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- PDB-7mic: Maize rayado fino virus protease in complex with Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 7mic
TitleMaize rayado fino virus protease in complex with Ubiquitin
Components
  • RNA replication protein
  • Ubiquitin
KeywordsVIRAL PROTEIN / HYDROLASE/SUBSTRATE / Protease / Deubiquitinase / PRO Replicase Protein / Ubiquitin / HYDROLASE-SUBSTRATE complex
Function / homology
Function and homology information


mRNA methyltransferase activity / mRNA modification / RNA processing / 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 ...mRNA methyltransferase activity / mRNA modification / RNA processing / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / Transferases; Transferring one-carbon groups; Methyltransferases / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Regulation of signaling by CBL / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN / Stabilization of p53 / Recognition of DNA damage by PCNA-containing replication complex / Regulation of TNFR1 signaling / Activation of NF-kappaB in B cells / Negative regulation of FGFR2 signaling / EGFR downregulation / Degradation of GLI1 by the proteasome / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / G2/M Checkpoints
Similarity search - Function
Peptidase C21 / Tymovirus endopeptidase domain / Salyut domain / Tymovirus endopeptidase / Salyut domain / Peptidase family C21 domain profile. / Tymovirus coat protein / Tymovirus coat protein / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain ...Peptidase C21 / Tymovirus endopeptidase domain / Salyut domain / Tymovirus endopeptidase / Salyut domain / Peptidase family C21 domain profile. / Tymovirus coat protein / Tymovirus coat protein / Viral methyltransferase / Alphavirus-like methyltransferase (MT) domain / Alphavirus-like methyltransferase (MT) domain profile. / Tymovirus, RNA-dependent RNA polymerase / RNA dependent RNA polymerase / Viral (Superfamily 1) RNA helicase / Viral coat protein subunit / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Ubiquitin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
3-AMINOPROPANE / Polyubiquitin-C / Genome polyprotein
Similarity search - Component
Biological speciesMaize rayado fino virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsPatel, A. / Mark, B.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: The endopeptidase of the maize-affecting Marafivirus type member maize rayado fino virus doubles as a deubiquitinase.
Authors: Patel, A. / McBride, J.A.M. / Mark, B.L.
History
DepositionApr 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA replication protein
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2425
Polymers24,9982
Non-polymers2433
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-6 kcal/mol
Surface area10080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.720, 75.720, 79.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-220-

HOH

21B-245-

HOH

31B-258-

HOH

41B-279-

HOH

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Components

#1: Protein RNA replication protein


Mass: 16437.484 Da / Num. of mol.: 1 / Fragment: Peptidase C21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maize rayado fino virus / Gene: ORF1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q91TW9
#2: Protein Ubiquitin


Mass: 8560.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Gly76 replaced by 1-aminopropane crosslinker, to react stably with co-crystallzed protease
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-3CN / 3-AMINOPROPANE


Mass: 59.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 100 mM phosphate citrate buffer (pH 3.8), 200 mM lithium sulfate and 25 % PEG 1000

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54187 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.09→31.16 Å / Num. obs: 13343 / % possible obs: 96.56 % / Redundancy: 2 % / Biso Wilson estimate: 16.94 Å2 / CC1/2: 0.91 / Net I/σ(I): 26.62
Reflection shellResolution: 2.09→2.17 Å / Num. unique obs: 1341 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7MIA, IUBQ

7mia


Resolution: 2.09→31.16 Å / SU ML: 0.1938 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.2708
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2628 1296 10.05 %
Rwork0.2048 11596 -
obs0.2107 12892 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.69 Å2
Refinement stepCycle: LAST / Resolution: 2.09→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 16 239 1930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211727
X-RAY DIFFRACTIONf_angle_d0.53282340
X-RAY DIFFRACTIONf_chiral_restr0.0385276
X-RAY DIFFRACTIONf_plane_restr0.0036302
X-RAY DIFFRACTIONf_dihedral_angle_d6.021240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.170.2641490.22631321X-RAY DIFFRACTION99.39
2.17-2.270.35871310.28491128X-RAY DIFFRACTION86
2.27-2.390.32381160.24271191X-RAY DIFFRACTION88.37
2.39-2.540.29011500.21411315X-RAY DIFFRACTION99.8
2.54-2.740.25061530.2141338X-RAY DIFFRACTION100
2.74-3.010.28861370.2071340X-RAY DIFFRACTION99.93
3.01-3.450.24181540.19061335X-RAY DIFFRACTION99.67
3.45-4.340.21411460.17421271X-RAY DIFFRACTION96.26
4.35-31.160.25311600.18771357X-RAY DIFFRACTION99.8

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