[English] 日本語
Yorodumi
- PDB-2pom: TAB1 with manganese ion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pom
TitleTAB1 with manganese ion
ComponentsMitogen-activated protein kinase kinase kinase 7-interacting protein 1
KeywordsSIGNALING PROTEIN/METAL BINDING PROTEIN / pp2c-like domain / SIGNALING PROTEIN-METAL BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


cardiac septum development / positive regulation of cGAS/STING signaling pathway / coronary vasculature development / non-canonical NF-kappaB signal transduction / aorta development / 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 ...cardiac septum development / positive regulation of cGAS/STING signaling pathway / coronary vasculature development / non-canonical NF-kappaB signal transduction / aorta development / 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 / transforming growth factor beta receptor signaling pathway / TRAF6-mediated induction of TAK1 complex within TLR4 complex / protein serine/threonine kinase activator activity / 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 / lung development / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / molecular adaptor activity / in utero embryonic development / positive regulation of MAPK cascade / endosome membrane / Ub-specific processing proteases / endoplasmic reticulum membrane / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / signal transduction / protein-containing complex / cytosol / cytoplasm
Similarity search - Function
PPM-type phosphatase domain / Phosphatase 2c; domain 1 / 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 / 4-Layer Sandwich / Alpha Beta
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: 2.27 Å
AuthorsLin, S.C.
CitationJournal: Mol.Cell / Year: 2007
Title: XIAP Induces NF-kappaB Activation via the BIR1/TAB1 Interaction and BIR1 Dimerization.
Authors: Lu, M. / Lin, S.C. / Huang, Y. / Kang, Y.J. / Rich, R. / Lo, Y.C. / Myszka, D. / Han, J. / Wu, H.
History
DepositionApr 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase kinase 7-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8422
Polymers40,7871
Non-polymers551
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.618, 141.618, 66.153
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsThe biological assembly is a monomer.

-
Components

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


Mass: 40786.797 Da / Num. of mol.: 1 / Fragment: N-TERMINAL PP2C-LIKE DOMAIN, RESIDUES 1-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K7IP1, TAB1 / Plasmid: pGEX-4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q15750
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 4.71 Å3/Da / Density % sol: 73.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M Li2SO4, 0.1M Hepes, 1mM MnCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 213 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 35865 / % possible obs: 95 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.069 / Χ2: 1.159 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.22-2.263.60.45913120.91171
2.26-2.33.80.40714500.7976.9
2.3-2.344.20.39814900.71880.7
2.34-2.394.40.38816390.70886.7
2.39-2.444.80.34517430.71193
2.44-2.55.10.34717950.65397.3
2.5-2.565.60.31618940.71299.5
2.56-2.636.30.27718560.73299.9
2.63-2.716.70.27718750.76100
2.71-2.870.2318630.757100
2.8-2.97.10.16819070.84100
2.9-3.017.10.13118760.91999.9
3.01-3.157.20.10818891.09699.9
3.15-3.327.20.08618851.293100
3.32-3.527.20.07218881.55999.9
3.52-3.87.20.06218881.623100
3.8-4.187.10.05818911.82100
4.18-4.7870.04819191.69699.6
4.78-6.026.80.04319251.67599.9
6.02-506.50.03718801.77993.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The TAB1 model solved by ourselves, but Not deposited yet

Resolution: 2.27→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2593 7.3 %random
Rwork0.211 ---
obs-32075 90.3 %-
Solvent computationBsol: 44.339 Å2
Displacement parametersBiso mean: 56.886 Å2
Baniso -1Baniso -2Baniso -3
1--7.398 Å2-7.776 Å20 Å2
2---7.398 Å20 Å2
3---14.796 Å2
Refinement stepCycle: LAST / Resolution: 2.27→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2736 0 1 15 2752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.27-2.370.442190.397X-RAY DIFFRACTION2867
2.37-2.50.3562820.326X-RAY DIFFRACTION3465
2.5-2.650.3133440.269X-RAY DIFFRACTION3993
2.65-2.860.2643280.245X-RAY DIFFRACTION4135
2.86-3.150.2813730.243X-RAY DIFFRACTION4299
3.15-3.60.2573670.226X-RAY DIFFRACTION4388
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param

+
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