[English] 日本語
Yorodumi
- PDB-6zqs: Crystal structure of double-phosphorylated p38alpha with ATF2(83-102) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zqs
TitleCrystal structure of double-phosphorylated p38alpha with ATF2(83-102)
Components
  • Cyclic AMP-dependent transcription factor ATF-2
  • Mitogen-activated protein kinase 14
KeywordsTRANSCRIPTION / MAPK SIGNALING PATHWAYS
Function / homology
Function and homology information


abducens nucleus development / hypoglossal nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / facial nucleus development / growth plate cartilage chondrocyte differentiation / positive regulation of cardiac muscle myoblast proliferation / positive regulation of transforming growth factor beta2 production / cellular response to anisomycin ...abducens nucleus development / hypoglossal nucleus development / detection of cell density / H4 histone acetyltransferase complex / growth plate cartilage chondrocyte proliferation / facial nucleus development / growth plate cartilage chondrocyte differentiation / positive regulation of cardiac muscle myoblast proliferation / positive regulation of transforming growth factor beta2 production / cellular response to anisomycin / cAMP response element binding / leucine zipper domain binding / cAMP response element binding protein binding / histone H2B acetyltransferase activity / positive regulation of mitochondrial membrane permeability involved in apoptotic process / brainstem development / cellular response to leucine starvation / NK T cell differentiation / apoptotic process involved in development / vacuole organization / neurofilament cytoskeleton organization / histone H4 acetyltransferase activity / NGF-stimulated transcription / positive regulation of cyclase activity / intrinsic apoptotic signaling pathway in response to hypoxia / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / mitotic intra-S DNA damage checkpoint signaling / regulation of synaptic membrane adhesion / : / motor neuron apoptotic process / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / CD163 mediating an anti-inflammatory response / stress-activated protein kinase signaling cascade / 3'-UTR-mediated mRNA stabilization / response to osmotic stress / positive regulation of myoblast fusion / : / KSRP (KHSRP) binds and destabilizes mRNA / cellular response to UV-B / cartilage condensation / mitogen-activated protein kinase p38 binding / positive regulation of muscle cell differentiation / peptidyl-threonine phosphorylation / Myogenesis / Platelet sensitization by LDL / positive regulation of myotube differentiation / NFAT protein binding / Activation of the AP-1 family of transcription factors / regulation of cytokine production involved in inflammatory response / hepatocyte apoptotic process / p38MAPK cascade / ERK/MAPK targets / cellular response to lipoteichoic acid / response to dietary excess / fatty acid oxidation / response to muramyl dipeptide / MAP kinase kinase activity / histone acetyltransferase activity / Regulation of MITF-M-dependent genes involved in pigmentation / outflow tract morphogenesis / white fat cell differentiation / MAP kinase activity / cellular response to vascular endothelial growth factor stimulus / regulation of ossification / mitogen-activated protein kinase / RHO GTPases Activate NADPH Oxidases / : / adipose tissue development / vascular endothelial growth factor receptor signaling pathway / chondrocyte differentiation / Response of EIF2AK4 (GCN2) to amino acid deficiency / BMP signaling pathway / negative regulation of hippo signaling / positive regulation of myoblast differentiation / hematopoietic progenitor cell differentiation / stress-activated MAPK cascade / skeletal muscle tissue development / positive regulation of cardiac muscle cell proliferation / cis-regulatory region sequence-specific DNA binding / positive regulation of brown fat cell differentiation / p38MAPK events / response to muscle stretch / signal transduction in response to DNA damage / JNK cascade / striated muscle cell differentiation / positive regulation of interleukin-12 production / positive regulation of erythrocyte differentiation / osteoclast differentiation / lipopolysaccharide-mediated signaling pathway / transcription initiation-coupled chromatin remodeling / placenta development / DNA damage checkpoint signaling / negative regulation of angiogenesis / Regulation of PTEN gene transcription / stem cell differentiation / tumor necrosis factor-mediated signaling pathway / positive regulation of D-glucose import across plasma membrane / cellular response to ionizing radiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding
Similarity search - Function
Transcription factor cyclic AMP-dependent, CRE-BP1-type / : / bZIP transcription factor / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like ...Transcription factor cyclic AMP-dependent, CRE-BP1-type / : / bZIP transcription factor / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper (bZIP) domain profile. / basic region leucin zipper / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 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-3FF / Cyclic AMP-dependent transcription factor ATF-2 / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsKirsch, K. / Sok, P. / Poti, A.L. / Remenyi, A.
Funding support Hungary, 2items
OrganizationGrant numberCountry
National Research Development and Innovation Office (NKFIH)NN 114309 Hungary
National Research Development and Innovation Office (NKFIH)KKP 126963 Hungary
CitationJournal: Nat Commun / Year: 2020
Title: Co-regulation of the transcription controlling ATF2 phosphoswitch by JNK and p38.
Authors: Kirsch, K. / Zeke, A. / Toke, O. / Sok, P. / Sethi, A. / Sebo, A. / Kumar, G.S. / Egri, P. / Poti, A.L. / Gooley, P. / Peti, W. / Bento, I. / Alexa, A. / Remenyi, A.
History
DepositionJul 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mitogen-activated protein kinase 14
B: Cyclic AMP-dependent transcription factor ATF-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3743
Polymers43,9492
Non-polymers4251
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-10 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.401, 84.602, 122.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-629-

