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- PDB-5lrx: Structure of A20 OTU domain bound to ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5lrx
TitleStructure of A20 OTU domain bound to ubiquitin
Components
  • (Tumor necrosis factor alpha-induced protein 3) x 2
  • Polyubiquitin-B
KeywordsHYDROLASE / protease / deubiquitinase / OTU domain
Function / homology
Function and homology information


regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / tolerance induction to lipopolysaccharide / negative regulation of osteoclast proliferation / negative regulation of CD40 signaling pathway / negative regulation of B cell activation / negative regulation of toll-like receptor 3 signaling pathway / negative regulation of chronic inflammatory response ...regulation of vascular wound healing / negative regulation of toll-like receptor 5 signaling pathway / negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / establishment of protein localization to vacuole / tolerance induction to lipopolysaccharide / negative regulation of osteoclast proliferation / negative regulation of CD40 signaling pathway / negative regulation of B cell activation / negative regulation of toll-like receptor 3 signaling pathway / negative regulation of chronic inflammatory response / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / negative regulation of toll-like receptor 2 signaling pathway / protein K11-linked deubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / B-1 B cell homeostasis / protein K48-linked deubiquitination / regulation of defense response to virus by host / positive regulation of hepatocyte proliferation / regulation of tumor necrosis factor-mediated signaling pathway / regulation of germinal center formation / Transferases; Acyltransferases; Aminoacyltransferases / symbiont entry into host cell via disruption of host cell glycocalyx / negative regulation of bone resorption / protein K63-linked deubiquitination / TNFR1-induced proapoptotic signaling / negative regulation of interleukin-1 beta production / negative regulation of interleukin-2 production / K63-linked polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / symbiont entry into host cell via disruption of host cell envelope / virus tail / response to muramyl dipeptide / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / protein deubiquitination / positive regulation of Wnt signaling pathway / negative regulation of endothelial cell apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein K48-linked ubiquitination / negative regulation of protein ubiquitination / cytoskeleton organization / TNFR1-induced NF-kappa-B signaling pathway / negative regulation of canonical NF-kappaB signal transduction / negative regulation of innate immune response / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / ubiquitin binding / NOD1/2 Signaling Pathway / negative regulation of smooth muscle cell proliferation / response to molecule of bacterial origin / negative regulation of inflammatory response / kinase binding / cellular response to hydrogen peroxide / Ovarian tumor domain proteases / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / cell migration / cellular response to lipopolysaccharide / protease binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / inflammatory response / apoptotic process / DNA binding / extracellular exosome / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Zinc finger, A20-type / A20-like zinc finger / 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 ...: / Zinc finger, A20-type / A20-like zinc finger / 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
Tail fiber / Tumor necrosis factor alpha-induced protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor necrosis factor alpha-induced protein 3
B: Polyubiquitin-B
C: Tumor necrosis factor alpha-induced protein 3
D: Polyubiquitin-B
E: Tumor necrosis factor alpha-induced protein 3
F: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)191,2416
Polymers191,2416
Non-polymers00
Water00
1
A: Tumor necrosis factor alpha-induced protein 3
B: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)52,0742
Polymers52,0742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-10 kcal/mol
Surface area18220 Å2
MethodPISA
2
C: Tumor necrosis factor alpha-induced protein 3
D: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)52,0742
Polymers52,0742
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-12 kcal/mol
Surface area18400 Å2
MethodPISA
3
E: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)43,5471
Polymers43,5471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15840 Å2
MethodPISA
4
F: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)43,5471
Polymers43,5471
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.195, 71.950, 203.926
Angle α, β, γ (deg.)90.00, 94.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tumor necrosis factor alpha-induced protein 3 / TNF alpha-induced protein 3 / OTU domain-containing protein 7C / Putative DNA-binding protein A20 / ...TNF alpha-induced protein 3 / OTU domain-containing protein 7C / Putative DNA-binding protein A20 / Zinc finger protein A20


Mass: 43514.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP3, OTUD7C / Production host: Escherichia coli (E. coli)
References: UniProt: P21580, ubiquitinyl hydrolase 1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein Polyubiquitin-B


