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- PDB-5lrv: Structure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diub... -

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Basic information

Entry
Database: PDB / ID: 5lrv
TitleStructure of Cezanne/OTUD7B OTU domain bound to Lys11-linked diubiquitin
Components
  • (Polyubiquitin- ...) x 2
  • OTU domain-containing protein 7B
KeywordsHYDROLASE / protease / deubiquitinase / OTU domain
Function / homology
Function and homology information


protein deubiquitination involved in ubiquitin-dependent protein catabolic process / mucosal immune response / protein K11-linked deubiquitination / positive regulation of TORC2 signaling / negative regulation of interleukin-8 production / protein K48-linked deubiquitination / negative regulation of protein localization to nucleus / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / symbiont entry into host cell via disruption of host cell glycocalyx ...protein deubiquitination involved in ubiquitin-dependent protein catabolic process / mucosal immune response / protein K11-linked deubiquitination / positive regulation of TORC2 signaling / negative regulation of interleukin-8 production / protein K48-linked deubiquitination / negative regulation of protein localization to nucleus / K48-linked deubiquitinase activity / protein K63-linked deubiquitination / symbiont entry into host cell via disruption of host cell glycocalyx / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / symbiont entry into host cell via disruption of host cell envelope / virus tail / protein deubiquitination / negative regulation of TORC1 signaling / negative regulation of canonical NF-kappaB signal transduction / TNFR1-induced NF-kappa-B signaling pathway / cysteine-type peptidase activity / Regulation of TNFR1 signaling / Ovarian tumor domain proteases / adaptive immune response / in utero embryonic development / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / 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 / UBA-like domain / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / OTU domain / OTU domain profile. ...: / Zinc finger, A20-type / : / A20-like zinc finger / UBA-like domain / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / OTU domain / OTU domain profile. / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Ubiquitin family
Similarity search - Domain/homology
PHOSPHATE ION / Tail fiber / OTU domain-containing protein 7B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Polyubiquitin-B
C: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9768
Polymers53,5133
Non-polymers4635
Water543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-28 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.030, 56.520, 91.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Polyubiquitin- ... , 2 types, 2 molecules BC

#2: Protein Polyubiquitin-B


Mass: 8547.770 Da / Num. of mol.: 1 / Mutation: K11X / Source method: obtained synthetically
Details: Lys11 was replaced with a diaminobutyric acid (DAB) residue
Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47
#3: Protein Polyubiquitin-B


Mass: 8604.884 Da / Num. of mol.: 1 / Mutation: G76X / Source method: obtained synthetically
Details: Gly76 was replaced with a ligation handle for diubiquitin probe generation
Source: (synth.) Homo sapiens (human) / References: UniProt: P0CG47

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Non-polymers , 3 types, 8 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M phosphate citrate (pH 4.2), 20% (w/v) PEG 8K, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.8→56.52 Å / Num. obs: 11505 / % possible obs: 94.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 9.5
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 2 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.162 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.88
RfactorNum. reflection% reflection
Rfree0.2442 550 4.79 %
Rwork0.2072 --
obs0.209 11478 93.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 29 3 3356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023422
X-RAY DIFFRACTIONf_angle_d0.5214667
X-RAY DIFFRACTIONf_dihedral_angle_d12.0871215
X-RAY DIFFRACTIONf_chiral_restr0.022538
X-RAY DIFFRACTIONf_plane_restr0.003595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.08170.311420.28172712X-RAY DIFFRACTION95
3.0817-3.52760.28161300.24362738X-RAY DIFFRACTION95
3.5276-4.44390.22711410.18742708X-RAY DIFFRACTION93
4.4439-48.16940.21161370.17622770X-RAY DIFFRACTION91
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)
12.2536-0.605-0.89621.04070.30751.57330.0478-0.1373-0.1236-0.0119-0.05120.0467-0.05710.0131-0.00060.3174-0.0489-0.03640.21170.0140.238-8.659-0.8852-9.5667
27.2012-4.05010.04085.44071.6792.10370.0161-0.29320.07820.01150.0421-0.2195-0.1765-0.0334-0.01710.405-0.0507-0.00820.2560.02960.202617.4816-17.3895-10.8205
31.0874-0.37251.46514.3056-2.91798.8034-0.3315-1.6781-0.10080.70210.2973-0.1065-0.16980.4570.06980.4950.0908-0.04951.06340.1230.4235-1.8403-5.390117.5648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'

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