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- PDB-3oj4: Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex -

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Basic information

Entry
Database: PDB / ID: 3oj4
TitleCrystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex
Components
  • Tumor necrosis factor alpha-induced protein 3
  • Ubiquitin
  • Ubiquitin-conjugating enzyme E2 D1
KeywordsLIGASE/PROTEIN BINDING / ubiquitin / zinc finger / ubiquitin conjugating enzyme / zinc ion / LIGASE-PROTEIN BINDING 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 / 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 nucleotide-binding oligomerization domain containing 2 signaling pathway ...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 nucleotide-binding oligomerization domain containing 2 signaling pathway / negative regulation of chronic inflammatory response / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / negative regulation of toll-like receptor 2 signaling pathway / positive regulation of protein polyubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein K11-linked deubiquitination / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / negative regulation of toll-like receptor 4 signaling pathway / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / B-1 B cell homeostasis / Phosphorylation of the APC/C / regulation of defense response to virus by host / protein K48-linked deubiquitination / Signaling by BMP / positive regulation of hepatocyte proliferation / (E3-independent) E2 ubiquitin-conjugating enzyme / regulation of tumor necrosis factor-mediated signaling pathway / regulation of germinal center formation / Transferases; Acyltransferases; Aminoacyltransferases / hypothalamus gonadotrophin-releasing hormone neuron development / protein K63-linked deubiquitination / negative regulation of bone resorption / female meiosis I / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / fat pad development / mitochondrion transport along microtubule / negative regulation of interleukin-1 beta production / K63-linked deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / E2 ubiquitin-conjugating enzyme / negative regulation of interleukin-2 production / female gonad development / seminiferous tubule development / male meiosis I / response to muramyl dipeptide / ubiquitin conjugating enzyme activity / Regulation of APC/C activators between G1/S and early anaphase / negative regulation of interleukin-6 production / Transcriptional Regulation by VENTX / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of tumor necrosis factor production / protein deubiquitination / negative regulation of BMP signaling pathway / positive regulation of Wnt signaling pathway / negative regulation of endothelial cell apoptotic process / protein K48-linked ubiquitination / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / negative regulation of TORC1 signaling / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / negative regulation of protein ubiquitination / FLT3 signaling by CBL mutants / negative regulation of canonical NF-kappaB signal transduction / cytoskeleton organization / 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 / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival
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. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme ...: / 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. / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-B / Polyubiquitin-C / Tumor necrosis factor alpha-induced protein 3 / Ubiquitin-conjugating enzyme E2 D1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBosanac, I. / Hymowitz, S.G.
CitationJournal: Mol.Cell / Year: 2010
Title: Ubiquitin Binding to A20 ZnF4 Is Required for Modulation of NF-κB 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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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_ncs_dom_lim / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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-conjugating enzyme E2 D1
B: Ubiquitin
C: Tumor necrosis factor alpha-induced protein 3
D: Ubiquitin-conjugating enzyme E2 D1
E: Ubiquitin
F: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2418
Polymers63,1106
Non-polymers1312
Water00
1
A: Ubiquitin-conjugating enzyme E2 D1
B: Ubiquitin
C: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6204
Polymers31,5553
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ubiquitin-conjugating enzyme E2 D1
E: Ubiquitin
F: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6204
Polymers31,5553
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.646, 102.646, 112.686
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMETAA1 - 1477 - 153
21METMETMETMETDD1 - 1477 - 153
12METMETARGARGBB1 - 724 - 75
22METMETARGARGEE1 - 724 - 75
13SERSERLYSLYSCC605 - 63519 - 49
23SERSERLYSLYSFF605 - 63519 - 49

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 D1 / Ubiquitin-protein ligase D1 / Ubiquitin carrier protein D1 / UbcH5 / Ubiquitin-conjugating enzyme ...Ubiquitin-protein ligase D1 / Ubiquitin carrier protein D1 / UbcH5 / Ubiquitin-conjugating enzyme E2-17 kDa 1 / Ubiquitin-conjugating enzyme E2(17)KB 1 / UBC4/5 homolog / Stimulator of Fe transport / SFT


