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- PDB-5z7g: Crystal structure of TAX1BP1 SKICH region in complex with NAP1 -

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Basic information

Entry
Database: PDB / ID: 5z7g
TitleCrystal structure of TAX1BP1 SKICH region in complex with NAP1
Components
  • 5-azacytidine-induced protein 2
  • Tax1-binding protein 1
KeywordsSIGNALING PROTEIN / TAX1BP1 / NAP1 / SKICH domain / Autophagy receptor / Selective autophagy
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 / dendritic cell differentiation / serine/threonine protein kinase complex / dendritic cell proliferation / phagophore assembly site / type I interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / autophagosome ...protein localization to phagocytic vesicle / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / dendritic cell differentiation / serine/threonine protein kinase complex / dendritic cell proliferation / phagophore assembly site / type I interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / autophagosome / canonical NF-kappaB signal transduction / negative regulation of canonical NF-kappaB signal transduction / T cell activation / Negative regulators of DDX58/IFIH1 signaling / Regulation of TNFR1 signaling / autophagy / kinase binding / protein-macromolecule adaptor activity / mitotic cell cycle / cytoplasmic vesicle / defense response to virus / innate immune response / apoptotic process / negative regulation of apoptotic process / mitochondrion / extracellular exosome / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Immunoglobulin-like - #2840 / Tbk1/Ikki binding domain / TBD domain / 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 - #2840 / Tbk1/Ikki binding domain / TBD domain / 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 / 5-azacytidine-induced protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsPan, L.F. / Fu, T. / Liu, J.P. / Xie, X.Q. / Wang, Y.L. / Hu, S.C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470749 China
National Natural Science Foundation of China21621002 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanistic insights into the interactions of NAP1 with the SKICH domains of NDP52 and TAX1BP1
Authors: Fu, T. / Liu, J. / Wang, Y. / Xie, X. / Hu, S. / Pan, L.
History
DepositionJan 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: 5-azacytidine-induced protein 2
D: 5-azacytidine-induced protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6707
Polymers38,3934
Non-polymers2763
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-38 kcal/mol
Surface area16470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.487, 118.487, 64.344
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 14137.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAX1BP1, T6BP, PRO0105 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q86VP1
#2: Protein/peptide 5-azacytidine-induced protein 2 / NF-kappa-B-activating kinase-associated protein 1 / Nak-associated protein 1 / TILP


Mass: 5058.892 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AZI2, NAP1, TBKBP2 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q9H6S1
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 3.4 Å3/Da / Density % sol: 63.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 8000, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 22896 / % possible obs: 99.5 % / Redundancy: 19.8 % / Net I/σ(I): 36.33
Reflection shellResolution: 2.3→2.34 Å / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z7A

5z7a


Resolution: 2.301→29.622 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 1181 5.16 %
Rwork0.1868 --
obs0.1891 22878 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→29.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2519 0 18 106 2643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082634
X-RAY DIFFRACTIONf_angle_d0.8533575
X-RAY DIFFRACTIONf_dihedral_angle_d9.9421913
X-RAY DIFFRACTIONf_chiral_restr0.052367
X-RAY DIFFRACTIONf_plane_restr0.005453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3014-2.40610.3231480.23492683X-RAY DIFFRACTION99
2.4061-2.53290.25661780.22392661X-RAY DIFFRACTION100
2.5329-2.69150.26991520.21472731X-RAY DIFFRACTION100
2.6915-2.89910.26841440.21172690X-RAY DIFFRACTION100
2.8991-3.19060.24911230.20242749X-RAY DIFFRACTION100
3.1906-3.65150.2231390.18622693X-RAY DIFFRACTION99
3.6515-4.59780.22181390.16422747X-RAY DIFFRACTION100
4.5978-29.62420.20261580.17172743X-RAY DIFFRACTION98
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)
14.23222.2547-0.57584.6784-0.73794.3096-0.2687-0.5083-0.28490.54630.0967-0.50.30160.13070.13520.3825-0.024-0.0080.3625-0.02920.41040.256854.7122-64.855
23.25940.3873-0.3821.5061-0.34332.43980.11910.4829-0.1946-0.27460.0880.02930.0252-0.1352-0.19220.2532-0.0239-0.0340.2449-0.04160.2607-9.683355.3761-68.999
32.74340.0915-0.09511.84240.67052.86480.0440.0671-0.892-0.41560.22770.02820.8274-0.076-0.19460.3398-0.0294-0.06630.2455-0.04680.4405-9.99143.0907-66.7099
41.63442.4141-0.95144.1207-0.51863.392-0.12940.9033-0.0999-0.47640.6284-0.1058-0.07-0.4309-0.33050.395-0.03280.0120.5112-0.03440.3762-0.362958.8783-80.0578
51.5530.49250.07561.04950.42131.3840.0028-0.1136-0.0773-0.20730.12970.18910.2592-0.2563-0.13020.2764-0.0441-0.08320.3297-0.0050.3184-15.217750.0274-66.0649
60.91740.59311.98365.22272.58895.09030.13070.154-0.6035-0.64250.0702-0.58440.09940.54430.06120.34540.01440.01460.392-0.10070.48771.126746.7227-70.16
77.583.09821.75362.9398-0.71241.9899-0.0591-0.64050.41140.55970.040.3356-0.0686-0.2422-0.00550.23820.0215-0.00610.2971-0.03880.2703-16.247752.2794-57.3883
84.4236-2.0632-0.00541.2725-0.84092.7845-0.0985-1.6098-2.38240.30120.68020.260.2971-0.41410.13010.4728-0.06550.07431.17690.34681.0687-5.429540.1597-32.9627
90.74230.54440.2930.9244-0.76722.27050.0854-0.6253-2.48610.5879-0.2583-0.2122-0.1644-0.05740.04410.2739-0.0179-0.05840.92510.48451.3623.47235.5338-35.3359
100.1460.0047-0.51.14470.43691.5607-0.62-0.3747-1.14951.1839-0.43780.52590.64290.1983-0.50380.8947-0.17070.06931.26720.8861.940.26325.7847-26.6507
112.57080.4398-0.65991.8894-0.30743.49650.1216-1.4194-1.87930.40220.2708-0.4397-0.1646-0.38640.0960.34510.05-0.14290.91790.29390.91290.769143.0933-35.6983
124.36270.2058-1.41812.96340.69611.14550.28910.1965-0.19030.2072-0.32680.20730.03220.09290.06740.2852-0.0627-0.01390.46130.09890.2141-20.417352.3002-43.7899
133.3496-0.8272-2.95033.36291.67734.1880.4255-1.03290.17410.24240.1103-0.1129-0.18950.9497-0.19650.3528-0.18830.00940.61810.01660.2759-15.527456.9412-42.4836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 80 )
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 105 )
6X-RAY DIFFRACTION6chain 'A' and (resid 106 through 114 )
7X-RAY DIFFRACTION7chain 'A' and (resid 115 through 121 )
8X-RAY DIFFRACTION8chain 'B' and (resid 13 through 31 )
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 68 )
10X-RAY DIFFRACTION10chain 'B' and (resid 69 through 87 )
11X-RAY DIFFRACTION11chain 'B' and (resid 88 through 121 )
12X-RAY DIFFRACTION12chain 'C' and (resid 33 through 75 )
13X-RAY DIFFRACTION13chain 'D' and (resid 33 through 75 )

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