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- PDB-3oj3: Crystal structure of the A20 ZnF4 and ubiquitin complex -

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Basic information

Entry
Database: PDB / ID: 3oj3
TitleCrystal structure of the A20 ZnF4 and ubiquitin complex
Components
  • Tumor necrosis factor alpha-induced protein 3
  • Ubiquitin
KeywordsPROTEIN BINDING/HYDROLASE / ubiquitin / zinc finger / zinc ion / PROTEIN BINDING-HYDROLASE complex
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 / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / protein K33-linked deubiquitination / protein K29-linked deubiquitination ...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 / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / protein K33-linked deubiquitination / protein K29-linked deubiquitination / negative regulation of B cell activation / 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 / regulation of germinal center formation / B-1 B cell homeostasis / regulation of defense response to virus by host / protein K48-linked deubiquitination / regulation of tumor necrosis factor-mediated signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / positive regulation of hepatocyte proliferation / protein K63-linked deubiquitination / hypothalamus gonadotrophin-releasing hormone neuron development / negative regulation of bone resorption / female meiosis I / TNFR1-induced proapoptotic signaling / positive regulation of protein monoubiquitination / negative regulation of interleukin-1 beta production / fat pad development / mitochondrion transport along microtubule / K63-linked deubiquitinase activity / negative regulation of NF-kappaB transcription factor activity / negative regulation of interleukin-2 production / K63-linked polyubiquitin modification-dependent protein binding / female gonad development / seminiferous tubule development / male meiosis I / response to muramyl dipeptide / negative regulation of interleukin-6 production / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of tumor necrosis factor production / positive regulation of Wnt signaling pathway / protein deubiquitination / protein K48-linked ubiquitination / negative regulation of endothelial cell apoptotic process / negative regulation of canonical NF-kappaB signal transduction / regulation of neuron apoptotic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of proteasomal protein catabolic process / energy homeostasis / cytoskeleton organization / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of protein ubiquitination / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Constitutive Signaling by NOTCH1 HD Domain Mutants / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / negative regulation of innate immune response / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation
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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : ...: / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin-like (UB roll) / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Tumor necrosis factor alpha-induced protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBosanac, I. / Hymowitz, S.G.
CitationJournal: Mol.Cell / Year: 2010
Title: Ubiquitin Binding to A20 ZnF4 Is Required for Modulation of NF-KB Signaling
Authors: Bosanac, I. / Wertz, I.E. / Pan, B. / Yu, C. / Kusam, S. / Lam, C. / Phu, L. / Phung, Q. / Maurer, B. / Arnott, D. / Kirkpatrick, D.S. / Dixit, V.M. / Hymowitz, S.G.
History
DepositionAug 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: Ubiquitin
D: Ubiquitin
E: Ubiquitin
F: Ubiquitin
G: Ubiquitin
H: Ubiquitin
I: Tumor necrosis factor alpha-induced protein 3
J: Tumor necrosis factor alpha-induced protein 3
K: Tumor necrosis factor alpha-induced protein 3
L: Tumor necrosis factor alpha-induced protein 3
M: Tumor necrosis factor alpha-induced protein 3
N: Tumor necrosis factor alpha-induced protein 3
O: Tumor necrosis factor alpha-induced protein 3
P: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,74124
Polymers114,21816
Non-polymers5238
Water2,144119
1
A: Ubiquitin
I: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3433
Polymers14,2772
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
J: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3433
Polymers14,2772
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin
K: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3433
Polymers14,2772
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin
L: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3433
Polymers14,2772
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Ubiquitin
M: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3433
Polymers14,2772
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Ubiquitin
N: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3433
Polymers14,2772
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Ubiquitin
O: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3433
Polymers14,2772
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Ubiquitin
P: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3433
Polymers14,2772
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Ubiquitin
C: Ubiquitin
D: Ubiquitin
I: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0615
Polymers31,9954
Non-polymers651
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.830, 170.030, 66.239
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
52
62
72

