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- PDB-6ei1: Crystal structure of the covalent complex between deubiquitinase ... -

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Basic information

Entry
Database: PDB / ID: 6ei1
TitleCrystal structure of the covalent complex between deubiquitinase ZUFSP (ZUP1) and Ubiquitin-PA
Components
  • Polyubiquitin-B
  • Zinc finger with UFM1-specific peptidase domain protein
KeywordsHYDROLASE / K63 / ubiquitin / deubiquitinase / cysteine peptidase / ZUP1
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
Cathepsin B; Chain A - #130 / Peptidase C78, ubiquitin fold modifier-specific peptidase 1/ 2 / Peptidase family C78 / : / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Cathepsin B; Chain A / Pectin lyase fold / Pectin lyase fold/virulence factor / zinc finger ...Cathepsin B; Chain A - #130 / Peptidase C78, ubiquitin fold modifier-specific peptidase 1/ 2 / Peptidase family C78 / : / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Cathepsin B; Chain A / Pectin lyase fold / Pectin lyase fold/virulence factor / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Ubiquitin family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
prop-2-en-1-amine / MALONATE ION / Tail fiber / Zinc finger-containing ubiquitin peptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.732 Å
AuthorsPichlo, C. / Baumann, U. / Hofmann, K. / Hermanns, T.
CitationJournal: Nat Commun / Year: 2018
Title: A family of unconventional deubiquitinases with modular chain specificity determinants.
Authors: Hermanns, T. / Pichlo, C. / Woiwode, I. / Klopffleisch, K. / Witting, K.F. / Ovaa, H. / Baumann, U. / Hofmann, K.
History
DepositionSep 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Structure summary / Category: struct / struct_keywords / Item: _struct.title / _struct_keywords.text
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Apr 9, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger with UFM1-specific peptidase domain protein
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5065
Polymers48,2552
Non-polymers2513
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Binding confirmed by mutational studies.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-2 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.230, 84.230, 201.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Zinc finger with UFM1-specific peptidase domain protein


Mass: 39735.348 Da / Num. of mol.: 1 / Fragment: UNP residues 232-578
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZUFSP, C6orf113 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: Q96AP4
#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 BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: P0CG47

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Non-polymers , 4 types, 288 molecules

#3: Chemical ChemComp-AYE / prop-2-en-1-amine / ALLYLAMINE


Mass: 57.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7N
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5 / Details: 0.2 M sodium malonate pH 5, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.73→49.45 Å / Num. obs: 44866 / % possible obs: 99 % / Redundancy: 10.8 % / Net I/σ(I): 16.6

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.732→49.448 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 18.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 1929 4.3 %
Rwork0.1714 --
obs0.1727 44862 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.732→49.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 17 285 3529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063341
X-RAY DIFFRACTIONf_angle_d0.7094504
X-RAY DIFFRACTIONf_dihedral_angle_d17.4111273
X-RAY DIFFRACTIONf_chiral_restr0.044494
X-RAY DIFFRACTIONf_plane_restr0.005590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7316-1.77490.25151310.22842913X-RAY DIFFRACTION97
1.7749-1.82290.27521360.21313031X-RAY DIFFRACTION100
1.8229-1.87660.26361350.21973006X-RAY DIFFRACTION100
1.8766-1.93710.23361350.20713004X-RAY DIFFRACTION100
1.9371-2.00640.24441370.19383042X-RAY DIFFRACTION100
2.0064-2.08670.23511360.18233013X-RAY DIFFRACTION100
2.0867-2.18170.19821340.16813020X-RAY DIFFRACTION100
2.1817-2.29670.19171380.16723044X-RAY DIFFRACTION100
2.2967-2.44060.22441360.16213047X-RAY DIFFRACTION100
2.4406-2.6290.20341400.16593081X-RAY DIFFRACTION100
2.629-2.89360.18181380.17223084X-RAY DIFFRACTION100
2.8936-3.31220.21151400.17333108X-RAY DIFFRACTION100
3.3122-4.17270.17981420.153167X-RAY DIFFRACTION100
4.1727-49.46810.18931510.16913373X-RAY DIFFRACTION100

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