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- PDB-5lrw: Structure of Cezanne/OTUD7B OTU domain bound to ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5lrw
TitleStructure of Cezanne/OTUD7B OTU domain bound to ubiquitin
Components
  • OTU domain-containing protein 7B
  • Polyubiquitin-B
KeywordsHYDROLASE / protease / deubiquitinase / OTU domain
Function / homology
Function and homology information


mucosal immune response / protein K11-linked deubiquitination / negative regulation of interleukin-8 production / protein K48-linked deubiquitination / protein K63-linked deubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of protein localization to nucleus / K48-linked deubiquitinase activity / female meiosis I / positive regulation of protein monoubiquitination ...mucosal immune response / protein K11-linked deubiquitination / negative regulation of interleukin-8 production / protein K48-linked deubiquitination / protein K63-linked deubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of protein localization to nucleus / K48-linked deubiquitinase activity / female meiosis I / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / mitochondrion transport along microtubule / K63-linked polyubiquitin modification-dependent protein binding / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / regulation of proteasomal protein catabolic process / energy homeostasis / cysteine-type peptidase activity / regulation of neuron apoptotic process / negative regulation of canonical NF-kappaB signal transduction / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Regulation of FZD by ubiquitination / 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 / p75NTR recruits signalling complexes / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / neuron projection morphogenesis / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / regulation of mitochondrial membrane potential / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of NF-kappa B signaling / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / NOTCH3 Activation and Transmission of Signal to the Nucleus / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Recognition of DNA damage by PCNA-containing replication complex
Similarity search - Function
Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / UBA-like domain / OTU domain / OTU domain profile. / Ubiquitin conserved site / Ubiquitin domain ...Zinc finger, A20-type / A20-like zinc finger / Zinc finger A20-type profile. / A20-like zinc fingers / OTU-like cysteine protease / UBA-like domain / OTU domain / OTU domain profile. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Polyubiquitin-B / OTU domain-containing protein 7B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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 2.0Sep 13, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization

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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: OTU domain-containing protein 7B
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3546
Polymers85,1704
Non-polymers1842
Water11,187621
1
A: OTU domain-containing protein 7B
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6773
Polymers42,5852
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-10 kcal/mol
Surface area16940 Å2
MethodPISA
2
C: OTU domain-containing protein 7B
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6773
Polymers42,5852
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-11 kcal/mol
Surface area16460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.560, 157.560, 75.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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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: 34037.910 Da / Num. of mol.: 2 / Mutation: residues 267-291 were replaced by QPG
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: Protein Polyubiquitin-B


Mass: 8546.848 Da / Num. of mol.: 2 / Mutation: G76X
Source method: isolated from a genetically manipulated source
Details: Gly76 was replaced with 2-bromoethylamine / Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate (pH 4.8), 6% (w/v) PEG 6K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→66.13 Å / Num. obs: 47250 / % possible obs: 100 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 8.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.854 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.484 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.58
RfactorNum. reflection% reflection
Rfree0.2171 2389 5.06 %
Rwork0.1761 --
obs0.1781 47215 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→45.484 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5517 0 12 621 6150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025755
X-RAY DIFFRACTIONf_angle_d0.6237837
X-RAY DIFFRACTIONf_dihedral_angle_d13.0562099
X-RAY DIFFRACTIONf_chiral_restr0.025886
X-RAY DIFFRACTIONf_plane_restr0.0031002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04090.28151390.25492613X-RAY DIFFRACTION100
2.0409-2.08530.29291260.24072669X-RAY DIFFRACTION100
2.0853-2.13380.28811210.22412639X-RAY DIFFRACTION100
2.1338-2.18720.23661480.22212642X-RAY DIFFRACTION100
2.1872-2.24630.23821400.21932623X-RAY DIFFRACTION100
2.2463-2.31240.24261380.20992645X-RAY DIFFRACTION100
2.3124-2.3870.26461410.20112628X-RAY DIFFRACTION100
2.387-2.47230.24141620.20022621X-RAY DIFFRACTION100
2.4723-2.57130.25811570.18842629X-RAY DIFFRACTION100
2.5713-2.68830.22981390.17932640X-RAY DIFFRACTION100
2.6883-2.83010.25381420.18182645X-RAY DIFFRACTION100
2.8301-3.00730.21961440.17492621X-RAY DIFFRACTION100
3.0073-3.23950.20361410.16912655X-RAY DIFFRACTION100
3.2395-3.56540.18741480.15792631X-RAY DIFFRACTION100
3.5654-4.0810.19831260.14642652X-RAY DIFFRACTION100
4.081-5.14050.17081330.13572650X-RAY DIFFRACTION100
5.1405-45.49540.17791440.15782623X-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)
11.0840.05810.3790.64660.07950.9860.02190.0123-0.0698-0.0064-0.00180.01020.0876-0.0452-0.00270.1088-0.02360.00750.06830.00210.09165.639424.2626-12.0961
20.3841-0.04380.26230.97740.11750.7022-0.05950.1637-0.81930.21040.1581-0.03490.3104-0.346-0.02360.234-0.171100.1845-0.08860.499349.06410.0976-15.5755
31.0720.1091-0.14790.7607-0.11591.89460.0442-0.00390.07060.0027-0.0177-0.0392-0.22250.2111-0.00910.1153-0.0079-0.00230.1321-0.00580.102512.849621.10790.752
41.5840.4382-0.99771.535-0.5261.2550.10920.43540.78970.2965-0.0955-0.4676-1.45860.3026-0.02610.8542-0.30040.00090.49450.09540.61329.290844.4789-4.3121
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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