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- PDB-3phw: OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3phw
TitleOTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin
Components
  • RNA-directed RNA polymerase L
  • Ubiquitin-40S ribosomal protein S27a
KeywordsHydrolase/Ribosomal Protein / OTU domain / De-ubiquitinase / De-ISGylase / Hydrolase-Ribosomal Protein complex
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination ...RNA-templated viral transcription / negative stranded viral RNA replication / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / small-subunit processome / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / cytosolic ribosome / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / 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 / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling
Similarity search - Function
: / RNA-directed RNA polymerase, nairovirus / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. ...: / RNA-directed RNA polymerase, nairovirus / Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / S27a-like superfamily / Cathepsin B; Chain A / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ETHANAMINE / Ubiquitin-ribosomal protein eS31 fusion protein / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus strain IbAr10200
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAkutsu, M. / Ye, Y. / Virdee, S. / Komander, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains.
Authors: Akutsu, M. / Ye, Y. / Virdee, S. / Chin, J.W. / Komander, D.
History
DepositionNov 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 6, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase L
B: Ubiquitin-40S ribosomal protein S27a
C: RNA-directed RNA polymerase L
D: Ubiquitin-40S ribosomal protein S27a
E: RNA-directed RNA polymerase L
F: Ubiquitin-40S ribosomal protein S27a
G: RNA-directed RNA polymerase L
H: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,30612
Polymers118,1258
Non-polymers1804
Water10,124562
1
A: RNA-directed RNA polymerase L
B: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5763
Polymers29,5312
Non-polymers451
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-10 kcal/mol
Surface area10960 Å2
MethodPISA
2
C: RNA-directed RNA polymerase L
D: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5763
Polymers29,5312
Non-polymers451
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-9 kcal/mol
Surface area11030 Å2
MethodPISA
3
E: RNA-directed RNA polymerase L
F: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5763
Polymers29,5312
Non-polymers451
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-9 kcal/mol
Surface area10760 Å2
MethodPISA
4
G: RNA-directed RNA polymerase L
H: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5763
Polymers29,5312
Non-polymers451
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-9 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.440, 106.170, 111.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
RNA-directed RNA polymerase L / Protein L / Large structural protein / Replicase / Transcriptase / Ubiquitin thiolesterase / RNA- ...Protein L / Large structural protein / Replicase / Transcriptase / Ubiquitin thiolesterase / RNA-directed RNA polymerase


Mass: 21011.580 Da / Num. of mol.: 4 / Fragment: UNP residues 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
Strain: Nigeria/IbAr10200/1970 / Gene: L / Production host: Escherichia coli (E. coli)
References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1, RNA-directed RNA polymerase
#2: Protein
Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 8519.778 Da / Num. of mol.: 4 / Fragment: UNP residues 1-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P62979
#3: Chemical
ChemComp-NEH / ETHANAMINE / Ethylamine


Mass: 45.084 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H7N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.27 M sodium phosphate dihydrogen, 1.53 M di-potassium phosphate hydrogen, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 59820

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Processing

Software
NameVersionClassification
PHASESphasing
PHENIX(phenix.refine: 1.4_122)refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.623 Å / SU ML: 0.29 / σ(F): 0.01 / Phase error: 29.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 2925 5.05 %
Rwork0.2131 --
obs0.2164 57879 89.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.758 Å2 / ksol: 0.381 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.0658 Å2-0 Å20 Å2
2---3.8838 Å2-0 Å2
3---8.9496 Å2
Refinement stepCycle: LAST / Resolution: 2→45.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7481 0 12 562 8055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057641
X-RAY DIFFRACTIONf_angle_d0.90310328
X-RAY DIFFRACTIONf_dihedral_angle_d15.7682807
X-RAY DIFFRACTIONf_chiral_restr0.0611150
X-RAY DIFFRACTIONf_plane_restr0.0031325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.31163100.22725487X-RAY DIFFRACTION91
2.0715-2.15440.32172700.22335556X-RAY DIFFRACTION92
2.1544-2.25250.34442780.25545362X-RAY DIFFRACTION88
2.2525-2.37120.33183080.24845337X-RAY DIFFRACTION88
2.3712-2.51980.29433000.21145631X-RAY DIFFRACTION93
2.5198-2.71430.29912810.21375642X-RAY DIFFRACTION93
2.7143-2.98740.2792870.20965656X-RAY DIFFRACTION93
2.9874-3.41960.25892830.20045591X-RAY DIFFRACTION91
3.4196-4.30780.24153040.18865406X-RAY DIFFRACTION88
4.3078-45.63470.23553040.19865286X-RAY DIFFRACTION83

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