[English] 日本語
Yorodumi
- PDB-5v3b: Human A20 OTU domain (WT) with acetamidylated C103 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v3b
TitleHuman A20 OTU domain (WT) with acetamidylated C103
ComponentsTumor necrosis factor alpha-induced protein 3
KeywordsHYDROLASE / LIGASE / OTU domain / acetamidylation / ubiquitin editing
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 chronic inflammatory response ...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 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 / 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 / regulation of germinal center formation / positive regulation of hepatocyte proliferation / Transferases; Acyltransferases; Aminoacyltransferases / TNFR1-induced proapoptotic signaling / negative regulation of bone resorption / protein K63-linked deubiquitination / negative regulation of interleukin-1 beta production / negative regulation of interleukin-2 production / K63-linked deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of NF-kappaB transcription factor activity / response to muramyl dipeptide / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / positive regulation of Wnt signaling pathway / protein deubiquitination / negative regulation of endothelial cell apoptotic process / protein K48-linked ubiquitination / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of canonical NF-kappaB signal transduction / cytoskeleton organization / negative regulation of protein ubiquitination / negative regulation of innate immune response / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / Negative regulators of DDX58/IFIH1 signaling / negative regulation of smooth muscle cell proliferation / Regulation of TNFR1 signaling / response to molecule of bacterial origin / NOD1/2 Signaling Pathway / negative regulation of inflammatory response / cellular response to hydrogen peroxide / kinase binding / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / Ovarian tumor domain proteases / cell migration / cellular response to lipopolysaccharide / protease binding / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / inflammatory response / apoptotic process / DNA binding / extracellular exosome / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
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.
Similarity search - Domain/homology
Tumor necrosis factor alpha-induced protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsLangley, D.B. / Christ, D. / Grey, S.
CitationJournal: Nat.Immunol. / Year: 2019
Title: Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity.
Authors: Zammit, N.W. / Siggs, O.M. / Gray, P.E. / Horikawa, K. / Langley, D.B. / Walters, S.N. / Daley, S.R. / Loetsch, C. / Warren, J. / Yap, J.Y. / Cultrone, D. / Russell, A. / Malle, E.K. / ...Authors: Zammit, N.W. / Siggs, O.M. / Gray, P.E. / Horikawa, K. / Langley, D.B. / Walters, S.N. / Daley, S.R. / Loetsch, C. / Warren, J. / Yap, J.Y. / Cultrone, D. / Russell, A. / Malle, E.K. / Villanueva, J.E. / Cowley, M.J. / Gayevskiy, V. / Dinger, M.E. / Brink, R. / Zahra, D. / Chaudhri, G. / Karupiah, G. / Whittle, B. / Roots, C. / Bertram, E. / Yamada, M. / Jeelall, Y. / Enders, A. / Clifton, B.E. / Mabbitt, P.D. / Jackson, C.J. / Watson, S.R. / Jenne, C.N. / Lanier, L.L. / Wiltshire, T. / Spitzer, M.H. / Nolan, G.P. / Schmitz, F. / Aderem, A. / Porebski, B.T. / Buckle, A.M. / Abbott, D.W. / Ziegler, J.B. / Craig, M.E. / Benitez-Aguirre, P. / Teo, J. / Tangye, S.G. / King, C. / Wong, M. / Cox, M.P. / Phung, W. / Tang, J. / Sandoval, W. / Wertz, I.E. / Christ, D. / Goodnow, C.C. / Grey, S.T.
History
DepositionMar 7, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMar 21, 2018ID: 4ZS5
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
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
C: Tumor necrosis factor alpha-induced protein 3
D: Tumor necrosis factor alpha-induced protein 3
E: Tumor necrosis factor alpha-induced protein 3
F: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)258,9636
Polymers258,9636
Non-polymers00
Water00
1
A: Tumor necrosis factor alpha-induced protein 3
B: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)86,3212
Polymers86,3212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-10 kcal/mol
Surface area27920 Å2
MethodPISA
2
C: Tumor necrosis factor alpha-induced protein 3
D: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)86,3212
Polymers86,3212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-11 kcal/mol
Surface area27340 Å2
MethodPISA
3
E: Tumor necrosis factor alpha-induced protein 3
F: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)86,3212
Polymers86,3212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-10 kcal/mol
Surface area28450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.719, 80.901, 153.429
Angle α, β, γ (deg.)90.000, 102.460, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALTRPTRPAA5 - 3565 - 356
21VALVALTRPTRPBB5 - 3565 - 356
12VALVALGLNGLNAA5 - 3575 - 357
22VALVALGLNGLNCC5 - 3575 - 357
13VALVALGLNGLNAA5 - 3575 - 357
23VALVALGLNGLNDD5 - 3575 - 357
14GLNGLNTRPTRPAA4 - 3564 - 356
24GLNGLNTRPTRPEE4 - 3564 - 356
15LEULEUGLNGLNAA6 - 3576 - 357
25LEULEUGLNGLNFF6 - 3576 - 357
16VALVALTRPTRPBB5 - 3565 - 356
26VALVALTRPTRPCC5 - 3565 - 356
17VALVALTRPTRPBB5 - 3565 - 356
27VALVALTRPTRPDD5 - 3565 - 356
18VALVALTRPTRPBB5 - 3565 - 356
28VALVALTRPTRPEE5 - 3565 - 356
19LEULEUTRPTRPBB6 - 3566 - 356
29LEULEUTRPTRPFF6 - 3566 - 356
110VALVALGLUGLUCC5 - 3585 - 358
210VALVALGLUGLUDD5 - 3585 - 358
111VALVALTRPTRPCC5 - 3565 - 356
211VALVALTRPTRPEE5 - 3565 - 356
112LEULEUGLUGLUCC6 - 3586 - 358
212LEULEUGLUGLUFF6 - 3586 - 358
113VALVALTRPTRPDD5 - 3565 - 356
213VALVALTRPTRPEE5 - 3565 - 356
114LEULEUGLUGLUDD6 - 3586 - 358
214LEULEUGLUGLUFF6 - 3586 - 358
115LEULEUTRPTRPEE6 - 3566 - 356
215LEULEUTRPTRPFF6 - 3566 - 356

