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- PDB-2vfj: Structure of the A20 Ovarian Tumour (OTU) domain -

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Basic information

Entry
Database: PDB / ID: 2vfj
TitleStructure of the A20 Ovarian Tumour (OTU) domain
ComponentsTUMOR NECROSIS FACTOR
KeywordsHYDROLASE / PHOSPHORYLATION / CYSTEINE PROTEASE / METAL-BINDING / OVARIAN TUMOUR / THIOL PROTEASE / DNA-BINDING / POLYMORPHISM / LYS63-LINKED / CYTOPLASM / UBIQUITIN / ZINC-FINGER / DEUBIQUITINATING ENZYME / CYTOKINE SIGNALLING / UBL CONJUGATION PATHWAY / OTU / ZINC / NF-KB / NUCLEUS / PROTEASE / APOPTOSIS
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 / regulation of tumor necrosis factor-mediated signaling pathway / regulation of germinal center formation / positive regulation of hepatocyte proliferation / Transferases; Acyltransferases; Aminoacyltransferases / 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 deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of NF-kappaB transcription factor activity / response to muramyl dipeptide / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / positive regulation of Wnt signaling pathway / protein deubiquitination / negative regulation of endothelial cell apoptotic process / protein K48-linked ubiquitination / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of canonical NF-kappaB signal transduction / cytoskeleton organization / negative regulation of protein ubiquitination / negative regulation of innate immune response / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / Negative regulators of DDX58/IFIH1 signaling / negative regulation of smooth muscle cell proliferation / Regulation of TNFR1 signaling / response to molecule of bacterial origin / NOD1/2 Signaling Pathway / negative regulation of inflammatory response / cellular response to hydrogen peroxide / kinase binding / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / Ovarian tumor domain proteases / 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.
Similarity search - Domain/homology
Tumor necrosis factor alpha-induced protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsKomander, D. / Barford, D.
CitationJournal: Biochem.J. / Year: 2008
Title: Structure of the A20 Otu Domain and Mechanistic Insights Into Deubiquitination
Authors: Komander, D. / Barford, D.
History
DepositionNov 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _software.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TUMOR NECROSIS FACTOR
B: TUMOR NECROSIS FACTOR
C: TUMOR NECROSIS FACTOR
D: TUMOR NECROSIS FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,8229
Polymers172,4144
Non-polymers4095
Water00
1
A: TUMOR NECROSIS FACTOR


Theoretical massNumber of molelcules
Total (without water)43,1031
Polymers43,1031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TUMOR NECROSIS FACTOR


Theoretical massNumber of molelcules
Total (without water)43,1031
Polymers43,1031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: TUMOR NECROSIS FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2963
Polymers43,1031
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: TUMOR NECROSIS FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3204
Polymers43,1031
Non-polymers2163
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.964, 83.023, 164.940
Angle α, β, γ (deg.)90.00, 98.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TUMOR NECROSIS FACTOR / ALPHA-INDUCED PROTEIN 3 / DNA-BINDING PROTEIN A20 / ZINC FINGER PROTEIN A20


Mass: 43103.480 Da / Num. of mol.: 4 / Fragment: OVARIAN TUMOUR (OTU) DOMAIN, RESIDUES 1-366
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-366 / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P21580, ubiquitinyl hydrolase 1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Sequence detailsRESIDUES 1-366 OF A20 SEVERAL RESIDUES WERE MODELLED AS ALA DUE TO DISORDER

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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: 3.4 Å3/Da / Density % sol: 63 % / Description: 3 WAVELENGTH MAD EXPERIMENT
Crystal growDetails: 1.3-1.6 M MAGNESIUM SULPHATE, 0.1 M MES [PH 6.5-6.9]

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 36226 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.9
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.6 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDEphasing
HKL2Mapphasing
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3.2→50.286 Å / σ(F): 1.4 / Stereochemistry target values: ML
Details: THE ANISO RECORDS CORRESPOND TO TLS FACTORS INCORPORATED BY PHENIX AND NOT ANISOTROPIC REFINEMENT OF INDIVIDUAL ATOMS.
RfactorNum. reflection% reflection
Rfree0.2429 3606 5.1 %
Rwork0.2044 --
obs0.2064 70382 95.63 %
Refinement stepCycle: LAST / Resolution: 3.2→50.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10182 0 21 0 10203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110444
X-RAY DIFFRACTIONf_angle_d1.37714236
X-RAY DIFFRACTIONf_dihedral_angle_d19.5113613
X-RAY DIFFRACTIONf_chiral_restr0.0941624
X-RAY DIFFRACTIONf_plane_restr0.0051810
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)
11.8733-0.14570.56521.4025-0.06461.5824-0.1283-0.034-0.43440.00450.08720.34690.0236-0.4090.02480.21220.028-0.10510.3589-0.00770.322920.250615.772621.9341
21.34420.1127-0.20210.3908-0.16681.257-0-0.211-0.00290.23920.0227-0.2561-0.01280.4446-0.01640.7439-0.08610.06480.7643-0.05570.307730.478257.961872.413
32.07331.11821.01011.82430.41821.4006-0.0881-0.11930.2926-0.14180.07340.205-0.2881-0.39690.06050.36640.1549-0.05850.25410.09590.21135.679351.498124.6551
40.9847-0.3446-0.17121.47290.21092.0742-0.082-0.4899-0.01220.11260.3143-0.3429-0.06130.8801-0.21340.38760.1255-0.12970.8380.00950.28162.590122.845945.8598
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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