HOH

21A-704-

HOH

-
Components

#1: Protein Mitogen-activated protein kinase 14 / MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSBP / MAP kinase MXI2 / ...MAPK 14 / Cytokine suppressive anti-inflammatory drug-binding protein / CSBP / MAP kinase MXI2 / MAX-interacting protein 2 / Mitogen-activated protein kinase p38 alpha / MAP kinase p38 alpha / Stress-activated protein kinase 2a / SAPK2a


Mass: 41647.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A / Plasmid: PET DERIVATIVE / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q16539, mitogen-activated protein kinase
#2: Protein/peptide Cyclic AMP-dependent transcription factor ATF-2 / cAMP-dependent transcription factor ATF-2 / Activating transcription factor 2 / Cyclic AMP- ...cAMP-dependent transcription factor ATF-2 / Activating transcription factor 2 / Cyclic AMP-responsive element-binding protein 2 / cAMP-responsive element-binding protein 2 / HB16 / Histone acetyltransferase ATF2 / cAMP response element-binding protein CRE-BP1


Mass: 2301.463 Da / Num. of mol.: 1 / Mutation: S90N / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15336, histone acetyltransferase
#3: Chemical ChemComp-3FF / 2-[(2,4-difluorophenyl)amino]-7-{[(2R)-2,3-dihydroxypropyl]oxy}-10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-one


Mass: 425.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H21F2NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 14% PEG 3350, 0.1 M cacodylate ph 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→69.62 Å / Num. obs: 30463 / % possible obs: 99.1 % / Redundancy: 12.5 % / Biso Wilson estimate: 38.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Rrim(I) all: 0.085 / Net I/σ(I): 17.8 / Num. measured all: 380252 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-26.21.5991.118420.4250.6641.74488.2
8.94-69.6210.30.0361.539710.0090.03199.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TCA

6tca


Resolution: 1.95→69.62 Å / SU ML: 0.2265 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2234 1502 4.94 %
Rwork0.1753 28878 -
obs0.1776 30380 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.28 Å2
Refinement stepCycle: LAST / Resolution: 1.95→69.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 31 351 3268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822988
X-RAY DIFFRACTIONf_angle_d1.08554070
X-RAY DIFFRACTIONf_chiral_restr0.0583456
X-RAY DIFFRACTIONf_plane_restr0.0056518
X-RAY DIFFRACTIONf_dihedral_angle_d17.4339407
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.3638930.2842336X-RAY DIFFRACTION88.97
2.01-2.080.24771480.23122592X-RAY DIFFRACTION99.49
2.09-2.170.26661600.21012586X-RAY DIFFRACTION99.82
2.17-2.270.2291360.19682596X-RAY DIFFRACTION99.85
2.27-2.390.25031350.19362613X-RAY DIFFRACTION99.82
2.39-2.540.27831350.19442618X-RAY DIFFRACTION99.93
2.54-2.730.24941390.18312651X-RAY DIFFRACTION99.96
2.73-3.010.26281350.18072671X-RAY DIFFRACTION99.93
3.01-3.440.22011350.16452661X-RAY DIFFRACTION99.86
3.44-4.340.17541450.14652694X-RAY DIFFRACTION99.82
4.34-69.620.21421410.17292860X-RAY DIFFRACTION99.93
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)
16.88898831514-2.090076975941.552911918772.22122668572-2.239530229597.767169458860.244589516083-0.0814946983066-0.360869821311-0.380791647573-0.08913191623270.7383052969740.184064519387-0.736336309691-0.1597813466410.4216653344920.0306185851379-0.03484083589890.385134348504-0.07729835357860.385120909005-18.4458567376-31.1436192915-3.00931090359
21.02181407594-0.2861129049650.1294617057961.49703842747-0.3589671759862.538668939730.0550980256993-0.112592195351-0.01665381469340.0945804664874-0.002895726331320.02638756263010.0643215532903-0.0910078119136-0.04955901517590.250469851661-0.0481242686812-0.01182354489970.29701427034-0.03148686047390.276829472583-10.8985061464-32.074746689621.5872150906
32.5507088055-0.985264001507-0.4571118138391.113101474950.4767028005221.87432912035-0.140851637489-0.3013399127270.2177187419940.1931276376290.121934855623-0.3076232320320.1170862040650.0940549174734-0.01306776885970.331867620576-0.0225255452678-0.09493749483560.387977603929-0.03733868330340.346800327229-0.192115554885-35.638179961328.852651272
49.28240221903-1.2796527782-4.739818021567.297743777971.610704406986.678835952740.2262912101280.2665020436910.570317908971-0.426157596512-0.0144842899873-0.402583260168-0.459280255338-0.0547704588981-0.2485874179390.319404909903-0.005919290043520.01566904477010.2125889101480.03240428713420.298300697651-14.6584648065-14.11396206057.52013366166
56.804678221921.81957343491-2.207515572943.30613279294-3.26573140733.255620291280.091630682991-0.7287126378730.5108810069770.5969019122970.04518833137510.802185755421-0.011049290522-0.93435108395-0.2280448794620.535093828604-0.1081279180490.01027356514290.888023102773-0.02874498920590.505090680637-25.5235357991-31.385516345339.5738677176
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 47 )AA5 - 472 - 44
22chain 'A' and (resid 48 through 261 )AA48 - 26145 - 258
33chain 'A' and (resid 262 through 333 )AA262 - 333259 - 330
44chain 'A' and (resid 334 through 352 )AA334 - 352331 - 349
55chain 'B' and (resid 88 through 101 )BC88 - 1011 - 14

+
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