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- PDB-3vuy: Crystal structure of A20 ZF7 in complex with linear tetraubiquitin -

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Basic information

Entry
Database: PDB / ID: 3vuy
TitleCrystal structure of A20 ZF7 in complex with linear tetraubiquitin
Components
  • Polyubiquitin-C
  • Tumor necrosis factor alpha-induced protein 3
KeywordsPROTEIN BINDING/METAL BINDING PROTEIN / zinc finger / PROTEIN BINDING-METAL BINDING PROTEIN 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 / negative regulation of B cell activation / 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 / negative regulation of osteoclast proliferation / tolerance induction to lipopolysaccharide / negative regulation of CD40 signaling pathway / negative regulation of toll-like receptor 3 signaling pathway / negative regulation of B cell activation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / : / negative regulation of toll-like receptor 2 signaling pathway / protein K11-linked deubiquitination / negative regulation of chronic inflammatory response / negative regulation of toll-like receptor 4 signaling pathway / regulation of germinal center formation / protein K48-linked deubiquitination / B-1 B cell homeostasis / regulation of defense response to virus by host / regulation of tumor necrosis factor-mediated signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / protein K63-linked deubiquitination / positive regulation of hepatocyte proliferation / negative regulation of bone resorption / 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 / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of interleukin-6 production / response to muramyl dipeptide / negative regulation of tumor necrosis factor production / positive regulation of Wnt signaling pathway / protein K48-linked ubiquitination / negative regulation of endothelial cell apoptotic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / 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 / cytoskeleton organization / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / 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 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / 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 / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / negative regulation of innate immune response / NF-kB is activated and signals survival / 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 / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / 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 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / APC/C:Cdc20 mediated degradation of Securin
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 / 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 / OTU domain / OTU domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / Polyubiquitin-C / Tumor necrosis factor alpha-induced protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsNishimasu, H. / Ishitani, R. / Nureki, O.
CitationJournal: Embo J. / Year: 2012
Title: Specific recognition of linear polyubiquitin by A20 zinc finger 7 is involved in NF-kappaB regulation
Authors: Tokunaga, F. / Nishimasu, H. / Ishitani, R. / Goto, E. / Noguchi, T. / Mio, K. / Kamei, K. / Ma, A. / Iwai, K. / Nureki, O.
History
DepositionJul 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_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_asym_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_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: Polyubiquitin-C
D: Tumor necrosis factor alpha-induced protein 3
C: Polyubiquitin-C
F: Tumor necrosis factor alpha-induced protein 3
B: Polyubiquitin-C
E: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,97412
Polymers37,6606
Non-polymers3146
Water3,315184
1
A: Polyubiquitin-C
D: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6584
Polymers12,5532
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-18 kcal/mol
Surface area6520 Å2
MethodPISA
2
C: Polyubiquitin-C
F: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6584
Polymers12,5532
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-20 kcal/mol
Surface area6270 Å2
MethodPISA
3
B: Polyubiquitin-C
E: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6584
Polymers12,5532
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-19 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.438, 62.438, 85.355
