[English] 日本語
Yorodumi
- PDB-4i5h: Crystal Structure of a Double Mutant Rat Erk2 Complexed With a Ty... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4i5h
TitleCrystal Structure of a Double Mutant Rat Erk2 Complexed With a Type II Quinazoline Inhibitor
ComponentsMitogen-activated protein kinase 1
KeywordsTransferase/Transferase Inhibitor / MAP kinase / DFG-out / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs ...phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / MAPK1 (ERK2) activation / Signaling by NODAL / Frs2-mediated activation / ERK/MAPK targets / ERKs are inactivated / Activation of the AP-1 family of transcription factors / RHO GTPases Activate WASPs and WAVEs / IFNG signaling activates MAPKs / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Golgi Cisternae Pericentriolar Stack Reorganization / Regulation of actin dynamics for phagocytic cup formation / Estrogen-stimulated signaling through PRKCZ / Growth hormone receptor signaling / Spry regulation of FGF signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Oxidative Stress Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oncogene Induced Senescence / Signaling by Activin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Signal attenuation / NCAM signaling for neurite out-growth / Negative regulation of FGFR1 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Regulation of the apoptosome activity / Signal transduction by L1 / Negative regulation of FGFR2 signaling / RHO GTPases Activate NADPH Oxidases / Negative regulation of MAPK pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interferon gamma signaling / FCERI mediated MAPK activation / Regulation of HSF1-mediated heat shock response / MAP2K and MAPK activation / Recycling pathway of L1 / neural crest cell development / diadenosine tetraphosphate biosynthetic process / cardiac neural crest cell development involved in heart development / caveolin-mediated endocytosis / cytosine metabolic process / response to epidermal growth factor / mitogen-activated protein kinase kinase kinase binding / positive regulation of macrophage proliferation / outer ear morphogenesis / regulation of cellular pH / regulation of Golgi inheritance / Thrombin signalling through proteinase activated receptors (PARs) / RAF/MAP kinase cascade / ERBB signaling pathway / labyrinthine layer blood vessel development / mammary gland epithelial cell proliferation / trachea formation / Neutrophil degranulation / regulation of early endosome to late endosome transport / regulation of stress-activated MAPK cascade / : / positive regulation of macrophage chemotaxis / lung morphogenesis / ERBB2-ERBB3 signaling pathway / response to exogenous dsRNA / regulation of cytoskeleton organization / face development / progesterone receptor signaling pathway / androgen receptor signaling pathway / pseudopodium / negative regulation of cell differentiation / Bergmann glial cell differentiation / positive regulation of telomere capping / thyroid gland development / steroid hormone receptor signaling pathway / decidualization / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / phosphatase binding / Schwann cell development / stress-activated MAPK cascade / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / sensory perception of pain / positive regulation of telomere maintenance via telomerase / cellular response to cadmium ion / ERK1 and ERK2 cascade / cellular response to amino acid starvation / myelination / dendrite cytoplasm / phosphotyrosine residue binding / RNA polymerase II CTD heptapeptide repeat kinase activity / insulin-like growth factor receptor signaling pathway / thymus development / positive regulation of peptidyl-threonine phosphorylation / caveola / positive regulation of translation / long-term synaptic potentiation / animal organ morphogenesis
Similarity search - Function
Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase, ERK1/2 / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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, ATP binding site / Protein kinases ATP-binding region signature. / 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-G17 / Mitogen-activated protein kinase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsHari, S.B. / Maly, D.J. / Merritt, E.A.
CitationJournal: Chem.Biol. / Year: 2013
Title: Sequence determinants of a specific inactive protein kinase conformation.
Authors: Hari, S.B. / Merritt, E.A. / Maly, D.J.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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

-
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)41,8162
Polymers41,3541
Non-polymers4621
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.240, 77.240, 121.791
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Detailsbiological unit is the same as asym.

