[English] 日本語
Yorodumi
- PDB-3v3v: Structural and functional analysis of quercetagetin, a natural JN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3v3v
TitleStructural and functional analysis of quercetagetin, a natural JNK1 inhibitor
Components
  • C-Jun-amino-terminal kinase-interacting protein 1
  • Mitogen-activated protein kinase 8
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / PHOSPHORYLATION / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / JUN phosphorylation / positive regulation of cell killing / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / basal dendrite / negative regulation of JUN kinase activity / positive regulation of establishment of protein localization to mitochondrion / Activation of BIM and translocation to mitochondria ...dentate gyrus mossy fiber / regulation of CD8-positive, alpha-beta T cell proliferation / JUN phosphorylation / positive regulation of cell killing / Activation of BMF and translocation to mitochondria / Interleukin-38 signaling / basal dendrite / negative regulation of JUN kinase activity / positive regulation of establishment of protein localization to mitochondrion / Activation of BIM and translocation to mitochondria / WNT5:FZD7-mediated leishmania damping / MAP-kinase scaffold activity / JUN kinase binding / positive regulation of cyclase activity / regulation of JNK cascade / mitogen-activated protein kinase kinase kinase binding / histone deacetylase regulator activity / mitogen-activated protein kinase kinase binding / NRAGE signals death through JNK / positive regulation of NLRP3 inflammasome complex assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / dendritic growth cone / positive regulation of protein metabolic process / JUN kinase activity / kinesin binding / peptidyl-threonine phosphorylation / mitogen-activated protein kinase / regulation of macroautophagy / response to mechanical stimulus / axonal growth cone / response to UV / stress-activated MAPK cascade / energy homeostasis / vesicle-mediated transport / negative regulation of protein binding / JNK cascade / cellular response to amino acid starvation / protein serine/threonine kinase binding / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / cellular response to reactive oxygen species / FCERI mediated MAPK activation / positive regulation of JNK cascade / regulation of circadian rhythm / mitochondrial membrane / cellular response to mechanical stimulus / histone deacetylase binding / peptidyl-serine phosphorylation / cellular senescence / rhythmic process / Signaling by ALK fusions and activated point mutants / MAPK cascade / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to lipopolysaccharide / cellular response to oxidative stress / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / neuron projection / protein phosphorylation / positive regulation of apoptotic process / axon / protein serine kinase activity / neuronal cell body / protein serine/threonine kinase activity / synapse / dendrite / positive regulation of gene expression / regulation of DNA-templated transcription / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / signal transduction / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
JIP1, SH3 domain / : / Mitogen-activated protein (MAP) kinase, JNK / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. ...JIP1, SH3 domain / : / Mitogen-activated protein (MAP) kinase, JNK / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Variant SH3 domain / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MYU / Mitogen-activated protein kinase 8 / C-Jun-amino-terminal kinase-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBaek, S. / Kang, N.J. / Popowicz, G.M. / Arciniega, M. / Jung, S.K. / Byun, S. / Song, N.R. / Heo, Y.S. / Kim, B.Y. / Lee, H.J. ...Baek, S. / Kang, N.J. / Popowicz, G.M. / Arciniega, M. / Jung, S.K. / Byun, S. / Song, N.R. / Heo, Y.S. / Kim, B.Y. / Lee, H.J. / Holak, T.A. / Augustin, M. / Bode, A.M. / Huber, R. / Dong, Z. / Lee, K.W.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural and Functional Analysis of the Natural JNK1 Inhibitor Quercetagetin.
Authors: Baek, S. / Kang, N.J. / Popowicz, G.M. / Arciniega, M. / Jung, S.K. / Byun, S. / Song, N.R. / Heo, Y.S. / Kim, B.Y. / Lee, H.J. / Holak, T.A. / Augustin, M. / Bode, A.M. / Huber, R. / Dong, Z. / Lee, K.W.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase 8
B: C-Jun-amino-terminal kinase-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,03811
Polymers45,0122
Non-polymers1,0269
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-101 kcal/mol
Surface area16790 Å2
MethodPISA
2
A: Mitogen-activated protein kinase 8
B: C-Jun-amino-terminal kinase-interacting protein 1
hetero molecules

A: Mitogen-activated protein kinase 8
B: C-Jun-amino-terminal kinase-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,07622
Polymers90,0244
Non-polymers2,05218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8540 Å2
ΔGint-226 kcal/mol
Surface area31200 Å2
MethodPISA
3
A: Mitogen-activated protein kinase 8
B: C-Jun-amino-terminal kinase-interacting protein 1
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)368,30588
Polymers360,09616
Non-polymers8,20972
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area40190 Å2
ΔGint-1094 kcal/mol
Surface area120230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.370, 172.370, 86.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Mitogen-activated protein kinase 8 / MAP kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated ...MAP kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1


Mass: 43666.426 Da / Num. of mol.: 1 / Fragment: UNP residues 1-363
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P45983, mitogen-activated protein kinase
#2: Protein/peptide C-Jun-amino-terminal kinase-interacting protein 1 / JIP-1 / JNK-interacting protein 1 / Islet-brain-1 / IB-1 / JNK MAP kinase scaffold protein 1 / ...JIP-1 / JNK-interacting protein 1 / Islet-brain-1 / IB-1 / JNK MAP kinase scaffold protein 1 / Mitogen-activated protein kinase 8-interacting protein 1


Mass: 1345.612 Da / Num. of mol.: 1 / Fragment: UNP residues 153-163 / Source method: obtained synthetically / Details: FMOC synthesis / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q9WVI9

-
Non-polymers , 4 types, 36 molecules

#3: Chemical ChemComp-MYU / 3,5,6,7-TETRAHYDROXY-2-(3,4-DIHYDROXYPHENYL)-4H-CHROMEN-4-ONE / 2-(3,4-DIHYDROXYPHENYL)-3,5,6,7-TETRAHYDROXY-4H-1-BENZOPYRAN-4-ONE / 2-(3,4-DIHYDROXYPHENYL)-4H-CHROMENE-3,5,6,7-TETRAOL / QUERCETAGETIN


Mass: 318.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O8
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE SEQUENCE MATCHES TO UNP ENTRY P45983-4(ISOFORM 4).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.1M Ammonium Sulfate 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2011 / Details: monochromator and mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 18111 / Num. obs: 13950 / % possible obs: 77 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 2.98 / % possible all: 43.6

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UKH

1ukh


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.912 / SU B: 16.648 / SU ML: 0.318 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.961 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26553 611 4.4 %RANDOM
Rwork0.22676 ---
all0.2285 13950 --
obs0.22849 13278 76.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.572 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2866 0 59 27 2952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222981
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.994044
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6535357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69724.496129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.68315520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8711515
X-RAY DIFFRACTIONr_chiral_restr0.0920.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212209
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6061.51804
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14422923
X-RAY DIFFRACTIONr_scbond_it1.26131177
X-RAY DIFFRACTIONr_scangle_it2.1694.51121
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.505 26 -
Rwork0.504 521 -
obs--42.44 %

+
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