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- PDB-3znh: Crimean Congo Hemorrhagic Fever Virus OTU domain in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3znh
TitleCrimean Congo Hemorrhagic Fever Virus OTU domain in complex with ubiquitin-propargyl.
Components
  • POLYUBIQUITIN-B
  • UBIQUITIN THIOESTERASE
KeywordsHYDROLASE/SIGNALING PROTEIN / HYDROLASE-SIGNALING PROTEIN COMPLEX / DEUBIQUITINASE
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I ...RNA-templated viral transcription / negative stranded viral RNA replication / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic 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 / 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 / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / 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 / Pexophagy / InlA-mediated entry of Listeria monocytogenes into host cells / 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 / NF-kB is activated and signals survival / Regulation of PTEN localization / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Gap-filling DNA repair synthesis and ligation in GG-NER / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / neuron projection morphogenesis / 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 / regulation of mitochondrial membrane potential / 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 / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / 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 / Recognition of DNA damage by PCNA-containing replication complex / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity
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. / Cathepsin B; Chain A / 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. / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsEkkebus, R. / vanKasteren, S.I. / Kulathu, Y. / Scholten, A. / Berlin, I. / deJong, A. / Goerdayal, G. / Neefjes, J. / Heck, A.J.R. / Komander, D. / Ovaa, H.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: On Terminal Alkynes that Can React with Active-Site Cysteine Nucleophiles in Proteases.
Authors: Ekkebus, R. / Van Kasteren, S.I. / Kulathu, Y. / Scholten, A. / Berlin, I. / Geurink, P.P. / De Jong, A. / Goerdayal, G. / Neefjes, J. / Heck, A.J.R. / Komander, D. / Ovaa, H.
History
DepositionFeb 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Mar 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBIQUITIN THIOESTERASE
B: POLYUBIQUITIN-B


Theoretical massNumber of molelcules
Total (without water)29,4162
Polymers29,4162
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-7.3 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.050, 146.050, 58.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

21A-2030-

HOH

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Components

#1: Protein UBIQUITIN THIOESTERASE / OTU DOMAIN OF CRIMEAN CONGO HEMORRHAGIC FEVER VIRUS CCHFV


Mass: 20857.414 Da / Num. of mol.: 1 / Fragment: OTU DOMAIN, RESIDUES 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CRIMEAN-CONGO HEMORRHAGIC FEVER VIRUS / Strain: IBAR10200 / Description: DNA GENERATED BY GENE SYNTHESIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA2 PLACI / References: UniProt: Q6TQR6, ubiquitinyl hydrolase 1
#2: Protein POLYUBIQUITIN-B / UBIQUITIN PROPARGYL / UBIQUITIN


Mass: 8558.857 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically / Details: GLY76 IS REPLACED WITH A PROPARGYL GROUP / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P0CG47
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsALLYLAMINE (AYE): THIS IS THE PRODUCT OF COVALENT MODIFICATION FROM PROPARGYL UBIQUITIN WITH A CYS. ...ALLYLAMINE (AYE): THIS IS THE PRODUCT OF COVALENT MODIFICATION FROM PROPARGYL UBIQUITIN WITH A CYS. THE ETHANAMINE IS COVALENTLY LINKED TO CYS40 OF MOLECULE A.
Sequence detailsRESIDUES 1-183 RESIDUE 76 IS REPLACED WITH A PROPARGYL MOIETY, WHICH FORMS A QUATERNARY VINYL ...RESIDUES 1-183 RESIDUE 76 IS REPLACED WITH A PROPARGYL MOIETY, WHICH FORMS A QUATERNARY VINYL THIOETHER WITH CYS40 OF MOLECULE A.

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6.5
Details: 20-30% PEG 8000, 100 MM NA CACODYLATE PH 6.5, 100 MM MG ACETATE, AND 2% N-OCTYL-BETA-D-GLUCOSIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→53.12 Å / Num. obs: 16479 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.6 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PHW

3phw


Resolution: 2.3→126.48 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.793 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. COVALENT LINKS BETWEEN MOLECULE B GLY75,ETHANAMINE76 AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY. COVALENT LINKS BETWEEN MOLECULE B GLY75,ETHANAMINE76 AND MOLECULE A CYS40 HAVE BEEN REFINED IN REFMAC. DISORDERED RESIDUES WERE MODELLED WITH SIDE CHAINS REMOVED OR MUTATED TO ALA.
RfactorNum. reflection% reflectionSelection details
Rfree0.27465 838 5.1 %RANDOM
Rwork0.21076 ---
obs0.21385 15629 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.362 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å21.09 Å20 Å2
2--2.18 Å20 Å2
3----3.27 Å2
Refinement stepCycle: LAST / Resolution: 2.3→126.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 0 48 1822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021810
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.962457
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03624.37580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65115299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.752159
X-RAY DIFFRACTIONr_chiral_restr0.1220.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211362
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 62 -
Rwork0.258 995 -
obs--96.44 %

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