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- PDB-5v3p: Human A20 OTU domain (I325N) with acetamidylated C103 -

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Basic information

Entry
Database: PDB / ID: 5v3p
TitleHuman A20 OTU domain (I325N) 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 / 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 / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / 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 / negative regulation of protein ubiquitination / cytoskeleton organization / negative regulation of innate immune response / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / Negative regulators of DDX58/IFIH1 signaling / negative regulation of smooth muscle cell proliferation / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / response to molecule of bacterial origin / kinase binding / cellular response to hydrogen peroxide / negative regulation of inflammatory response / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / : / Ovarian tumor domain proteases / cell migration / protease binding / cellular response to lipopolysaccharide / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / lysosome / inflammatory response / apoptotic process / proteolysis / 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: 2.5 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: 4ZRH, 5DOD
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Advisory / Data collection / Database references
Category: citation / citation_author / pdbx_database_PDB_obs_spr
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 / _pdbx_database_PDB_obs_spr.replace_pdb_id
Revision 1.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)258,9696
Polymers258,9696
Non-polymers00
Water37821
1
A: Tumor necrosis factor alpha-induced protein 3
D: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)86,3232
Polymers86,3232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tumor necrosis factor alpha-induced protein 3
C: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)86,3232
Polymers86,3232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Tumor necrosis factor alpha-induced protein 3
F: Tumor necrosis factor alpha-induced protein 3


Theoretical massNumber of molelcules
Total (without water)86,3232
Polymers86,3232
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.870, 81.870, 297.343
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
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: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLNGLNAA5 - 3575 - 357
21VALVALGLNGLNBB5 - 3575 - 357
12VALVALGLNGLNAA5 - 3575 - 357
22VALVALGLNGLNCC5 - 3575 - 357
13VALVALGLNGLNAA5 - 3575 - 357
23VALVALGLNGLNDD5 - 3575 - 357
14LEULEUTRPTRPAA6 - 3566 - 356
24LEULEUTRPTRPEE6 - 3566 - 356
15LEULEULYSLYSAA6 - 3556 - 355
25LEULEULYSLYSFF6 - 3556 - 355
16VALVALGLUGLUBB5 - 3585 - 358
26VALVALGLUGLUCC5 - 3585 - 358
17VALVALGLUGLUBB5 - 3585 - 358
27VALVALGLUGLUDD5 - 3585 - 358
18LEULEUGLUGLUBB6 - 3586 - 358
28LEULEUGLUGLUEE6 - 3586 - 358
19LEULEULYSLYSBB6 - 3556 - 355
29LEULEULYSLYSFF6 - 3556 - 355
110VALVALGLUGLUCC5 - 3585 - 358
210VALVALGLUGLUDD5 - 3585 - 358
111LEULEUGLUGLUCC6 - 3586 - 358
211LEULEUGLUGLUEE6 - 3586 - 358
112LEULEULYSLYSCC6 - 3556 - 355
212LEULEULYSLYSFF6 - 3556 - 355
113LEULEUGLUGLUDD6 - 3586 - 358
213LEULEUGLUGLUEE6 - 3586 - 358
114LEULEULYSLYSDD6 - 3556 - 355
214LEULEULYSLYSFF6 - 3556 - 355
115LEULEULYSLYSEE6 - 3546 - 354
215LEULEULYSLYSFF6 - 3546 - 354

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

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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: 43161.477 Da / Num. of mol.: 6 / Fragment: OTU domain (UNP residues 1-366) / Mutation: I325N
Source method: isolated from a genetically manipulated source
Details: C103 has been alkylated with iodoacetamide such that it has become an acetamidylated adduct (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)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.22 Å3/Da / Density % sol: 44.63 % / Description: triangular rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 50 mM CaCl2, 100 mM MES (pH 6.0), 5.0 % PEG1500

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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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.263
11-K, -H, -L20.214
11-h,-k,l30.306
11K, H, -L40.217
ReflectionResolution: 2.5→40.62 Å / Num. obs: 76908 / % possible obs: 99.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 47.7 Å2 / CC1/2: 0.929 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.076 / Rrim(I) all: 0.158 / Net I/av σ(I): 7.8 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 4.6 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.5-2.550.9062.20.7130.4711.023100
12.5-40.620.0940.980.0490.10791.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.14data scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 3DKB

3dkb


Resolution: 2.5→39.47 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.924 / SU B: 13.017 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.048
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 3838 5 %RANDOM
Rwork0.1614 ---
obs0.1633 73040 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 121.58 Å2 / Biso mean: 55.407 Å2 / Biso min: 18.38 Å2
Baniso -1Baniso -2Baniso -3
1-16.03 Å20 Å20 Å2
2--16.03 Å20 Å2
3----32.07 Å2
Refinement stepCycle: final / Resolution: 2.5→39.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14765 0 0 21 14786
Biso mean---31.2 -
Num. residues----1777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01915088
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214153
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.95720380
X-RAY DIFFRACTIONr_angle_other_deg0.971332801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20551736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75824.097742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.139152771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3541596
X-RAY DIFFRACTIONr_chiral_restr0.0860.22264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116168
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023056
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A196280.07
12B196280.07
21A195800.08
22C195800.08
31A196640.08
32D196640.08
41A184120.09
42E184120.09
51A166140.09
52F166140.09
61B191640.09
62C191640.09
71B194580.09
72D194580.09
81B183120.09
82E183120.09
91B165720.11
92F165720.11
101C194860.09
102D194860.09
111C181880.09
112E181880.09
121C164680.1
122F164680.1
131D184500.1
132E184500.1
141D165000.1
142F165000.1
151E158880.1
152F158880.1
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 298 -
Rwork0.177 5430 -
all-5728 -
obs--99.98 %
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)
10.3304-0.15850.10170.9779-0.66071.6831-0.04990.00520.01210.05240.0865-0.011-0.2017-0.0218-0.03660.11460.01160.01610.01650.01290.042647.93268.8438.91
20.49840.12370.10550.8862-0.57821.546-0.001-0.0072-0.0171-0.02210.04310.01450.1459-0.0582-0.04210.12090.0079-0.00040.01370.01920.032947.94425.74864.721
30.51080.1633-0.05440.2406-0.13381.13070.1595-0.06010.0343-0.0118-0.12440.0625-0.1288-0.0238-0.03510.1287-0.0035-0.02150.1048-0.01910.022542.60930.547111.613
40.3176-0.01130.05750.4232-0.12281.10850.12820.0296-0.02810.0381-0.05820.09970.0706-0.0718-0.070.06950.02820.00110.13260.00220.02941.98964.225-8.789
50.05890.0374-0.17240.4189-0.04871.2192-0.03790.06140.0731-0.08720.05570.0110.177-0.1076-0.01770.0871-0.0184-0.01460.07760.09660.152387.06646.53551.982
60.32080.050.21190.49030.29931.57090.06290.00370.11890.2285-0.07770.1188-0.1406-0.06590.01480.2282-0.01510.03150.0172-0.03220.170388.07548.41197.314
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 357
2X-RAY DIFFRACTION1A401 - 403
3X-RAY DIFFRACTION1B408
4X-RAY DIFFRACTION2B5 - 358
5X-RAY DIFFRACTION2B401 - 407
6X-RAY DIFFRACTION3C4 - 358
7X-RAY DIFFRACTION3C401 - 402
8X-RAY DIFFRACTION4D5 - 358
9X-RAY DIFFRACTION4D401 - 406
10X-RAY DIFFRACTION5E6 - 358
11X-RAY DIFFRACTION6F6 - 355
12X-RAY DIFFRACTION6F401 - 402

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