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 3 / Fragment: Ubiquitin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Plasmid: pT7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P0CG48
#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: 3976.549 Da / Num. of mol.: 3 / Fragment: A20-type 7 Zinc finger domain, residues 757-790
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P21580
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.55 Å3/Da / Density % sol: 51.78 % / Mosaicity: 0.344 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10mM Tris-HCl, 150mM NaCl, 0.2M Na/K tartrate, 8% PEG 3350, pH 8.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 25855 / Num. obs: 25855 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.096 / Χ2: 1.59 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.98-2.014.40.47912930.749198.3
2.01-2.0550.47412480.777199.8
2.05-2.095.40.47413480.922199.6
2.09-2.135.40.43112540.872199.5
2.13-2.185.70.42312900.884199.8
2.18-2.235.90.39413140.9199.8
2.23-2.296.20.35612790.966199.8
2.29-2.356.60.32212970.998199.8
2.35-2.426.70.32513101.073199.8
2.42-2.4970.29212941.0991100
2.49-2.587.30.25912871.155199.9
2.58-2.697.80.22312751.2761100
2.69-2.818.20.16312991.317199.9
2.81-2.968.50.15213001.4251100
2.96-3.149.10.12813091.6051100
3.14-3.399.60.09212741.7711100
3.39-3.7310.20.07113052.0591100
3.73-4.2610.70.05512902.304199.9
4.26-5.37110.04912812.637199.8
5.37-5010.70.05213083.213199.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.981→45.678 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.68 / σ(F): 2.04 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 1288 4.99 %random
Rwork0.2164 ---
obs0.2184 25820 99.68 %-
all-25820 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.682 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 116.59 Å2 / Biso mean: 42.3906 Å2 / Biso min: 17.46 Å2
Baniso -1Baniso -2Baniso -3
1-5.0841 Å2-0 Å2-0 Å2
2--5.0841 Å2-0 Å2
3----10.1682 Å2
Refinement stepCycle: LAST / Resolution: 1.981→45.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 6 184 2731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122591
X-RAY DIFFRACTIONf_angle_d0.6273461
X-RAY DIFFRACTIONf_chiral_restr0.046380
X-RAY DIFFRACTIONf_plane_restr0.002455
X-RAY DIFFRACTIONf_dihedral_angle_d14.097989
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9809-2.06020.39381430.37382711285499
2.0602-2.1540.38371390.324827242863100
2.154-2.26750.31561440.279127292873100
2.2675-2.40960.27371430.253927272870100
2.4096-2.59560.29871420.241127402882100
2.5956-2.85680.26621450.223327322877100
2.8568-3.27010.24861480.195827142862100
3.2701-4.11960.19731430.168627362879100
4.1196-45.69040.20981410.171727192860100
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)
12.2150.5223-0.91394.26180.58762.3690.0937-0.0544-0.0860.21570.05380.34270.3819-0.7265-0.14720.2336-0.11070.00390.47810.03380.1983-3.944828.5367-12.6407
27.65981.1150.30783.2130.53566.8955-0.1618-0.0313-0.4536-0.2710.0943-0.43240.6840.54120.09320.3923-0.02660.04920.31760.07940.2676.8511-2.32367.78
33.47542.6450.9915.80690.03443.7777-0.1455-0.2236-0.2336-0.32830.0707-0.23740.17850.31670.02340.11630.02150.02130.36890.06470.21728.421210.36678.9544
42.1759-0.15030.29011.8761-0.40095.92570.1829-0.3374-0.17520.0009-0.1809-0.15980.09810.5282-0.02230.2666-0.1753-0.02460.42070.04590.23255.668431.8925-29.6266
58.2677-2.2778-0.55698.0051.95357.9979-0.1851-0.23510.20440.1420.1445-0.0825-0.10350.40750.01640.5193-0.00810.03260.2518-0.0180.1993.35427.3509-8.5294
63.612-1.7014-0.90834.0328-0.78414.55920.05060.1590.2859-0.0559-0.00270.2244-0.7554-0.7649-0.06660.46560.193-0.08870.4691-0.02950.274224.740820.274225.104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:76)A1 - 76
2X-RAY DIFFRACTION2(CHAIN B AND RESID 1:76)B1 - 76
3X-RAY DIFFRACTION3(CHAIN C AND RESID 1:76)C1 - 76
4X-RAY DIFFRACTION4(CHAIN D AND (RESID 757:789 OR RESID 801:802) )D757 - 789
5X-RAY DIFFRACTION4(CHAIN D AND (RESID 757:789 OR RESID 801:802) )D801 - 802
6X-RAY DIFFRACTION5(CHAIN E AND (RESID 759:790 OR RESID 801:802) )E759 - 790
7X-RAY DIFFRACTION5(CHAIN E AND (RESID 759:790 OR RESID 801:802) )E801 - 802
8X-RAY DIFFRACTION6(CHAIN F AND (RESID 759:789 OR RESID 801:802) )F759 - 789
9X-RAY DIFFRACTION6(CHAIN F AND (RESID 759:789 OR RESID 801:802) )F801 - 802

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