[English] 日本語
Yorodumi
- PDB-8xi8: The Crystal Structure of TAB1 from Biortus. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xi8
TitleThe Crystal Structure of TAB1 from Biortus.
ComponentsTGF-beta-activated kinase 1 and MAP3K7-binding protein 1
KeywordsSIGNALING PROTEIN / Glycoprotein / Phosphoprotein / Ubl conjugation
Function / homology
Function and homology information


positive regulation of cGAS/STING signaling pathway / cardiac septum development / coronary vasculature development / aorta development / non-canonical NF-kappaB signal transduction / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / heart morphogenesis / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway ...positive regulation of cGAS/STING signaling pathway / cardiac septum development / coronary vasculature development / aorta development / non-canonical NF-kappaB signal transduction / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / heart morphogenesis / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / protein serine/threonine kinase activator activity / transforming growth factor beta receptor signaling pathway / lung development / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / activated TAK1 mediates p38 MAPK activation / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / positive regulation of protein serine/threonine kinase activity / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / in utero embryonic development / positive regulation of MAPK cascade / molecular adaptor activity / endosome membrane / Ub-specific processing proteases / nuclear speck / endoplasmic reticulum membrane / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / protein-containing complex / cytoplasm / cytosol
Similarity search - Function
Protein phosphatase 2C / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily
Similarity search - Domain/homology
TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Ju, C. / Bao, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of TAB1 from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Ju, C. / Bao, C.
History
DepositionDec 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TGF-beta-activated kinase 1 and MAP3K7-binding protein 1


Theoretical massNumber of molelcules
Total (without water)40,6431
Polymers40,6431
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.525, 144.525, 66.218
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

-
Components

#1: Protein TGF-beta-activated kinase 1 and MAP3K7-binding protein 1 / Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase ...Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 / TGF-beta-activated kinase 1-binding protein 1 / TAK1-binding protein 1


Mass: 40642.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAB1, MAP3K7IP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15750
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 4.91 Å3/Da / Density % sol: 74.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 16% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→48.82 Å / Num. obs: 11715 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.184 / Net I/σ(I): 9.5
Reflection shellResolution: 3.35→3.62 Å / Rmerge(I) obs: 1.168 / Num. unique obs: 2390

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→48.82 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 23.68 / SU ML: 0.348 / Cross valid method: FREE R-VALUE / ESU R: 2.999 / ESU R Free: 0.427
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2521 555 4.738 %
Rwork0.2007 11159 -
all0.203 --
obs-11714 99.923 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 115.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.867 Å20.433 Å20 Å2
2--0.867 Å2-0 Å2
3----2.812 Å2
Refinement stepCycle: LAST / Resolution: 3.35→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 0 18 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0122783
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162640
X-RAY DIFFRACTIONr_angle_refined_deg0.8191.6483769
X-RAY DIFFRACTIONr_angle_other_deg0.2691.5756072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7275354
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.218519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58610474
X-RAY DIFFRACTIONr_dihedral_angle_6_deg10.00110133
X-RAY DIFFRACTIONr_chiral_restr0.0350.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02634
X-RAY DIFFRACTIONr_nbd_refined0.2060.2618
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22581
X-RAY DIFFRACTIONr_nbtor_refined0.170.21383
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.265
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0440.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0190.22
X-RAY DIFFRACTIONr_nbd_other0.1220.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2410.24
X-RAY DIFFRACTIONr_mcbond_it5.39611.3961419
X-RAY DIFFRACTIONr_mcbond_other5.39611.3931418
X-RAY DIFFRACTIONr_mcangle_it8.97220.491772
X-RAY DIFFRACTIONr_mcangle_other8.9720.4921773
X-RAY DIFFRACTIONr_scbond_it5.12412.0311364
X-RAY DIFFRACTIONr_scbond_other5.12312.0311364
X-RAY DIFFRACTIONr_scangle_it8.89321.8891997
X-RAY DIFFRACTIONr_scangle_other8.89121.8891998
X-RAY DIFFRACTIONr_lrange_it12.753101.9913059
X-RAY DIFFRACTIONr_lrange_other12.752102.0013060
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.4370.321490.336810X-RAY DIFFRACTION99.8837
3.437-3.530.402430.336786X-RAY DIFFRACTION100
3.53-3.6320.361390.31767X-RAY DIFFRACTION100
3.632-3.7430.319400.295726X-RAY DIFFRACTION99.8696
3.743-3.8650.258320.26729X-RAY DIFFRACTION100
3.865-40.235360.24703X-RAY DIFFRACTION100
4-4.150.343250.211697X-RAY DIFFRACTION100
4.15-4.3180.303180.194669X-RAY DIFFRACTION100
4.318-4.5090.187300.185624X-RAY DIFFRACTION99.8473
4.509-4.7270.196450.175594X-RAY DIFFRACTION100
4.727-4.980.26340.175564X-RAY DIFFRACTION100
4.98-5.2780.231200.181555X-RAY DIFFRACTION100
5.278-5.6380.247230.188508X-RAY DIFFRACTION100
5.638-6.0830.223280.179481X-RAY DIFFRACTION100
6.083-6.6530.269250.17449X-RAY DIFFRACTION100
6.653-7.4220.233220.158406X-RAY DIFFRACTION100
7.422-8.5370.219100.144363X-RAY DIFFRACTION100
8.537-10.3770.217180.13313X-RAY DIFFRACTION100
10.377-14.3550.187130.16251X-RAY DIFFRACTION100
14.355-48.820.31150.243164X-RAY DIFFRACTION100

+
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://pdbjlc1.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