[English] 日本語
Yorodumi
- PDB-5dq6: Mus musculus A20 OTU domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dq6
TitleMus musculus A20 OTU domain
ComponentsTumor necrosis factor alpha-induced protein 3
KeywordsHYDROLASE / A20 OTU
Function / homology
Function and homology information


negative regulation of granuloma formation / positive regulation of protein catabolic process => GO:0045732 / protein K33-linked deubiquitination / protein K29-linked deubiquitination / TNFR1-induced proapoptotic signaling / 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 CD40 signaling pathway ...negative regulation of granuloma formation / positive regulation of protein catabolic process => GO:0045732 / protein K33-linked deubiquitination / protein K29-linked deubiquitination / TNFR1-induced proapoptotic signaling / 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 CD40 signaling pathway / protein deubiquitination involved in ubiquitin-dependent protein catabolic process / negative regulation of toll-like receptor 3 signaling pathway / Negative regulators of DDX58/IFIH1 signaling / negative regulation of B cell activation / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / marginal zone B cell differentiation / : / Regulation of TNFR1 signaling / protein K11-linked deubiquitination / Ovarian tumor domain proteases / negative regulation of chronic inflammatory response / : / negative regulation of heterotypic cell-cell adhesion / regulation of germinal center formation / protein K48-linked deubiquitination / B-1 B cell homeostasis / NOD1/2 Signaling Pathway / negative regulation of cyclin-dependent protein serine/threonine kinase activity / Transferases; Acyltransferases; Aminoacyltransferases / protein K63-linked deubiquitination / regulation of immunoglobulin production / positive regulation of hepatocyte proliferation / 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 / regulation of innate immune response / 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 extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of canonical NF-kappaB signal transduction / negative regulation of protein ubiquitination / cytoskeleton organization / negative regulation of innate immune response / negative regulation of autophagy / ubiquitin binding / negative regulation of smooth muscle cell proliferation / response to molecule of bacterial origin / kinase binding / negative regulation of inflammatory response / response to wounding / cellular response to hydrogen peroxide / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / : / cell migration / cellular response to lipopolysaccharide / protease binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / inflammatory response / apoptotic process / DNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
A20 peptidase / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMabbitt, P.D. / Jackson, C.J.
CitationJournal: To Be Published
Title: Mus musculus A20 OTU domain
Authors: Mabbitt, P.D. / Jackson, C.J.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tumor necrosis factor alpha-induced protein 3
B: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)84,2832
Polymers84,2832
Non-polymers00
Water46826
1
A: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)42,1411
Polymers42,1411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)42,1411
Polymers42,1411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.340, 71.340, 143.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein Tumor necrosis factor alpha-induced protein 3 / TNF alpha-induced protein 3 / Putative DNA-binding protein A20 / Zinc finger protein A20


Mass: 42141.414 Da / Num. of mol.: 2 / Fragment: OTU domain (UNP residues 1-360)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tnfaip3, Tnfip3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q60769, ubiquitinyl hydrolase 1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.4 M NaCl, 0.1 M MES / PH range: 6-6.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→37.77 Å / Num. obs: 19279 / % possible obs: 92.1 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.06639 / Net I/σ(I): 11.4

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZJF

3zjf


Resolution: 2.8→37.77 Å / Cross valid method: FREE R-VALUE / σ(F): 1.65 / Phase error: 40.07 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2905 1077 5.59 %
Rwork0.2527 --
obs0.2555 19279 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5511 0 0 26 5537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115633
X-RAY DIFFRACTIONf_angle_d1.4347607
X-RAY DIFFRACTIONf_dihedral_angle_d16.1952144
X-RAY DIFFRACTIONf_chiral_restr0.06835
X-RAY DIFFRACTIONf_plane_restr0.007965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8006-2.92750.32451270.32012325X-RAY DIFFRACTION93
2.9275-3.08110.38681260.32322321X-RAY DIFFRACTION93
3.0811-3.2730.32021580.30122264X-RAY DIFFRACTION91
3.273-3.52390.39171500.31592248X-RAY DIFFRACTION90
3.5239-3.87510.34981380.30542273X-RAY DIFFRACTION91
3.8751-4.42820.27691380.26162233X-RAY DIFFRACTION89
4.4282-5.55030.2971370.23242217X-RAY DIFFRACTION89
5.5503-17.69850.21991030.19622242X-RAY DIFFRACTION90
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)
12.39620.08960.50578.2506-3.85376.47040.2224-0.3816-0.3645-0.1561-0.0017-1.3411-0.81071.69490.33050.3044-0.3068-0.16781.75650.30940.8102-5.8715-9.1361-14.272
24.2386-0.21590.20489.472-1.5576.32760.13260.1988-0.28040.6868-1.23540.8396-0.18991.81020.46790.50130.0472-0.03240.81380.2050.7094-13.8019-15.0354-8.3584
35.43615.5412-1.95327.0123-2.27869.02060.1420.7576-0.1779-0.4372-0.98910.97690.0662-0.09420.7181.06970.4381-0.36360.7711-0.11811.007-18.4322-33.5523-12.3534
49.1578-1.2034-0.89566.6166-2.04976.95720.6485-0.5457-0.93051.0053-1.5142-0.5388-0.79511.7260.78440.8929-0.118-0.1511.18440.35570.7668-12.5397-20.50630.2763
5-0.34310.09480.46752.10210.50111.35390.3381-0.4052-0.13671.2053-0.6987-0.7356-0.28890.45860.53431.072-0.2349-0.19461.55470.41551.0965-5.3612-21.15675.7466
65.08863.0856-0.37114.4979-0.41522.1240.547-1.47040.74741.8984-1.8880.11870.1780.33190.45761.7542-0.4832-0.70061.40130.20520.724-7.469110.0856-12.127
77.6069-2.6166-2.02046.21940.40815.95310.0960.6565-0.96470.3637-0.59791.26340.5554-0.77270.47270.8651-0.12890.25370.7226-0.10570.860713.78953.049711.9352
86.3374-1.6414-2.00723.5581.40071.2618-1.4456-1.571-0.72731.09980.5502-0.66131.37721.07280.40681.82510.25630.30161.1929-0.23930.694236.157-7.800115.2524
99.9334-2.6-0.28535.58830.70064.9477-0.19310.8317-0.04130.3106-0.27950.04130.6019-0.70230.52541.0406-0.2250.13450.6739-0.13690.625722.8124-0.25394.1701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 202 )
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 285 )
5X-RAY DIFFRACTION5chain 'A' and (resid 286 through 341 )
6X-RAY DIFFRACTION6chain 'A' and (resid 342 through 359 )
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 120 )
8X-RAY DIFFRACTION8chain 'B' and (resid 121 through 145 )
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 357 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more