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- PDB-4nlh: SKICH domain of human TAX1BP1 -

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Basic information

Entry
Database: PDB / ID: 4nlh
TitleSKICH domain of human TAX1BP1
ComponentsTax1-binding protein 1
KeywordsPROTEIN BINDING / Ig like fold
Function / homology
Function and homology information


protein localization to phagocytic vesicle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of NF-kappaB transcription factor activity / autophagosome / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / autophagy / kinase binding ...protein localization to phagocytic vesicle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / phagophore assembly site / negative regulation of NF-kappaB transcription factor activity / autophagosome / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / autophagy / kinase binding / cytoplasmic vesicle / protein-macromolecule adaptor activity / innate immune response / apoptotic process / negative regulation of apoptotic process / mitochondrion / extracellular exosome / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin-like - #2840 / Calcium binding and coiled-coil domain-like / Calcium binding and coiled-coil domain (CALCOCO1) like / Autophagy receptor zinc finger-C2H2 domain / SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Immunoglobulin-like ...Immunoglobulin-like - #2840 / Calcium binding and coiled-coil domain-like / Calcium binding and coiled-coil domain (CALCOCO1) like / Autophagy receptor zinc finger-C2H2 domain / SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Tax1-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYang, Y. / Wang, G. / Huang, X. / Zhu, J. / Du, Z.
CitationJournal: To be published
Title: SKICH domain of human TAX1BP1
Authors: Yang, Y. / Wang, G. / Huang, X. / Zhu, J. / Du, Z.
History
DepositionNov 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tax1-binding protein 1
B: Tax1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)31,4052
Polymers31,4052
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tax1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)15,7031
Polymers15,7031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Tax1-binding protein 1


Theoretical massNumber of molelcules
Total (without water)15,7031
Polymers15,7031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.160, 64.020, 101.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tax1-binding protein 1 / TRAF6-binding protein


Mass: 15702.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN TAX1BP1, PRO0105, T6BP, TAX1BP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86VP1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, MES 7.2, KBr, pH 8.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 23821

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.689 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7119 / SU ML: 0.39 / σ(F): 0 / Phase error: 33.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2777 1831 8.39 %
Rwork0.2382 --
obs0.2415 21836 91.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.44 Å2 / Biso mean: 37.5673 Å2 / Biso min: 13.35 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 0 225 2067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081920
X-RAY DIFFRACTIONf_angle_d1.1712627
X-RAY DIFFRACTIONf_chiral_restr0.082260
X-RAY DIFFRACTIONf_plane_restr0.006337
X-RAY DIFFRACTIONf_dihedral_angle_d12.927655
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.95150.69271010.70831059116064
1.9515-2.0090.40021230.37531368149183
2.009-2.07380.34181380.31181535167392
2.0738-2.14790.30571430.26211584172795
2.1479-2.23390.25991250.2771351147682
2.2339-2.33550.40461230.36911305142879
2.3355-2.45860.32041460.25681633177997
2.4586-2.61260.32741500.24661646179698
2.6126-2.81430.26141540.24141666182099
2.8143-3.09730.23671520.211516781830100
3.0973-3.54510.21771570.196117071864100
3.5451-4.4650.22481550.17471700185599
4.465-34.69440.22151640.16541773193797
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)
12.81840.29150.39410.3619-0.12740.2087-0.02960.64130.3352-0.1988-0.0952-0.12130.55810.0642-0.1660.27670.03870.05680.23540.00420.18580.2802-14.4780.3347
20.7653-0.282-0.01980.39260.54420.64460.0776-0.17130.09020.22420.0688-0.2851-0.1341-0.0406-0.0180.2922-0.00070.05420.1631-0.0190.15452.9135-14.343911.0843
31.0440.2828-0.03541.09770.63150.9699-0.27180.23510.4103-0.55270.06240.2914-0.5124-0.05520.30830.27860.0525-0.05880.1748-0.04460.2194-5.3035-5.196210.4651
40.1773-0.1747-0.21850.37830.26060.2885-0.014-0.58680.17920.09080.379-0.34850.2261.09070.01130.2417-0.0790.06850.4134-0.13170.266316.1002-11.11566.062
50.07530.4897-0.03581.09520.07320.4164-0.0116-0.10350.1542-0.177-0.05770.06230.0436-0.1483-0.02460.15590.02390.00140.2777-0.03860.1557-3.9154-12.184615.6102
61.2946-0.8187-0.27620.46080.27250.57580.23640.3269-0.00980.0612-0.2338-0.0391-0.1785-0.22920.06630.2241-0.00860.0170.1470.03690.1228-4.6304-12.97858.9996
70.01550.0216-0.0540.126-0.15580.2141-0.0870.12630.1220.2011-0.0613-0.3811-0.23580.53890.20180.3649-0.0297-0.06340.47740.27830.854121.791-32.081328.6981
80.39220.18590.00820.44930.13731.7445-0.0003-0.2319-0.4725-0.142-0.0836-0.53-0.0488-0.2634-0.46670.2173-0.0101-0.02380.2130.07120.34719.1957-34.33924.7447
90.00930.04750.01750.21050.02190.3922-0.0371-0.29490.2368-0.1379-0.1651-0.2279-0.74080.26-0.06710.6174-0.2953-0.74650.4226-0.02981.19722.8104-23.028235.1624
100.3412-0.17510.3240.3192-0.2060.28990.1745-0.02570.1909-0.1478-0.2432-0.40590.0971-0.1546-0.05280.2652-0.0864-0.01240.2760.10710.529514.386-23.61520.942
110.8190.08490.87260.06760.16311.7151-0.47380.23120.5627-0.6582-0.4429-1.2262-0.7740.1777-0.6680.5395-0.0780.16680.20950.17540.518714.6178-20.364619.2686
120.1635-0.0668-0.23440.0720.08960.79330.189-0.3507-0.3290.71890.2451-0.4866-0.5568-0.05430.50680.6053-0.1051-0.39560.58590.01460.758418.863-25.50341.7724
130.6186-0.05970.23673.3385-0.34061.75720.1382-0.3130.5819-0.48450.2464-2.3261-0.4538-0.20020.63350.1383-0.0570.10480.0490.4007-0.11579.5751-28.329721.472
140.1275-0.0321-0.22940.75260.01280.2966-0.6307-0.51060.33960.2742-0.2674-0.1808-0.51890.2506-0.55380.4-0.5674-0.20040.22930.41211.096123.4853-20.228327.0871
150.22590.1244-0.07670.6881-0.47590.33270.33190.5819-0.1836-1.174-0.2057-0.75960.9685-0.11640.31140.47180.03520.20070.31920.10010.374910.1034-36.718815.6289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 48 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 68 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 80 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 105 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 106 through 124 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 15 through 20 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 38 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 39 through 48 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 49 through 54 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 55 through 68 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 69 through 80 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 81 through 105 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 106 through 114 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 115 through 124 )B0

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