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- PDB-6a42: R1EN(5-223)-ubiquitin fusion -

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Basic information

Entry
Database: PDB / ID: 6a42
TitleR1EN(5-223)-ubiquitin fusion
ComponentsRNA-directed DNA polymerase homolog (R1),Polyubiquitin-C
KeywordsDNA BINDING PROTEIN / Endonuclease / Chimera
Function / homology
Function and homology information


Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A ...Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKBKE / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Activation of NF-kappaB in B cells / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / CLEC7A (Dectin-1) signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / Assembly of the pre-replicative complex
Similarity search - Function
Endonuclease-reverse transcriptase / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase superfamily / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Ubiquitin family ...Endonuclease-reverse transcriptase / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase superfamily / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
ACETIC ACID / Polyubiquitin-C / RNA-directed DNA polymerase homolog (R1)
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMaita, N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K13747 Japan
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Crystal Structure Determination of Ubiquitin by Fusion to a Protein That Forms a Highly Porous Crystal Lattice
Authors: Maita, N.
History
DepositionJun 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / 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
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed DNA polymerase homolog (R1),Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1782
Polymers33,1181
Non-polymers601
Water3,207178
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.206, 141.206, 37.905
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

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Components

#1: Protein RNA-directed DNA polymerase homolog (R1),Polyubiquitin-C


Mass: 33117.719 Da / Num. of mol.: 1 / Mutation: E44A
Source method: isolated from a genetically manipulated source
Details: Fusion protein, R1BmEN & Ubiquitin
Source: (gene. exp.) Bombyx mori (domestic silkworm), (gene. exp.) Bos taurus (cattle)
Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7M4J4, UniProt: P0CH28, RNA-directed DNA polymerase
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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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: 3.29 Å3/Da / Density % sol: 62.66 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 2.0M sodium acetate, 10mM ammonium sulfate, 1% Jeffamine M600,
PH range: 7.3-8.2

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 3, 2015
RadiationMonochromator: Silica / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 45813 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.06 / Rrim(I) all: 0.144 / Χ2: 0.97 / Net I/σ(I): 11.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1724 / CC1/2: 0.76 / Rpim(I) all: 0.408 / Rrim(I) all: 0.961 / Χ2: 0.83 / % possible all: 68.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ei9
Resolution: 1.7→36.23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.988 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22001 2156 4.7 %RANDOM
Rwork0.19105 ---
obs0.19245 43652 95.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.738 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.1 Å20 Å2
2--0.19 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.7→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 4 178 2462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0142388
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172135
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.6483244
X-RAY DIFFRACTIONr_angle_other_deg1.0221.6334999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3915302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15320.597134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98115397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0411523
X-RAY DIFFRACTIONr_chiral_restr0.0930.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022738
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02435
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9083.0281197
X-RAY DIFFRACTIONr_mcbond_other2.9033.0271195
X-RAY DIFFRACTIONr_mcangle_it4.1424.521496
X-RAY DIFFRACTIONr_mcangle_other4.1424.5231497
X-RAY DIFFRACTIONr_scbond_it4.0413.4921191
X-RAY DIFFRACTIONr_scbond_other4.0393.4911192
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0795.0321747
X-RAY DIFFRACTIONr_long_range_B_refined8.02129.1042200
X-RAY DIFFRACTIONr_long_range_B_other8.01929.1082201
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 107 -
Rwork0.286 2375 -
obs--70.37 %

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