[English] 日本語
Yorodumi
- PDB-4nlh: SKICH domain of human TAX1BP1 -

+
Open data


ID or keywords:

Loading...

-
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 / protein-macromolecule adaptor activity / cytoplasmic vesicle / innate immune response / apoptotic process / negative regulation of apoptotic process / mitochondrion / extracellular exosome / metal ion binding / cytosol
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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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