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- PDB-8adb: Viral tegument-like DUBs -

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Basic information

Entry
Database: PDB / ID: 8adb
TitleViral tegument-like DUBs
Components
  • Deubiquitinating enzyme
  • Ubiquitin
KeywordsHYDROLASE / DUBs / deubiquitinating enzymes / ubiquitin / tegument
Function / homology
Function and homology information


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 ...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 / cytosolic ribosome / 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 / 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 / Regulation of innate immune responses to cytosolic DNA / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / 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 / TICAM1, RIP1-mediated IKK complex recruitment / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / InlB-mediated entry of Listeria monocytogenes into host cell / Regulation of activated PAK-2p34 by proteasome mediated degradation / Josephin domain DUBs / Translesion synthesis by POLI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / 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 / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Regulation of signaling by CBL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Degradation of AXIN / Peroxisomal protein import / Hh mutants are degraded by ERAD / Stabilization of p53 / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling
Similarity search - Function
Cathepsin B; Chain A - #120 / Cathepsin B; Chain A / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. ...Cathepsin B; Chain A - #120 / Cathepsin B; Chain A / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
prop-2-en-1-amine / CITRIC ACID / Uncharacterized protein / Ubiquitin-ribosomal protein eL40 fusion protein
Similarity search - Component
Biological speciesWaddlia chondrophila (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsErven, I. / Abraham, E.T. / Hermanns, T. / Baumann, U. / Hofmann, K.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)HO 3783/3-1 Germany
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
Citation
Journal: Nat Commun / Year: 2022
Title: A widely distributed family of eukaryotic and bacterial deubiquitinases related to herpesviral large tegument proteins.
Authors: Erven, I. / Abraham, E. / Hermanns, T. / Baumann, U. / Hofmann, K.
#1: Journal: Nat Commun / Year: 2022
Title: A structural basis for the diverse linkage specificities within the ZUFSP deubiquitinase family.
Authors: Hermanns, T. / Pichlo, C. / Baumann, U. / Hofmann, K.
History
DepositionJul 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Sep 4, 2024Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deubiquitinating enzyme
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7224
Polymers32,4732
Non-polymers2492
Water2,504139
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)101.766, 101.766, 63.204
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-669-

HOH

21B-113-

HOH

31B-128-

HOH

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Components

#1: Protein Deubiquitinating enzyme / VTD (Viral tegument-like DUB)


Mass: 23952.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Waddlia chondrophila (bacteria) / Strain: ATCC VR-1470 / WSU 86-1044 / Gene: wcw_1294 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: D6YWY5
#2: Protein Ubiquitin


Mass: 8519.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA52, UBCEP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62987
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M BisTris propane pH 7.0, 2.0 M Ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→80 Å / Num. obs: 39677 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 30.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.153 / Net I/σ(I): 11.4
Reflection shellResolution: 1.73→1.84 Å / Redundancy: 19.2 % / Rmerge(I) obs: 2.82 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6346 / CC1/2: 0.497 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4478refinement
PHENIX1.20_4478refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: WC-VDT1, 1UBB

1ubb


Resolution: 1.73→51.36 Å / SU ML: 0.2239 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7922
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1928 1986 5.01 %
Rwork0.1671 37647 -
obs0.1684 39633 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.46 Å2
Refine analyzeLuzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.73→51.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 17 139 2385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092300
X-RAY DIFFRACTIONf_angle_d1.21613109
X-RAY DIFFRACTIONf_chiral_restr0.0626349
X-RAY DIFFRACTIONf_plane_restr0.0083409
X-RAY DIFFRACTIONf_dihedral_angle_d13.8715885
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.770.4121390.32692646X-RAY DIFFRACTION99.64
1.77-1.820.29111370.27852671X-RAY DIFFRACTION100
1.82-1.880.28981400.25392648X-RAY DIFFRACTION100
1.88-1.940.26131390.22352679X-RAY DIFFRACTION100
1.94-20.24321440.21172652X-RAY DIFFRACTION100
2.01-2.090.21721400.16792664X-RAY DIFFRACTION99.93
2.09-2.180.20741380.16142696X-RAY DIFFRACTION99.96
2.18-2.290.20271340.14612657X-RAY DIFFRACTION100
2.3-2.440.1891430.16512701X-RAY DIFFRACTION99.96
2.44-2.630.19431460.15852668X-RAY DIFFRACTION100
2.63-2.890.18251440.18052705X-RAY DIFFRACTION99.96
2.89-3.310.21181450.16342702X-RAY DIFFRACTION100
3.31-4.170.15711490.14522732X-RAY DIFFRACTION100
4.17-51.360.17441480.15492826X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.523302971098-0.025101846336-0.1232630380070.846315299398-0.3029299935591.525909423180.04244127862210.01683676305670.001036121217860.08699051273980.01472918367360.0156892349701-0.118679587234-0.05418804590030.003529837675850.2631853885040.01224972940770.02317705785050.210389823524-0.003890116421270.26501638927753.930740017714.010204799320.523797148
20.246687527247-0.167050144711-0.03323229090750.4912001212710.3849925201180.5185190483820.101186317650.0374056992541-0.194362752931-0.02004646010850.0279143568026-0.139514809270.1829110724660.39227429599-2.59512084905E-50.3560782524750.0687061866863-0.0358236568450.422735864667-0.0404091122960.36581162020774.7502605796-4.0416455306630.2721757467
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 280 through 493)AA280 - 4931 - 209
22(chain 'A' and resid 502)A502
32(chain 'B' and resid 1 through 75)BC - D1 - 751

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