[English] 日本語
Yorodumi
- PDB-5ep6: The crystal structure of NAP1 in complex with TBK1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ep6
TitleThe crystal structure of NAP1 in complex with TBK1
Components
  • 5-azacytidine-induced protein 2
  • Serine/threonine-protein kinase TBK1
KeywordsPROTEIN BINDING/TRANSFERASE / NAP1 / TBK1 / CALCOCO2 / PROTEIN BINDING-TRANSFERASE complex
Function / homology
Function and homology information


IRF3 mediated activation of type 1 IFN / positive regulation of xenophagy / STAT6-mediated induction of chemokines / positive regulation of TORC2 signaling / T follicular helper cell differentiation / regulation of type I interferon production / Interleukin-37 signaling / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / TNFR1-induced proapoptotic signaling ...IRF3 mediated activation of type 1 IFN / positive regulation of xenophagy / STAT6-mediated induction of chemokines / positive regulation of TORC2 signaling / T follicular helper cell differentiation / regulation of type I interferon production / Interleukin-37 signaling / positive regulation of type I interferon-mediated signaling pathway / IRF3-mediated induction of type I IFN / TNFR1-induced proapoptotic signaling / TRAF6 mediated IRF7 activation / toll-like receptor 4 signaling pathway / type I interferon-mediated signaling pathway / cGAS/STING signaling pathway / peptidyl-threonine phosphorylation / cytoplasmic pattern recognition receptor signaling pathway / positive regulation of macroautophagy / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / positive regulation of type I interferon production / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of autophagy / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / TICAM1-dependent activation of IRF3/IRF7 / negative regulation of canonical NF-kappaB signal transduction / Regulation of innate immune responses to cytosolic DNA / antiviral innate immune response / macroautophagy / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / Regulation of TNFR1 signaling / peptidyl-serine phosphorylation / response to virus / DDX58/IFIH1-mediated induction of interferon-alpha/beta / SARS-CoV-1 activates/modulates innate immune responses / TRAF3-dependent IRF activation pathway / protein phosphatase binding / defense response to virus / Potential therapeutics for SARS / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / inflammatory response / negative regulation of gene expression / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / Tbk1/Ikki binding domain / TBD domain / TANK binding kinase 1, ubiquitin-like domain / TANK-binding kinase 1, coiled-coil domain 1 / TANK-binding kinase 1 coiled-coil domain 1 / TANK binding kinase 1 ubiquitin-like domain / : / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...: / Tbk1/Ikki binding domain / TBD domain / TANK binding kinase 1, ubiquitin-like domain / TANK-binding kinase 1, coiled-coil domain 1 / TANK-binding kinase 1 coiled-coil domain 1 / TANK binding kinase 1 ubiquitin-like domain / : / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
5-azacytidine-induced protein 2 / Serine/threonine-protein kinase TBK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.451 Å
AuthorsLi, F. / Xie, X. / Liu, J. / Pan, L.
Funding support China, 2items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31470749 China
National Basic Research Program of China2013CB836900 China
CitationJournal: Nat Commun / Year: 2016
Title: Structural insights into the interaction and disease mechanism of neurodegenerative disease-associated optineurin and TBK1 proteins.
Authors: Li, F. / Xie, X. / Wang, Y. / Liu, J. / Cheng, X. / Guo, Y. / Gong, Y. / Hu, S. / Pan, L.
History
DepositionNov 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5-azacytidine-induced protein 2
C: 5-azacytidine-induced protein 2
B: Serine/threonine-protein kinase TBK1
D: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3729
Polymers23,9114
Non-polymers4605
Water1,820101
1
A: 5-azacytidine-induced protein 2
B: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1404
Polymers11,9562
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-18 kcal/mol
Surface area7030 Å2
MethodPISA
2
C: 5-azacytidine-induced protein 2
D: Serine/threonine-protein kinase TBK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2325
Polymers11,9562
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-22 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.360, 50.113, 84.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein/peptide 5-azacytidine-induced protein 2 / NF-kappa-B-activating kinase-associated protein 1 / Nak-associated protein 1 / TILP


Mass: 5631.463 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 215-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AZI2, NAP1, TBKBP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H6S1
#2: Protein Serine/threonine-protein kinase TBK1 / NF-kappa-B-activating kinase / T2K / TANK-binding kinase 1


Mass: 6324.202 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 677-729
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBK1, NAK / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UHD2, non-specific serine/threonine protein kinase
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% w/v Tryptone, 0.05 M HEPES sodium (pH 7.0), 12% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 298.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 31428 / % possible obs: 98.77 % / Redundancy: 6.8 % / Net I/σ(I): 27.5

-
Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.451→43.092 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 1583 5.05 %
Rwork0.1867 --
obs0.1883 31329 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.451→43.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 30 101 1430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061541
X-RAY DIFFRACTIONf_angle_d0.9942090
X-RAY DIFFRACTIONf_dihedral_angle_d17.787638
X-RAY DIFFRACTIONf_chiral_restr0.06232
X-RAY DIFFRACTIONf_plane_restr0.003266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4507-1.49750.24111300.20422394X-RAY DIFFRACTION89
1.4975-1.55110.25691430.17152687X-RAY DIFFRACTION99
1.5511-1.61320.20331400.15872738X-RAY DIFFRACTION100
1.6132-1.68660.20671420.15132688X-RAY DIFFRACTION100
1.6866-1.77550.23091680.15352691X-RAY DIFFRACTION100
1.7755-1.88680.20611370.16422729X-RAY DIFFRACTION100
1.8868-2.03240.23021300.16162744X-RAY DIFFRACTION100
2.0324-2.2370.17821480.15472744X-RAY DIFFRACTION100
2.237-2.56060.19111530.17162747X-RAY DIFFRACTION100
2.5606-3.2260.23781490.19992796X-RAY DIFFRACTION100
3.226-43.11090.22561430.21462788X-RAY DIFFRACTION95

+
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://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