc-binding / TRIM proteins / E2 conjugating enzyme / Ubiquitin / RING domain
Function / homology
Function and homology information


protein K6-linked ubiquitination / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / negative regulation of BMP signaling pathway / protein monoubiquitination / protein K48-linked ubiquitination ...protein K6-linked ubiquitination / Signaling by BMP / (E3-independent) E2 ubiquitin-conjugating enzyme / protein K11-linked ubiquitination / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / negative regulation of BMP signaling pathway / protein monoubiquitination / protein K48-linked ubiquitination / protein autoubiquitination / regulation of neuron apoptotic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / cellular response to leukemia inhibitory factor / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Degradation of AXIN / Stabilization of p53 / Hh mutants are degraded by ERAD
Similarity search - Function
: / NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains ...: / NHL repeat profile. / NHL repeat / NHL repeat / B-box, C-terminal / B-Box C-terminal domain / Zinc finger, RING-type, eukaryotic / RING-type zinc-finger / Filamin/ABP280 repeat / Filamin-type immunoglobulin domains / Filamin/ABP280 repeat / Filamin/ABP280 repeat profile. / Filamin/ABP280 repeat-like / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Six-bladed beta-propeller, TolB-like / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D3 / Tripartite motif-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPerez-Borrajero, C. / Kotova, I. / Murciano, B. / Hennig, J.
Funding support Germany, 2items
OrganizationGrant numberCountry
EIPOD fellowship under Marie Sklodowska-Curie Actions COFUND664726 Germany
German Research Foundation (DFG)HE 7291_1 Germany
Citation
Journal: To Be Published
Title: Structural and biophysical studies of TRIM2 and TRIM3
Authors: Perez-Borrajero, C. / Hennig, J.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
#3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: Features and development of Coot.
Authors: P Emsley / B Lohkamp / W G Scott / K Cowtan /
Abstract: Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations ...Coot is a molecular-graphics application for model building and validation of biological macromolecules. The program displays electron-density maps and atomic models and allows model manipulations such as idealization, real-space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers and Ramachandran idealization. Furthermore, tools are provided for model validation as well as interfaces to external programs for refinement, validation and graphics. The software is designed to be easy to learn for novice users, which is achieved by ensuring that tools for common tasks are 'discoverable' through familiar user-interface elements (menus and toolbars) or by intuitive behaviour (mouse controls). Recent developments have focused on providing tools for expert users, with customisable key bindings, extensions and an extensive scripting interface. The software is under rapid development, but has already achieved very widespread use within the crystallographic community. The current state of the software is presented, with a description of the facilities available and of some of the underlying methods employed.
#4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: XDS.
Authors: Kabsch, W.
#5: Journal: J Synchrotron Radiat / Year: 2020
Title: ID30A-3 (MASSIF-3) - a beamline for macromolecular crystallography at the ESRF with a small intense beam.
Authors: von Stetten, D. / Carpentier, P. / Flot, D. / Beteva, A. / Caserotto, H. / Dobias, F. / Guijarro, M. / Giraud, T. / Lentini, M. / McSweeney, S. / Royant, A. / Petitdemange, S. / Sinoir, J. / ...Authors: von Stetten, D. / Carpentier, P. / Flot, D. / Beteva, A. / Caserotto, H. / Dobias, F. / Guijarro, M. / Giraud, T. / Lentini, M. / McSweeney, S. / Royant, A. / Petitdemange, S. / Sinoir, J. / Surr, J. / Svensson, O. / Theveneau, P. / Leonard, G.A. / Mueller-Dieckmann, C.
History
DepositionAug 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D3
B: Ubiquitin-conjugating enzyme E2 D3
C: Tripartite motif-containing protein 2
D: Tripartite motif-containing protein 2
E: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,84019
Polymers79,3795
Non-polymers1,46114
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.120, 69.270, 151.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 0 and (name N or name...
d_2ens_1(chain "B" and (resid 0 or resid 2 through 15...
d_1ens_2(chain "C" and (resid 10 through 21 or (resid 22...
d_2ens_2(chain "D" and (resid 10 through 14 or (resid 15...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISHISA2
d_12ens_1ALAARGA4 - 17
d_13ens_1ALAGLNA21 - 22
d_14ens_1ARGPROA24 - 27
d_15ens_1GLYPHEA29 - 33
d_16ens_1TRPTRPA35
d_17ens_1ALASERA37 - 93
d_18ens_1TRPILEA95 - 101
d_19ens_1LYSPROA103 - 115
d_110ens_1PROASPA117 - 118
d_111ens_1PROTHRA120 - 131
d_112ens_1ARGASNA133 - 137
d_113ens_1ILEMETA139 - 149
d_21ens_1HISHISB2
d_22ens_1ALAARGB4 - 17
d_23ens_1ALAGLNB20 - 21
d_24ens_1ARGPROB23 - 26
d_25ens_1GLYPHEB28 - 32
d_26ens_1TRPTRPB34
d_27ens_1ALASERB36 - 92
d_28ens_1TRPILEB94 - 100
d_29ens_1LYSPROB102 - 114
d_210ens_1PROASPB116 - 117
d_211ens_1PROTHRB119 - 130
d_212ens_1ARGASNB132 - 136
d_213ens_1ILEMETB138 - 148
d_11ens_2SERLYSC1 - 22
d_12ens_2PROLEUC24 - 77
d_13ens_2ASPARGC79 - 83
d_21ens_2SERLYSD2 - 23
d_22ens_2PROLEUD25 - 78
d_23ens_2ASPARGD80 - 84

