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- PDB-2fa2: Crystal structure of Fus3 without a peptide from Ste5 -

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Basic information

Entry
Database: PDB / ID: 2fa2
TitleCrystal structure of Fus3 without a peptide from Ste5
ComponentsMitogen-activated protein kinase FUS3
KeywordsTRANSFERASE / MAP kinase
Function / homology
Function and homology information


MAPK3 (ERK1) activation / phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / Frs2-mediated activation / ERK/MAPK targets / Signalling to ERK5 / ERKs are inactivated / Senescence-Associated Secretory Phenotype (SASP) / NCAM signaling for neurite out-growth / Ca2+ pathway ...MAPK3 (ERK1) activation / phospho-PLA2 pathway / RAF-independent MAPK1/3 activation / Frs2-mediated activation / ERK/MAPK targets / Signalling to ERK5 / ERKs are inactivated / Senescence-Associated Secretory Phenotype (SASP) / NCAM signaling for neurite out-growth / Ca2+ pathway / RAF/MAP kinase cascade / Negative regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / Estrogen-stimulated signaling through PRKCZ / MAPK1 (ERK2) activation / Signal transduction by L1 / MAP2K and MAPK activation / Negative feedback regulation of MAPK pathway / pheromone response MAPK cascade / Recycling pathway of L1 / response to pheromone triggering conjugation with cellular fusion / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / Regulation of HSF1-mediated heat shock response / Activation of the AP-1 family of transcription factors / Transcriptional and post-translational regulation of MITF-M expression and activity / transposable element silencing / mating projection tip / MAPK6/MAPK4 signaling / MAP kinase activity / mitogen-activated protein kinase / negative regulation of MAPK cascade / Neutrophil degranulation / positive regulation of protein export from nucleus / cytoplasmic stress granule / periplasmic space / protein kinase activity / intracellular signal transduction / cell division / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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 ...Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / : / 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, 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
THIOCYANATE ION / Mitogen-activated protein kinase FUS3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsBhattacharyya, R.P. / Remenyi, A. / Good, M.C. / Bashor, C.J. / Falick, A.M. / Lim, W.A.
CitationJournal: Science / Year: 2006
Title: The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway
Authors: Bhattacharyya, R.P. / Remenyi, A. / Good, M.C. / Bashor, C.J. / Falick, A.M. / Lim, W.A.
History
DepositionDec 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase FUS3
B: Mitogen-activated protein kinase FUS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9678
Polymers81,6182
Non-polymers3486
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-31 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.143, 94.468, 113.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe assymetric unit contains two biological units. The structure is a homodimer of MAP kinase Fus3.

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Components

#1: Protein Mitogen-activated protein kinase FUS3 / MAP kinase FUS3


Mass: 40809.047 Da / Num. of mol.: 2 / Mutation: T180V, Y182F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FUS3, DAC2 / Plasmid: pBH4-Fus3VF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)plysS / References: UniProt: P16892, EC: 2.7.1.37
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 18% PEG3350, 0.1M MES, 10% MPD, 0.2M KSCN, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 13, 2004
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 19082 / Num. obs: 19082 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.074 / Net I/σ(I): 13.5
Reflection shellResolution: 2.85→2.95 Å / Mean I/σ(I) obs: 3.9 / Num. unique all: 1359 / Rsym value: 0.189 / % possible all: 68.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2B9F

2b9f


Resolution: 2.85→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1875 -random
Rwork0.209 ---
all0.209 18983 --
obs0.209 18983 93.3 %-
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5318 0 18 27 5363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6

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