[English] 日本語
Yorodumi
- PDB-8zjv: Crystal Structure of the ERK2 complexed with 5-Iodotubercidin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8zjv
TitleCrystal Structure of the ERK2 complexed with 5-Iodotubercidin
ComponentsMitogen-activated protein kinase 1
KeywordsTRANSFERASE / Inhibitor
Function / homology
Function and homology information


phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / cytosine metabolic process / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis ...phospho-PLA2 pathway / Signaling by MAPK mutants / RAF-independent MAPK1/3 activation / Suppression of apoptosis / Gastrin-CREB signalling pathway via PKC and MAPK / Signaling by Activin / cardiac neural crest cell development involved in heart development / cytosine metabolic process / interleukin-34-mediated signaling pathway / caveolin-mediated endocytosis / outer ear morphogenesis / trachea formation / labyrinthine layer blood vessel development / response to epidermal growth factor / Signaling by NODAL / RSK activation / Signaling by MAP2K mutants / ERKs are inactivated / Bergmann glial cell differentiation / lung morphogenesis / Regulation of the apoptosome activity / Golgi Cisternae Pericentriolar Stack Reorganization / positive regulation of macrophage proliferation / : / mammary gland epithelial cell proliferation / regulation of Golgi inheritance / Signaling by LTK in cancer / positive regulation of peptidyl-threonine phosphorylation / face development / ERBB signaling pathway / regulation of early endosome to late endosome transport / thyroid gland development / Negative feedback regulation of MAPK pathway / regulation of stress-activated MAPK cascade / positive regulation of neuroinflammatory response / IFNG signaling activates MAPKs / Frs2-mediated activation / response to exogenous dsRNA / Activation of the AP-1 family of transcription factors / ERBB2-ERBB3 signaling pathway / ERK/MAPK targets / RUNX2 regulates osteoblast differentiation / regulation of cytoskeleton organization / positive regulation of macrophage chemotaxis / MAPK1 (ERK2) activation / Recycling pathway of L1 / pseudopodium / positive regulation of telomere maintenance / regulation of ossification / MAP kinase activity / Advanced glycosylation endproduct receptor signaling / mitogen-activated protein kinase / Regulation of HSF1-mediated heat shock response / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / stress-activated MAPK cascade / ERK1 and ERK2 cascade / RHO GTPases Activate NADPH Oxidases / Signal attenuation / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / Growth hormone receptor signaling / Schwann cell development / thymus development / phosphatase binding / Estrogen-stimulated signaling through PRKCZ / myelination / NPAS4 regulates expression of target genes / lipopolysaccharide-mediated signaling pathway / phosphotyrosine residue binding / insulin-like growth factor receptor signaling pathway / ciliary tip / Nuclear events stimulated by ALK signaling in cancer / RNA polymerase II CTD heptapeptide repeat kinase activity / Transcriptional and post-translational regulation of MITF-M expression and activity / ESR-mediated signaling / NCAM signaling for neurite out-growth / cellular response to amino acid starvation / B cell receptor signaling pathway / Regulation of PTEN gene transcription / Signal transduction by L1 / chemokine-mediated signaling pathway / response to nicotine / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / cellular response to tumor necrosis factor / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Signaling by high-kinase activity BRAF mutants / positive regulation of cholesterol biosynthetic process / Spry regulation of FGF signaling / MAP2K and MAPK activation / Regulation of actin dynamics for phagocytic cup formation / Negative Regulation of CDH1 Gene Transcription / caveola / Oncogene Induced Senescence / long-term synaptic potentiation
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
Chem-5ID / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYang, Y. / Fu, L. / Chen, R. / Cheng, H. / Sun, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of the ERK2 complexed with 5-Iodotubercidin
Authors: Yang, Y. / Fu, L. / Chen, R. / Cheng, H. / Sun, X.
History
DepositionMay 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,75710
Polymers40,7591
Non-polymers9989
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mitogen-activated protein kinase 1
hetero molecules

A: Mitogen-activated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,51420
Polymers81,5182
Non-polymers1,99618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area5610 Å2
ΔGint-118 kcal/mol
Surface area31480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.979, 96.979, 95.530
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-409-

CL

21A-600-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Mitogen-activated protein kinase 1 / MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform ...MAP kinase 1 / MAPK 1 / ERT1 / Extracellular signal-regulated kinase 2 / ERK-2 / MAP kinase isoform p42 / p42-MAPK / Mitogen-activated protein kinase 2 / MAP kinase 2 / MAPK 2


Mass: 40758.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK1, ERK2, PRKM1, PRKM2 / Production host: Escherichia coli (E. coli)
References: UniProt: P28482, mitogen-activated protein kinase

-
Non-polymers , 5 types, 313 molecules

#2: Chemical ChemComp-5ID / (2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL / 5-IODOTUBERCIDIN


Mass: 392.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13IN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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.: 304 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M Lithium Sulfate monohydrate, 0.1 M Bis-Tris pH 5.5, 25% w/v Polyethylene Glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→41.52 Å / Num. obs: 48367 / % possible obs: 99.66 % / Redundancy: 15.1 % / Biso Wilson estimate: 25.44 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1282 / Net I/σ(I): 16.67
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 15.5 % / Rmerge(I) obs: 2.026 / Num. unique obs: 4796 / CC1/2: 0.685 / CC star: 0.902 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AX3

5ax3


Resolution: 1.8→41.52 Å / SU ML: 0.2029 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4819
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.22 2417 5 %
Rwork0.19 45938 -
obs0.1915 48355 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.22 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 0 53 304 3207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642967
X-RAY DIFFRACTIONf_angle_d0.79784021
X-RAY DIFFRACTIONf_chiral_restr0.0503437
X-RAY DIFFRACTIONf_plane_restr0.0078511
X-RAY DIFFRACTIONf_dihedral_angle_d12.74321110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.32111330.31262672X-RAY DIFFRACTION99.08
1.84-1.880.33141410.27092655X-RAY DIFFRACTION99.36
1.88-1.920.26871210.24332659X-RAY DIFFRACTION99.36
1.92-1.970.24741330.22182695X-RAY DIFFRACTION99.51
1.97-2.020.24781490.21922667X-RAY DIFFRACTION99.51
2.02-2.080.23371600.22632X-RAY DIFFRACTION99.29
2.08-2.150.22271400.20032676X-RAY DIFFRACTION99.68
2.15-2.220.2061730.20262670X-RAY DIFFRACTION99.61
2.23-2.310.21751090.20272699X-RAY DIFFRACTION99.82
2.31-2.420.21611480.20062697X-RAY DIFFRACTION99.82
2.42-2.550.20931330.19952705X-RAY DIFFRACTION99.86
2.55-2.710.22881310.20572722X-RAY DIFFRACTION99.93
2.71-2.920.2811400.19892721X-RAY DIFFRACTION100
2.92-3.210.24161910.19762662X-RAY DIFFRACTION99.96
3.21-3.670.20911620.17362740X-RAY DIFFRACTION100
3.68-4.630.18031190.15312780X-RAY DIFFRACTION100
4.63-41.520.18991340.17352886X-RAY DIFFRACTION99.7

+
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