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- PDB-3vuw: Crystal structure of A20 ZF7 in complex with linear ubiquitin, form I -

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Basic information

Entry
Database: PDB / ID: 3vuw
TitleCrystal structure of A20 ZF7 in complex with linear ubiquitin, form I
Components
  • Polyubiquitin-C
  • Tumor necrosis factor alpha-induced protein 3
KeywordsPROTEIN BINDING/METAL BINDING PROTEIN / zinc finger / cellular signaling / ubiquitination / 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 / 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 / Transferases; Acyltransferases; Aminoacyltransferases / protein K63-linked deubiquitination / positive regulation of hepatocyte proliferation / negative regulation of bone resorption / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of interleukin-2 production / negative regulation of interleukin-1 beta production / K63-linked deubiquitinase activity / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of interleukin-6 production / response to muramyl dipeptide / positive regulation of Wnt signaling pathway / negative regulation of tumor necrosis factor production / protein K48-linked ubiquitination / negative regulation of endothelial cell apoptotic process / negative regulation of canonical NF-kappaB signal transduction / cytoskeleton organization / 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 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / 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 / p75NTR recruits signalling complexes / 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 / InlA-mediated entry of Listeria monocytogenes into host cells / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / negative regulation of innate immune response / Translesion synthesis by REV1 / NF-kB is activated and signals survival / Regulation of PTEN localization / Translesion synthesis by POLK / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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: 1.95 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
B: Polyubiquitin-C
C: Polyubiquitin-C
E: Tumor necrosis factor alpha-induced protein 3
F: Tumor necrosis factor alpha-induced protein 3
G: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,80312
Polymers37,4896
Non-polymers3146
Water3,639202
1
A: Polyubiquitin-C
G: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6014
Polymers12,4962
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-18 kcal/mol
Surface area6110 Å2
MethodPISA
2
B: Polyubiquitin-C
F: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6014
Polymers12,4962
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-18 kcal/mol
Surface area6290 Å2
MethodPISA
3
C: Polyubiquitin-C
E: Tumor necrosis factor alpha-induced protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6014
Polymers12,4962
Non-polymers1052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-18 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.173, 51.991, 52.180
Angle α, β, γ (deg.)70.080, 80.250, 78.050
Int Tables number1
Space group name H-MP1

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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: 3919.497 Da / Num. of mol.: 3 / Fragment: A20-type 7 Zinc finger domain, residues 757-789
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.: 202 / 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: 2.59 Å3/Da / Density % sol: 52.55 % / Mosaicity: 0.424 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10mM Tris-HCl, 150mM NaCl, pH 8.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.2 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 21, 2011
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 26390 / Num. obs: 26390 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.057 / Χ2: 2.128 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.9810.40.2710821.444178.7
1.98-2.0210.60.25612911.439194.9
2.02-2.0610.70.23713491.527195.5
2.06-2.110.70.19212791.572196.2
2.1-2.1510.70.16613411.6195.9
2.15-2.210.70.15313191.634196.3
2.2-2.2510.70.13712951.714196.1
2.25-2.3110.60.11613671.727196.9
2.31-2.3810.70.11213041.815196.8
2.38-2.4610.60.10213351.937196.9
2.46-2.5410.70.08613162.007197.1
2.54-2.6510.70.07913412.159197.4
2.65-2.7710.60.0713412.224197.5
2.77-2.9110.60.06413522.332197.8
2.91-3.110.60.05713392.543198.1
3.1-3.3310.50.0513432.623198.2
3.33-3.6710.40.04713562.946198.6
3.67-4.210.30.04313522.982199
4.2-5.2910.20.0413623.016199.1
5.29-509.60.04413263.319196.4

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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: 1.95→41.501 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.54 / σ(F): 1.99 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1318 5 %random
Rwork0.1782 ---
all0.1803 26354 --
obs0.1803 26354 96.04 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.409 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 109.65 Å2 / Biso mean: 36.3715 Å2 / Biso min: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1-5.0859 Å21.2496 Å2-0.7978 Å2
2---5.7236 Å2-7.2338 Å2
3---0.6377 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 6 202 2714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092602
X-RAY DIFFRACTIONf_angle_d1.1413493
X-RAY DIFFRACTIONf_chiral_restr0.078385
X-RAY DIFFRACTIONf_plane_restr0.005463
X-RAY DIFFRACTIONf_dihedral_angle_d16.2071003
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 (%)
1.9501-2.02820.30571310.22022503263487
2.0282-2.12050.27141420.19622771291396
2.1205-2.23230.26171510.20352784293596
2.2323-2.37210.27181450.18752823296897
2.3721-2.55520.22911480.18282782293097
2.5552-2.81230.22981500.17992845299597
2.8123-3.21910.22511490.18962836298598
3.2191-4.05520.20181500.1682859300999
4.0552-41.51090.19431520.16322833298598
Refinement TLS params.Method: refined / Origin x: 0.3574 Å / Origin y: -1.2583 Å / Origin z: -0.8419 Å
111213212223313233
T0.1408 Å2-0.028 Å20.0042 Å2-0.2073 Å20.0182 Å2--0.2024 Å2
L0.1459 °2-0.6499 °2-0.2271 °2-2.393 °21.226 °2--1.3319 °2
S0.0466 Å °0.0094 Å °0.0233 Å °-0.2457 Å °-0.0305 Å °-0.0037 Å °-0.1221 Å °-0.0605 Å °-0.011 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 74
2X-RAY DIFFRACTION1ALLB1 - 74
3X-RAY DIFFRACTION1ALLC1 - 75
4X-RAY DIFFRACTION1ALLE759 - 75
5X-RAY DIFFRACTION1ALLF758 - 852
6X-RAY DIFFRACTION1ALLG759 - 852
7X-RAY DIFFRACTION1ALLB - F1 - 922

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