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- PDB-9fpa: DUBS Parachlamydia sp. PcJOS orthorhombic crystal form -

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Basic information

Entry
Database: PDB / ID: 9fpa
TitleDUBS Parachlamydia sp. PcJOS orthorhombic crystal form
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 / 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 / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / 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 / Regulation of innate immune responses to cytosolic DNA / NF-kB is activated and signals survival / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / neuron projection morphogenesis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / regulation of mitochondrial membrane potential / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / 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 / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / activated TAK1 mediates p38 MAPK activation / Negative regulators of DDX58/IFIH1 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 / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Degradation of AXIN / Regulation of TNFR1 signaling / Negative regulation of FGFR2 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
CITRIC ACID / Peptidase C39-like domain-containing protein / Polyubiquitin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
Parachlamydia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsBaumann, U. / Hermanns, T. / Uthoff, M.
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 13, 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
B: Ubiquitin
C: Peptidase C39-like domain-containing protein
A: Peptidase C39-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8605
Polymers73,4763
Non-polymers3842
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: 2 PcJOS:1 diubioquitin
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-9 kcal/mol
Surface area27540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.220, 108.180, 149.610
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 Ubiquitin


Mass: 17135.654 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 B (bacteria) / References: UniProt: P0CG47
#2: Protein Peptidase C39-like domain-containing protein


Mass: 28170.064 Da / Num. of mol.: 2 / Mutation: C162A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parachlamydia sp. (bacteria) / Gene: CK425_03690 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H9SU66
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Midas G6. 35 % v/v glycerol ethoxylate, 0.2 M lithium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 46803 / % possible obs: 99.9 % / Redundancy: 7.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.137 / Rrim(I) all: 0.143 / Net I/σ(I): 10.03
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.18-2.241.3291.3733820.6131.4431
2.24-2.31.09933160.7511.1741
2.3-2.360.86332570.8220.9221
2.36-2.440.76131350.8540.8131
2.44-2.520.62830530.8950.6721
2.52-2.610.5229670.9240.5561
2.61-2.70.40828570.9480.4361
2.7-2.810.32227390.9660.3451
2.81-2.940.25426520.9780.2721
2.94-3.080.19925260.9860.2131
3.08-3.250.15424340.9930.1651
3.25-3.450.12322840.9930.1321
3.45-3.680.10221610.9950.1091
3.68-3.980.09320240.9950.11
3.98-4.360.0818650.9960.0861
4.36-4.870.07217040.9960.0781
4.87-5.630.06915060.9960.0741
5.63-6.890.06413120.9970.0691
6.89-9.750.04910290.9980.0531
9.75-500.0396000.9980.0421

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→43.9 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 2263 4.84 %
Rwork0.1844 --
obs0.1857 46730 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4684 0 26 230 4940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084784
X-RAY DIFFRACTIONf_angle_d0.9156482
X-RAY DIFFRACTIONf_dihedral_angle_d13.91796
X-RAY DIFFRACTIONf_chiral_restr0.053745
X-RAY DIFFRACTIONf_plane_restr0.009845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.230.32281360.28172697X-RAY DIFFRACTION99
2.23-2.280.26381400.25752759X-RAY DIFFRACTION100
2.28-2.340.26781350.2372734X-RAY DIFFRACTION100
2.34-2.40.24431420.22812743X-RAY DIFFRACTION100
2.4-2.470.25471480.21082761X-RAY DIFFRACTION100
2.47-2.550.2321300.20152716X-RAY DIFFRACTION100
2.55-2.640.2231460.19622771X-RAY DIFFRACTION100
2.64-2.750.23381470.19482749X-RAY DIFFRACTION100
2.75-2.870.24321260.19882781X-RAY DIFFRACTION100
2.87-3.020.24811430.21152777X-RAY DIFFRACTION100
3.02-3.210.24531500.19822746X-RAY DIFFRACTION100
3.21-3.460.23411370.22793X-RAY DIFFRACTION100
3.46-3.810.21231420.18892792X-RAY DIFFRACTION100
3.81-4.360.18141460.1582815X-RAY DIFFRACTION100
4.36-5.490.16171460.14042872X-RAY DIFFRACTION100
5.49-43.90.18161490.16272961X-RAY DIFFRACTION99
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)
14.81870.9742-0.26772.6803-0.68313.83910.3887-0.4196-0.17320.4627-0.2671-0.05580.05-0.0312-0.14440.4287-0.0721-0.02140.5610.1020.349519.470411.974134.9543
23.7165-1.1341-0.73253.4446-0.27774.16640.0106-0.1533-0.25320.20310.0779-0.06740.44830.0527-0.11970.49330.0406-0.06990.3783-0.01020.418921.5229-4.3496-1.1145
34.28310.812-0.52073.1298-0.21624.3712-0.390.6527-0.0238-0.40770.35590.1226-0.1565-0.32980.04750.4723-0.1134-0.00910.5964-0.06990.29620.81967.5402-36.2196
40.9557-1.07271.30961.9257-0.29167.7347-0.01940.0643-0.6199-0.0210.2099-0.36371.66430.3141-0.08230.74020.08440.00580.4308-0.12110.796430.0798-16.7483-16.9699
52.01010.72820.3442.690.083.5368-0.19150.2322-0.1709-0.0560.155-0.44450.09550.28330.05720.3758-0.0310.01020.5257-0.12010.452531.3731.2089-26.4844
63.03380.6180.62161.8671-0.0232.20450.09370.1089-0.153-0.1048-0.02430.06330.2563-0.018-0.06730.32820.01350.00120.30440.0120.291711.013914.4112.9999
71.8561.28320.57263.9234-2.71946.98160.2068-0.54560.00040.6888-0.5044-0.2342-0.10311.01520.29460.3636-0.0643-0.01110.6430.06890.348234.879618.955524.3684
83.61710.557-0.90027.8163-2.14833.82780.019-0.1037-0.07570.5226-0.0445-0.29440.0340.43820.02040.3226-0.0104-0.03590.4906-0.00620.290927.344421.182719.4934
91.8593-0.23840.341.5927-0.00623.28910.0439-0.05310.00640.0809-0.0636-0.0020.07-0.0884-0.00030.2543-0.01130.00360.33380.02270.299711.543321.57778.6805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 76)
2X-RAY DIFFRACTION2chain 'B' and (resid 77 through 150 )
3X-RAY DIFFRACTION3chain 'C' and (resid 98 through 161 )
4X-RAY DIFFRACTION4chain 'C' and (resid 162 through 213 )
5X-RAY DIFFRACTION5chain 'C' and (resid 214 through 324 )
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 177)
7X-RAY DIFFRACTION7chain 'A' and (resid 178 through 205 )
8X-RAY DIFFRACTION8chain 'A' and (resid 206 through 225 )
9X-RAY DIFFRACTION9chain 'A' and (resid 226 through 324 )

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