Mass: 8558.857 Da / Num. of mol.: 2 / Mutation: G76X
Source method: isolated from a genetically manipulated source
Details: Gly76 was replaced with propargylamide / Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Protein Tumor necrosis factor alpha-induced protein 3 / TNF alpha-induced protein 3 / OTU domain-containing protein 7C / Putative DNA-binding protein A20 / ...TNF alpha-induced protein 3 / OTU domain-containing protein 7C / Putative DNA-binding protein A20 / Zinc finger protein A20


Mass: 43546.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cys103 is oxidized / Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP3, OTUD7C / Production host: Escherichia coli (E. coli)
References: UniProt: P21580, ubiquitinyl hydrolase 1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES/imidazole (pH 6.5), 7% (w/v) PEG 8K, 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96863 Å / Relative weight: 1
ReflectionResolution: 2.85→49.33 Å / Num. obs: 43448 / % possible obs: 99.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.6
Reflection shellResolution: 2.85→2.96 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→49.325 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 2218 5.11 %
Rwork0.1952 --
obs0.1977 43393 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→49.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11566 0 0 0 11566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211838
X-RAY DIFFRACTIONf_angle_d0.53516175
X-RAY DIFFRACTIONf_dihedral_angle_d16.4876996
X-RAY DIFFRACTIONf_chiral_restr0.0421889
X-RAY DIFFRACTIONf_plane_restr0.0042069
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9120.34991520.29072582X-RAY DIFFRACTION100
2.912-2.97970.28341290.26012523X-RAY DIFFRACTION100
2.9797-3.05420.30631520.23822563X-RAY DIFFRACTION99
3.0542-3.13680.32441580.24862535X-RAY DIFFRACTION99
3.1368-3.22910.32931110.23072568X-RAY DIFFRACTION99
3.2291-3.33330.29131390.21662550X-RAY DIFFRACTION99
3.3333-3.45240.251640.20482544X-RAY DIFFRACTION100
3.4524-3.59060.21761490.20092587X-RAY DIFFRACTION100
3.5906-3.75390.28961460.19982524X-RAY DIFFRACTION99
3.7539-3.95180.26561070.19222567X-RAY DIFFRACTION99
3.9518-4.19920.21871320.16762617X-RAY DIFFRACTION100
4.1992-4.52320.17731560.1562545X-RAY DIFFRACTION99
4.5232-4.9780.22241210.15332609X-RAY DIFFRACTION99
4.978-5.69750.23491330.18082591X-RAY DIFFRACTION99
5.6975-7.17470.27751180.2162648X-RAY DIFFRACTION99
7.1747-49.33270.221510.19692622X-RAY DIFFRACTION98
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)
12.24220.0236-1.2061.6784-0.33254.20250.0412-0.02080.2443-0.19110.1744-0.1436-0.10520.3217-0.18590.2963-0.07190.00940.454-0.03510.341912.7188-8.204234.4361
25.01060.4927-2.47752.84520.0623.51080.0324-0.0842-0.00450.14120.05980.03140.0263-0.5053-0.05020.3238-0.0433-0.08240.66440.02890.3609-17.8015-12.299843.6352
32.49520.055-0.05371.8419-0.70323.77810.0830.3354-0.0957-0.1528-0.0039-0.05880.28950.1776-0.07110.44120.0476-0.08450.4236-0.03520.357234.5828-40.635272.8741
44.1679-1.6334-4.01827.21333.25726.1240.13311.1811-0.1678-0.9573-0.0281-0.83760.1503-0.484-0.11260.92260.1077-0.00230.9229-0.16590.656361.046-45.539855.4106
52.1634-0.30490.83121.2178-0.55463.51320.07440.04420.0389-0.2251-0.0486-0.0881-0.05570.0618-0.0430.35210.00610.03120.27590.00330.335542.8612-54.9258119.3378
62.89811.24180.57562.19210.87652.51790.15950.26250.43340.13730.06430.2505-0.24110.5475-0.21030.6738-0.12190.12820.7155-0.03050.427917.4871-21.1743-13.7268
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'

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