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.550713783446, -0.777427585624, 0.303843179673), (0.798002508116, 0.597123957774, 0.0814553625745), (-0.244757687851, 0.197609028548, 0.949233557179)23.7658187242, -19.2166396075, -13.0491156012
2given(0.612428262141, 0.764070327129, -0.20280078632), (0.752874713601, -0.641968820656, -0.145105819751), (-0.241062832788, -0.0638166789022, -0.968409077891)29.5389773189, -65.6162503806, -9.53999310035

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Components

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Protein , 3 types, 5 molecules ABCDE

#1: Protein Ubiquitin-conjugating enzyme E2 D3 / (E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


Mass: 16955.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D3, UBC5C, UBCH5C / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P61077, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Protein Tripartite motif-containing protein 2 / E3 ubiquitin-protein ligase TRIM2 / RING finger protein 86 / RING-type E3 ubiquitin transferase TRIM2


Mass: 16914.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM2, KIAA0517, RNF86 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9C040, RING-type E3 ubiquitin transferase
#3: Protein Polyubiquitin-C


Mass: 11639.206 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48

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Non-polymers , 4 types, 172 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.26 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium formate, 0.1 M bis-tris propane, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.295→40.92 Å / Num. obs: 32226 / % possible obs: 97.52 % / Redundancy: 12.7 % / Biso Wilson estimate: 50.47 Å2 / CC1/2: 0.993 / Net I/σ(I): 14.54
Reflection shellResolution: 2.295→2.377 Å / Num. unique obs: 2629 / CC1/2: 0.549

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJan 10, 2022data scaling
XDSJan 10, 2022data reduction
MxCuBEdata collection
PHENIX1.20.1_4487phasing
Coot0.9.8.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RING domain of TRIM2, Ubiquitin

Resolution: 2.4→40.92 Å / SU ML: 0.3798 / Cross valid method: FREE R-VALUE / Phase error: 27.072
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2326 1606 4.97 %
Rwork0.2141 51463 -
obs0.215 32103 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.47 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4088 0 83 158 4329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124332
X-RAY DIFFRACTIONf_angle_d1.67835912
X-RAY DIFFRACTIONf_chiral_restr0.0837693
X-RAY DIFFRACTIONf_plane_restr0.0057753
X-RAY DIFFRACTIONf_dihedral_angle_d17.1871613
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONcartesian NCS0.742597886007
ens_2d_2CX-RAY DIFFRACTIONcartesian NCS0.714085992862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.40721390.40322698X-RAY DIFFRACTION99.27
2.44-2.490.43711430.34292725X-RAY DIFFRACTION99.51
2.49-2.540.34031440.29172683X-RAY DIFFRACTION99.72
2.54-2.60.24061410.26362698X-RAY DIFFRACTION99.72
2.6-2.660.28841420.2712698X-RAY DIFFRACTION99.86
2.66-2.720.26451420.26512713X-RAY DIFFRACTION99.72
2.72-2.80.37351400.28852711X-RAY DIFFRACTION99.72
2.8-2.880.3261410.2632730X-RAY DIFFRACTION99.93
2.88-2.970.28711430.24132703X-RAY DIFFRACTION100
2.97-3.080.2611410.23942701X-RAY DIFFRACTION100
3.08-3.20.28781360.23482720X-RAY DIFFRACTION100
3.2-3.350.28531440.21562733X-RAY DIFFRACTION99.93
3.35-3.520.23411470.20412692X-RAY DIFFRACTION100
3.52-3.740.19991460.19292721X-RAY DIFFRACTION99.97
3.74-4.030.17741390.17582722X-RAY DIFFRACTION99.97
4.03-4.440.18611390.17422705X-RAY DIFFRACTION99.89
4.44-5.080.1641410.16962705X-RAY DIFFRACTION99.79
5.08-6.40.20261430.20432727X-RAY DIFFRACTION99.97
6.4-40.920.2111410.20622678X-RAY DIFFRACTION98.77

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