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:71 )
211chain B and (resseq 1:71 )
311chain C and (resseq 1:71 )
411chain D and (resseq 1:71 )
511chain E and (resseq 1:71 )
611chain F and (resseq 1:71 )
711chain G and (resseq 1:71 )
811chain H and (resseq 1:71 )
112chain I and (resseq 605:634 )
212chain P and (resseq 605:634 )
312chain J and (resseq 605:634 )
412chain K and (resseq 605:634 )
512chain L and (resseq 605:634 )
612chain M and (resseq 605:634 )
712chain N and (resseq 605:634 )

NCS ensembles :
ID
1
2

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Components

#1: Protein
Ubiquitin


Mass: 8859.106 Da / Num. of mol.: 8 / Fragment: Ubiquitin, UNP residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon + RIL / References: UniProt: P0CG47
#2: Protein/peptide
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: 5418.088 Da / Num. of mol.: 8 / Fragment: Zinc finger A20-type 4, UNP residues 592-635
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP3, OTUD7C / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon + RIL / References: UniProt: P21580
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 41.88 %
Crystal growTemperature: 292 K / pH: 6.5
Details: 0.1 M MES pH 6.5 and 30% PEG 4000, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 29, 2006
Details: VERTICALLY COLLIMATING PREMIRROR, LN2 COOLED DOUBLE- CRYSTAL SILICON (111) MONOCHROMATOR, TOROIDAL FOCUSING M2 MIRROR
RadiationMonochromator: LIQUID NITROGEN COOLED DUAL CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.351
ReflectionResolution: 2.5→50 Å / Num. obs: 31541 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rsym value: 0.08 / Net I/σ(I): 15.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.409 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 1UBQ PDB ENTRY: 2FID

1ubq

2fid


Resolution: 2.5→43.064 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.882 / σ(F): 1.4 / Phase error: 36.54 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2258 1689 5.37 %
Rwork0.2028 --
obs0.2041 31426 96.13 %
all-31511 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.281 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0903 Å20 Å2-0.1441 Å2
2---0.4154 Å2-0 Å2
3----0.6749 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.064 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6602 0 8 119 6729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096690
X-RAY DIFFRACTIONf_angle_d1.0358974
X-RAY DIFFRACTIONf_dihedral_angle_d15.1652598
X-RAY DIFFRACTIONf_chiral_restr0.061026
X-RAY DIFFRACTIONf_plane_restr0.0041146
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A563X-RAY DIFFRACTIONPOSITIONAL
12B563X-RAY DIFFRACTIONPOSITIONAL0.047
13C563X-RAY DIFFRACTIONPOSITIONAL0.045
14D563X-RAY DIFFRACTIONPOSITIONAL0.046
15E563X-RAY DIFFRACTIONPOSITIONAL0.04
16F563X-RAY DIFFRACTIONPOSITIONAL0.049
17G563X-RAY DIFFRACTIONPOSITIONAL0.048
18H563X-RAY DIFFRACTIONPOSITIONAL0.047
21I240X-RAY DIFFRACTIONPOSITIONAL
22P240X-RAY DIFFRACTIONPOSITIONAL0.05
23J240X-RAY DIFFRACTIONPOSITIONAL0.041
24K240X-RAY DIFFRACTIONPOSITIONAL0.042
25L240X-RAY DIFFRACTIONPOSITIONAL0.048
26M240X-RAY DIFFRACTIONPOSITIONAL0.039
27N240X-RAY DIFFRACTIONPOSITIONAL0.045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.601-2.68490.34542000.3682355X-RAY DIFFRACTION89
2.6849-2.78090.34311720.33362393X-RAY DIFFRACTION91
2.7809-2.89220.33431680.31982400X-RAY DIFFRACTION91
2.8922-3.02380.30171700.28612427X-RAY DIFFRACTION91
3.0238-3.18320.26551230.26882405X-RAY DIFFRACTION92
3.1832-3.38250.26631170.23712409X-RAY DIFFRACTION92
3.3825-3.64360.20461260.21872391X-RAY DIFFRACTION91
3.6436-4.010.211090.17852405X-RAY DIFFRACTION91
4.01-4.58970.19181560.1382350X-RAY DIFFRACTION89
4.5897-5.78030.19361580.13892353X-RAY DIFFRACTION89
5.7803-43.070.16611310.15282342X-RAY DIFFRACTION87

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