Mass: 17277.756 Da / Num. of mol.: 2 / Fragment: Ubiquitin-conjugating enzyme E2 D1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D1, SFT, UBC5A, UBCH5, UBCH5A / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon + RIL / References: UniProt: P51668, ubiquitin-protein ligase
#2: Protein Ubiquitin


Mass: 8859.106 Da / Num. of mol.: 2 / 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, UniProt: P0CG48*PLUS
#3: 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.: 2 / 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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.1
Details: 0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 13, 2006
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→25 Å / Num. all: 9814 / Num. obs: 9637 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rsym value: 0.115 / Net I/σ(I): 16.8
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 955 / Rsym value: 0.75 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY: 1UBQ, 1X23

1ubq

1x23


Resolution: 3.4→25 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.842 / SU B: 102.112 / SU ML: 0.724 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.767 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31882 962 10 %RANDOM
Rwork0.27984 ---
all0.284 9612 --
obs0.28381 8650 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.095 Å2
Baniso -1Baniso -2Baniso -3
1--3.19 Å2-1.6 Å20 Å2
2---3.19 Å20 Å2
3---4.79 Å2
Refinement stepCycle: LAST / Resolution: 3.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 2 0 3988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224090
X-RAY DIFFRACTIONr_angle_refined_deg1.0131.9755538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3135494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84824.556180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.90915722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3951520
X-RAY DIFFRACTIONr_chiral_restr0.070.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023074
X-RAY DIFFRACTIONr_nbd_refined0.1940.21669
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22715
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.25
X-RAY DIFFRACTIONr_mcbond_it0.8342.52587
X-RAY DIFFRACTIONr_mcangle_it1.28154086
X-RAY DIFFRACTIONr_scbond_it1.2532.51707
X-RAY DIFFRACTIONr_scangle_it1.82351452
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A588tight positional0.010.05
2B288tight positional0.020.05
3C124tight positional0.010.05
1A582medium positional0.150.5
2B286medium positional0.180.5
3C125medium positional0.090.5
1A588tight thermal0.020.5
2B288tight thermal0.020.5
3C124tight thermal0.020.5
1A582medium thermal0.162
2B286medium thermal0.152
3C125medium thermal0.142
LS refinement shellResolution: 3.4→3.469 Å / Rfactor Rfree error: 43.6 / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.436 61 -
Rwork0.43 502 -
obs-563 100 %
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)
113.26093.45892.42286.15513.63810.1513-0.2905-0.43070.3014-0.41240.3140.4103-1.03571.1709-0.0234-0.5801-0.0904-0.0359-0.48410.0597-0.4289-36.746120.302664.2197
26.33641.94091.777415.37054.606510.6419-0.78081.04660.3943-2.19311.3058-0.2936-2.32311.9386-0.5250.5577-0.90760.03980.1725-0.141-0.4883-25.919517.78943.6012
350.84428.46463.222342.261114.996344.9484-0.36651.3702-4.13350.11521.5811-1.95161.82132.8831-1.2146-0.7426-0.0592-0.1028-0.2453-0.2041-0.2868-27.7701-4.393844.3441
45.417-1.70571.184414.22524.487210.34870.60.03230.23120.0111-0.64260.49081.6588-0.25490.0426-0.38850.01550.0786-0.6307-0.0109-0.4151-35.94721.6829-7.8757
510.83254.62864.00299.832.473110.34151.1882-0.843-0.56922.1166-0.46780.20282.3933-0.7979-0.72041.0243-0.5801-0.1239-0.2837-0.037-0.4339-28.349313.53512.7369
638.92950.04227.175852.13968.345538.17170.64730.16770.47371.64470.5544-4.14331.2432.7195-1.2016-0.28060.2274-0.0646-0.6408-0.1888-0.318-10.087126.250212.0151
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 147
2X-RAY DIFFRACTION2B1 - 73
3X-RAY DIFFRACTION3C605 - 635
4X-RAY DIFFRACTION4D1 - 147
5X-RAY DIFFRACTION5E1 - 73
6X-RAY DIFFRACTION6F605 - 635

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