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- PDB-6gzs: Structure of Chlamydia trachomatis effector protein ChlaDUB1 boun... -

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Basic information

Entry
Database: PDB / ID: 6gzs
TitleStructure of Chlamydia trachomatis effector protein ChlaDUB1 bound to ubiquitin
Components
  • Deubiquitinase and deneddylase Dub1
  • Polyubiquitin-B
KeywordsHYDROLASE / Enzyme / CE clan / Deubiquitinase / Acetyltransferase
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / mitochondrion transport along microtubule / positive regulation of protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein deubiquitination / neuron projection morphogenesis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) ...deNEDDylase activity / protein deneddylation / mitochondrion transport along microtubule / positive regulation of protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein deubiquitination / neuron projection morphogenesis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / regulation of neuron apoptotic process / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / 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 / Prevention of phagosomal-lysosomal fusion / regulation of mitochondrial membrane potential / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / 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 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / positive regulation of protein ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / regulation of proteasomal protein catabolic process / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / PD-L1(CD274) glycosylation and translocation to plasma membrane / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Regulation of BACH1 activity / Translesion synthesis by POLK / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / InlB-mediated entry of Listeria monocytogenes into host cell / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / Regulation of activated PAK-2p34 by proteasome mediated degradation / TCF dependent signaling in response to WNT / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Maturation of DENV proteins / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / NOTCH3 Activation and Transmission of Signal to the Nucleus / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Negative regulation of FGFR3 signaling / Ubiquitin-dependent degradation of Cyclin D / Fanconi Anemia Pathway / Peroxisomal protein import / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Stabilization of p53 / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR2 signaling / Enterobacterial factors antagonize host defense / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Termination of translesion DNA synthesis / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / EGFR downregulation / Regulation of TNFR1 signaling
Similarity search - Function
Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues ...Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Papain-like cysteine peptidase superfamily / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
prop-2-en-1-amine / Deubiquitinase and deneddylase Dub1 / Polyubiquitin-B
Similarity search - Component
Biological speciesChlamydia trachomatis serovar L2 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPruneda, J.N. / Komander, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council724804 United Kingdom
CitationJournal: Nat Microbiol / Year: 2018
Title: A Chlamydia effector combining deubiquitination and acetylation activities induces Golgi fragmentation.
Authors: Pruneda, J.N. / Bastidas, R.J. / Bertsoulaki, E. / Swatek, K.N. / Santhanam, B. / Clague, M.J. / Valdivia, R.H. / Urbe, S. / Komander, D.
History
DepositionJul 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deubiquitinase and deneddylase Dub1
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0725
Polymers39,8272
Non-polymers2453
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-29 kcal/mol
Surface area14730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.798, 55.768, 58.574
Angle α, β, γ (deg.)90.00, 93.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Deubiquitinase and deneddylase Dub1 / ChlaDub1


Mass: 31307.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B) (bacteria)
Strain: 434/Bu / ATCC VR-902B / Gene: cdu1, CTL0247 / Production host: Escherichia coli (E. coli)
References: UniProt: B0B9A0, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Polyubiquitin-B


Mass: 8519.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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Non-polymers , 4 types, 187 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES (pH 6.0), 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9798 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→26.85 Å / Num. obs: 27450 / % possible obs: 99.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.476 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→26.847 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.79
RfactorNum. reflection% reflection
Rfree0.2132 1414 5.16 %
Rwork0.1811 --
obs0.1828 27425 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→26.847 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2515 0 15 184 2714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012590
X-RAY DIFFRACTIONf_angle_d1.3713530
X-RAY DIFFRACTIONf_dihedral_angle_d14.902937
X-RAY DIFFRACTIONf_chiral_restr0.059401
X-RAY DIFFRACTIONf_plane_restr0.008452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.28691330.25842608X-RAY DIFFRACTION100
1.9679-2.04670.25481380.23382558X-RAY DIFFRACTION100
2.0467-2.13980.26481590.20342587X-RAY DIFFRACTION100
2.1398-2.25250.24321420.19392592X-RAY DIFFRACTION100
2.2525-2.39360.22531550.18612543X-RAY DIFFRACTION100
2.3936-2.57830.21961430.18292603X-RAY DIFFRACTION100
2.5783-2.83750.22431270.18582611X-RAY DIFFRACTION100
2.8375-3.24750.2071290.19242614X-RAY DIFFRACTION100
3.2475-4.08910.21631150.16732655X-RAY DIFFRACTION100
4.0891-26.84950.18571730.16452640X-RAY DIFFRACTION100
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)
13.4296-1.3717-0.28745.22890.05352.24990.19080.5399-0.0723-0.8784-0.18070.9047-0.0778-0.285-0.01110.2710.0261-0.14560.2706-0.02840.35368.48857.765576.871
22.7181-0.27940.28031.2839-1.77922.7034-0.67212.16310.9399-0.72470.0634-0.592-0.32031.10760.31111.2914-0.09440.2641.41590.15120.539127.742312.262555.8046
33.2930.72190.47360.8427-1.13632.3092-0.17270.35420.1584-0.19030.05110.0107-0.12350.54320.14731.12330.0616-0.26180.64770.03090.134911.490714.450863.1932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 70)
3X-RAY DIFFRACTION3chain 'B' and (resid 71 through 75 )

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