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
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: 43160.531 Da / Num. of mol.: 6 / Fragment: OTU domain (UNP residues 1-366)
Source method: isolated from a genetically manipulated source
Details: C103 has been alkylated by iodoacetamide to produce an acetamidylated adduct identified as YCM
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFAIP3, OTUD7C / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P21580, ubiquitinyl hydrolase 1, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.76 % / Description: Long rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 50 mM CaCl2, 100 mM MES (pH 6.0), 7.5% PEG1500

-
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: Mar 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3→34.56 Å / Num. obs: 46536 / % possible obs: 97.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 79 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.056 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) all% possible all
3-3.115.61.4771.50.7030.68799.1
11.62-34.564.80.0380.99894.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3DKB

3dkb


Resolution: 3→34.56 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.901 / SU B: 32.862 / SU ML: 0.534 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.493
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2817 2340 5 %RANDOM
Rwork0.2378 ---
obs0.24 44077 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 221.19 Å2 / Biso mean: 77.343 Å2 / Biso min: 38.38 Å2
Baniso -1Baniso -2Baniso -3
1-6.76 Å20 Å2-3.9 Å2
2--1.97 Å20 Å2
3----6.38 Å2
Refinement stepCycle: final / Resolution: 3→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14207 0 0 0 14207
Num. residues----1905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914560
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212624
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.94419944
X-RAY DIFFRACTIONr_angle_other_deg1.076328755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15251873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45523.24571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.698151943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4291567
X-RAY DIFFRACTIONr_chiral_restr0.1030.22339
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116462
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023105
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A177520.08
12B177520.08
21A176280.08
22C176280.08
31A174320.07
32D174320.07
41A178120.08
42E178120.08
51A175840.08
52F175840.08
61B175880.07
62C175880.07
71B175420.07
72D175420.07
81B177460.07
82E177460.07
91B172460.09
92F172460.09
101C172120.08
102D172120.08
111C175340.07
112E175340.07
121C170340.09
122F170340.09
131D173080.08
132E173080.08
141D167860.08
142F167860.08
151E171160.08
152F171160.08
LS refinement shellResolution: 3→3.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 159 -
Rwork0.363 3273 -
all-3432 -
obs--98.85 %

+
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://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