-
Components

#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: 41353.504 Da / Num. of mol.: 1 / Mutation: Q103A, C164L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Erk2, Mapk, Mapk1, Prkm1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63086, mitogen-activated protein kinase
#2: Chemical ChemComp-G17 / N-{3-[2-(cyclopropylamino)quinazolin-6-yl]-4-methylphenyl}-3-(trifluoromethyl)benzamide


Mass: 462.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H21F3N4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 90 mM sodium citrate, 20% (w/v) PEG 6000, 0.7% n-butanol, pH 5.8, sitting drop, temperature 295K, VAPOR DIFFUSION, SITTING DROP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.9→15.462 Å / Num. all: 33356 / Num. obs: 33356 / % possible obs: 98.7 % / Redundancy: 9 % / Rsym value: 0.09 / Net I/σ(I): 12.7
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-23.80.71719544961.15892.8
2-2.126.212865945890.77999.7
2.12-2.2710.11.64366743430.474100
2.27-2.4510.52.24251440420.352100
2.45-2.6910.63.53962437410.216100
2.69-310.55.83575634000.128100
3-3.4710.69.23183830170.075100
3.47-4.2510.712.92757125840.05100
4.25-6.0110.410.52108020350.057100
6.01-15.4629.711.71072411090.03994.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.54 Å15.46 Å
Translation6.54 Å15.46 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→15.462 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2422 / WRfactor Rwork: 0.2038 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8108 / SU B: 8.243 / SU ML: 0.123 / SU R Cruickshank DPI: 0.1614 / SU Rfree: 0.1509 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 1684 5.1 %RANDOM
Rwork0.2182 ---
obs0.2201 33316 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.3 Å2 / Biso mean: 41.536 Å2 / Biso min: 19.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å2-0.79 Å2-0 Å2
2---0.79 Å2-0 Å2
3---2.57 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 34 134 2903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192837
X-RAY DIFFRACTIONr_bond_other_d0.0020.022747
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9913847
X-RAY DIFFRACTIONr_angle_other_deg0.8323.0026320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6655332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01523.939132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94215504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9741518
X-RAY DIFFRACTIONr_chiral_restr0.0880.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02651
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 116 -
Rwork0.367 2060 -
all-2176 -
obs--88.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2964-0.208-0.30971.809-0.55842.94490.1383-0.0152-0.4036-0.05360.02480.28870.222-0.3006-0.16310.1622-0.0088-0.130.08790.01950.1739-25.187168.3339130.144
21.13510.2560.13711.68580.17481.39870.04040.0108-0.1186-0.10430.01320.33450-0.1765-0.05360.1520.0482-0.04510.13240.02310.1103-17.045776.7112137.5094
31.80490.0536-0.53022.7613-0.46271.45350.07660.33780.0816-0.3627-0.00090.0965-0.1021-0.0489-0.07580.17850.0608-0.03810.1535-0.00040.0224-11.963695.8218132.8556
42.33881.10090.97264.74035.162210.64210.10640.19670.20580.0205-0.02390.1451-0.6061-0.1756-0.08240.22540.03480.06490.16030.06760.0483-5.7846105.3817123.3155
51.533-0.40240.21442.7227-0.51361.31550.012-0.0070.0829-0.0248-0.0375-0.1504-0.02790.02840.02550.16510.0272-0.02870.1737-0.01010.0978-1.729389.0944142.2116
64.7505-0.92170.82686.5262-2.91336.75930.1020.4702-0.4165-0.1793-0.1603-0.4070.32890.29530.05830.24350.0761-0.12540.1765-0.10530.156-16.376662.4273118.495
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 76
2X-RAY DIFFRACTION2A77 - 187
3X-RAY DIFFRACTION3A188 - 248
4X-RAY DIFFRACTION4A249 - 268
5X-RAY DIFFRACTION5A269 - 328
6X-RAY DIFFRACTION6A335 - 356

+
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://pdbjlvh1.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