[English] 日本語
Yorodumi
- PDB-5z7g: Crystal structure of TAX1BP1 SKICH region in complex with NAP1 -

+
Open data


ID or keywords:

Loading...

-
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 / 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 ...: / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 )

+
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