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- PDB-9fn4: DUBS Parachlamydia sp. PcJOS -

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Basic information

Entry
Database: PDB / ID: 9fn4
TitleDUBS Parachlamydia sp. PcJOS
Components
  • Peptidase C39-like domain-containing protein
  • Ubiquitin
KeywordsHYDROLASE / Debiquitinylating enzyme
Function / homology
Function and homology information


hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / energy homeostasis ...hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / 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 / neuron projection morphogenesis / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / 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 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / 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 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of protein ubiquitination / 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 / TCF dependent signaling in response to WNT / regulation of mitochondrial membrane potential / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling
Similarity search - Function
: / 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
L(+)-TARTARIC ACID / Peptidase C39-like domain-containing protein / Polyubiquitin-B
Similarity search - Component
Biological speciesParachlamydia sp. (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsBaumann, U. / Hermanns, T.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
CitationJournal: Mol.Cell / Year: 2025
Title: A family of bacterial Josephin-like deubiquitinases with an irreversible cleavage mode.
Authors: Hermanns, T. / Kolek, S. / Uthoff, M. / de Heiden, R.A. / Mulder, M.P.C. / Baumann, U. / Hofmann, K.
History
DepositionJun 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase C39-like domain-containing protein
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6903
Polymers45,5402
Non-polymers1501
Water2,216123
1
A: Peptidase C39-like domain-containing protein
B: Ubiquitin
hetero molecules

B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)62,8264
Polymers62,6763
Non-polymers1501
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z+1/41
Unit cell
Length a, b, c (Å)88.765, 88.765, 147.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Peptidase C39-like domain-containing protein


Mass: 28404.537 Da / Num. of mol.: 1 / Mutation: C84A
Source method: isolated from a genetically manipulated source
Details: C162A Mutation / Source: (gene. exp.) Parachlamydia sp. (bacteria) / Gene: CK425_03690
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2H9SU66
#2: Protein Ubiquitin


Mass: 17135.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: linear di-ubiquitin. Contained in the asymmetric unit is only either the C-terminal moiety (as in this entry) of the N-terminal ubiquitin moiety; the other one is related by crystal symmetry. ...Details: linear di-ubiquitin. Contained in the asymmetric unit is only either the C-terminal moiety (as in this entry) of the N-terminal ubiquitin moiety; the other one is related by crystal symmetry. See section on assembly.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P0CG47
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Molecular Dimensions Morpheus B7, 298 K.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.15→100 Å / Num. obs: 61201 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.125 / Net I/σ(I): 10.9
Reflection shellResolution: 2.15→2.28 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.86 / Num. unique obs: 9889 / CC1/2: 0.18 / Rrim(I) all: 2.05 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata scaling
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→57.76 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 3066 5.02 %random
Rwork0.184 ---
obs0.1848 61109 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→57.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 10 123 2517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032438
X-RAY DIFFRACTIONf_angle_d0.573303
X-RAY DIFFRACTIONf_dihedral_angle_d13.052914
X-RAY DIFFRACTIONf_chiral_restr0.042381
X-RAY DIFFRACTIONf_plane_restr0.004431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.38231380.36992596X-RAY DIFFRACTION98
2.18-2.220.37091370.32592653X-RAY DIFFRACTION100
2.22-2.260.3391410.31552625X-RAY DIFFRACTION100
2.26-2.30.27751460.28582633X-RAY DIFFRACTION100
2.3-2.340.24011370.26562631X-RAY DIFFRACTION100
2.34-2.390.29221400.25072690X-RAY DIFFRACTION100
2.39-2.440.24981500.24272573X-RAY DIFFRACTION100
2.44-2.50.20421290.22782690X-RAY DIFFRACTION100
2.5-2.560.2691440.23032629X-RAY DIFFRACTION100
2.56-2.630.26731350.23292624X-RAY DIFFRACTION100
2.63-2.710.26741290.22592647X-RAY DIFFRACTION100
2.71-2.80.19861350.21092658X-RAY DIFFRACTION100
2.8-2.90.21151490.19162595X-RAY DIFFRACTION100
2.9-3.010.18211470.18282692X-RAY DIFFRACTION100
3.01-3.150.20911290.18652631X-RAY DIFFRACTION100
3.15-3.320.23481470.18642631X-RAY DIFFRACTION100
3.32-3.520.20131380.1852652X-RAY DIFFRACTION100
3.53-3.80.17561370.16282635X-RAY DIFFRACTION100
3.8-4.180.15851420.15462639X-RAY DIFFRACTION100
4.18-4.780.13911330.12962637X-RAY DIFFRACTION100
4.78-6.020.16451480.14672640X-RAY DIFFRACTION100
6.03-57.760.18631350.16422642X-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)
13.95181.5016-1.59712.0232.43567.2384-0.18750.1885-0.7719-0.22510.14250.01220.94420.31660.02120.7185-0.0122-0.00240.36960.02710.617431.132-15.8979-1.65
21.3682-0.02010.12711.11820.28912.8508-0.05540.06430.0648-0.12170.09430.0638-0.0754-0.2677-0.01850.35430.0107-0.00540.33770.07190.373426.65455.658.7061
32.8393-0.30330.1662.5370.11033.0750.0308-0.0890.09540.15050.09680.095-0.18850.0482-0.13040.414-0.03980.04660.36940.00990.386945.89.2656-5.0551
41.45750.3481-0.31341.6861-0.95783.13020.0227-0.146-0.15210.158-0.0177-0.3163-0.15570.524-0.04150.4337-0.0437-0.06130.5034-0.0470.440154.06667.3119-3.0109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 95 through 121 )
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 324 )
3X-RAY DIFFRACTION3chain 'B' and (resid -1 through 44 )
4X-RAY DIFFRACTION4chain 'B' and (resid 45 through 74 )

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