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- PDB-2f9g: Crystal structure of Fus3 phosphorylated on Tyr182 -

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Basic information

Entry
Database: PDB / ID: 2f9g
TitleCrystal structure of Fus3 phosphorylated on Tyr182
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 / Transcriptional and post-translational regulation of MITF-M expression and activity / Regulation of HSF1-mediated heat shock response / Activation of the AP-1 family of transcription factors / 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. / : / 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, 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
ADENOSINE-5'-DIPHOSPHATE / Mitogen-activated protein kinase FUS3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details
Remark 400COMPOUND ONE OF THE TWO RESIDUES IN THE ACTIVATION LOOP (TYR182) IS PHOSPHORYLATED. (NOTE: FOR MAP ...COMPOUND ONE OF THE TWO RESIDUES IN THE ACTIVATION LOOP (TYR182) IS PHOSPHORYLATED. (NOTE: FOR MAP KINASES PHOSPHORYLATION OF BOTH RESIDUES (THR180 AND TYR182) IS REQUIRED FOR FULL ACTIVATION.) TYR182 PHOSPHORYLATION RENDERS THE FUS3 ACTIVATION LOOP MORE FLEXIBLE. THE PHOSPHORYLATED RESIDUE CAN NOT BE SEEN IN THE ELECTRON DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,3593
Polymers40,9071
Non-polymers4522
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.811, 62.533, 86.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 40906.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: Recombinant Fus3 was incubated with an activator peptide from Ste5 to achieve full phosphorylation on Tyr182 by autophsophorylation.
Gene: FUS3, DAC2 / Plasmid: pBH4-Fus3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)plysS / References: UniProt: P16892, EC: 2.7.1.37
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.87 Å3/Da / Density % sol: 34.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 25-28% PEG1000, 0.1M MES, 5-10% MPD, 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: 1.115889 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2004
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115889 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 18096 / Num. obs: 18096 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.09 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 1574 / Rsym value: 0.346 / % possible all: 86.6

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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: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1764 -random
Rwork0.211 ---
all0.211 18007 --
obs0.211 18007 97.4 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2685 0 28 102 2815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6

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