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- PDB-5lru: Structure of Cezanne/OTUD7B OTU domain -

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Basic information

Entry
Database: PDB / ID: 5lru
TitleStructure of Cezanne/OTUD7B OTU domain
ComponentsOTU domain-containing protein 7B
KeywordsHYDROLASE / protease / deubiquitinase / OTU domain
Function / homology
Function and homology information


mucosal immune response / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / protein K11-linked deubiquitination / negative regulation of interleukin-8 production / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / negative regulation of protein localization to nucleus / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding ...mucosal immune response / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / protein K11-linked deubiquitination / negative regulation of interleukin-8 production / protein K48-linked deubiquitination / protein K63-linked deubiquitination / K48-linked deubiquitinase activity / negative regulation of protein localization to nucleus / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / protein deubiquitination / negative regulation of canonical NF-kappaB signal transduction / cysteine-type peptidase activity / TNFR1-induced NF-kappa-B signaling pathway / Regulation of TNFR1 signaling / Ovarian tumor domain proteases / in utero embryonic development / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / adaptive immune response / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / : / UBA-like domain / OTU-like cysteine protease / OTU domain / OTU domain profile.
Similarity search - Domain/homology
OTU domain-containing protein 7B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMevissen, T.E.T. / Kulathu, Y. / Mulder, M.P.C. / Geurink, P.P. / Maslen, S.L. / Gersch, M. / Elliott, P.R. / Burke, J.E. / van Tol, B.D.M. / Akutsu, M. ...Mevissen, T.E.T. / Kulathu, Y. / Mulder, M.P.C. / Geurink, P.P. / Maslen, S.L. / Gersch, M. / Elliott, P.R. / Burke, J.E. / van Tol, B.D.M. / Akutsu, M. / El Oualid, F. / Kawasaki, M. / Freund, S.M.V. / Ovaa, H. / Komander, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105192732 United Kingdom
European Research Council309756 United Kingdom
CitationJournal: Nature / Year: 2016
Title: Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne.
Authors: Mevissen, T.E. / Kulathu, Y. / Mulder, M.P. / Geurink, P.P. / Maslen, S.L. / Gersch, M. / Elliott, P.R. / Burke, J.E. / van Tol, B.D. / Akutsu, M. / El Oualid, F. / Kawasaki, M. / Freund, S. ...Authors: Mevissen, T.E. / Kulathu, Y. / Mulder, M.P. / Geurink, P.P. / Maslen, S.L. / Gersch, M. / Elliott, P.R. / Burke, J.E. / van Tol, B.D. / Akutsu, M. / El Oualid, F. / Kawasaki, M. / Freund, S.M. / Ovaa, H. / Komander, D.
History
DepositionAug 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: OTU domain-containing protein 7B


Theoretical massNumber of molelcules
Total (without water)36,3601
Polymers36,3601
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.349, 103.349, 90.199
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 OTU domain-containing protein 7B / Cellular zinc finger anti-NF-kappa-B protein / Zinc finger A20 domain-containing protein 1 / Zinc ...Cellular zinc finger anti-NF-kappa-B protein / Zinc finger A20 domain-containing protein 1 / Zinc finger protein Cezanne


Mass: 36360.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OTUD7B, ZA20D1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GQQ9, ubiquitinyl hydrolase 1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris (pH 6.1), 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.2→90.2 Å / Num. obs: 25409 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 1.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→73.079 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.77
RfactorNum. reflection% reflection
Rfree0.2189 1298 5.12 %
Rwork0.1984 --
obs0.1995 25351 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→73.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 0 90 2227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022197
X-RAY DIFFRACTIONf_angle_d0.5932999
X-RAY DIFFRACTIONf_dihedral_angle_d12.763751
X-RAY DIFFRACTIONf_chiral_restr0.024343
X-RAY DIFFRACTIONf_plane_restr0.003379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.28820.34491400.30012618X-RAY DIFFRACTION100
2.2882-2.39240.29891480.26012604X-RAY DIFFRACTION100
2.3924-2.51850.24161460.22632637X-RAY DIFFRACTION100
2.5185-2.67630.23371530.22492618X-RAY DIFFRACTION100
2.6763-2.8830.25881340.22512652X-RAY DIFFRACTION100
2.883-3.17310.25531360.21672664X-RAY DIFFRACTION100
3.1731-3.63220.22511610.20072661X-RAY DIFFRACTION100
3.6322-4.57610.19521350.17442732X-RAY DIFFRACTION100
4.5761-73.11910.1921450.18462867X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 28.589 Å / Origin y: 9.7271 Å / Origin z: -12.7548 Å
111213212223313233
T0.3299 Å2-0.008 Å2-0.0289 Å2-0.3335 Å2-0.0559 Å2--0.4045 Å2
L3.8436 °2-0.4639 °20.2344 °2-3.6972 °2-1.164 °2--3.767 °2
S0.0643 Å °0.2529 Å °-0.4918 Å °-0.231 Å °0.0345 Å °0.2673 Å °0.2337 Å °-0.1985 Å °-0.0637 Å °
Refinement TLS groupSelection details: chain 'A'

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