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- PDB-2b9i: Crystal structure of Fus3 with a docking motif from Msg5 -

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Basic information

Entry
Database: PDB / ID: 2b9i
TitleCrystal structure of Fus3 with a docking motif from Msg5
Components
  • Mitogen-activated protein kinase FUS3
  • Tyrosine-protein phosphatase MSG5
KeywordsTRANSFERASE
Function / homology
Function and homology information


MAPK3 (ERK1) activation / Frs2-mediated activation / ERK/MAPK targets / Senescence-Associated Secretory Phenotype (SASP) / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / MAP2K and MAPK activation / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / RAF-independent MAPK1/3 activation ...MAPK3 (ERK1) activation / Frs2-mediated activation / ERK/MAPK targets / Senescence-Associated Secretory Phenotype (SASP) / NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / MAP2K and MAPK activation / Negative feedback regulation of MAPK pathway / Gastrin-CREB signalling pathway via PKC and MAPK / RAF-independent MAPK1/3 activation / ERKs are inactivated / Negative regulation of MAPK pathway / Signal transduction by L1 / pheromone response MAPK cascade / Regulation of HSF1-mediated heat shock response / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / Activation of the AP-1 family of transcription factors / retrotransposon silencing / mating projection tip / negative regulation of MAPK cascade / MAP kinase activity / mitogen-activated protein kinase / positive regulation of protein export from nucleus / cytoplasmic stress granule / periplasmic space / protein kinase activity / intracellular signal transduction / cell cycle / cell division / phosphorylation / 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 / Serine/Threonine protein kinases, catalytic 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: 2.5 Å
AuthorsRemenyi, A. / Good, M.C. / Bhattacharyya, R.P. / Lim, W.A.
CitationJournal: Mol.Cell / Year: 2005
Title: The role of docking interactions in mediating signaling input, output, and discrimination in the yeast MAPK network.
Authors: Remenyi, A. / Good, M.C. / Bhattacharyya, R.P. / Lim, W.A.
History
DepositionOct 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 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 / pdbx_struct_conn_angle ...database_2 / 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 1.4Aug 23, 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
C: Tyrosine-protein phosphatase MSG5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6234
Polymers43,1722
Non-polymers4522
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-24 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.081, 63.618, 99.950
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: 40809.047 Da / Num. of mol.: 1 / Mutation: T180V, Y182F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
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: Protein/peptide Tyrosine-protein phosphatase MSG5 / MSG5


Mass: 2362.688 Da / Num. of mol.: 1 / Fragment: Msg5 docking motif / Source method: obtained synthetically
Details: The Msg5 docking motif was chemically synthesized. The sequence of this peptide naturally exists in Saccharomyces cerevisiae (Baker's yeast).
References: protein-tyrosine-phosphatase
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 15-20% PEG8000, 0.1M MES pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13279 / % possible obs: 98.1 % / Redundancy: 3.4 % / Rsym value: 0.048 / Net I/σ(I): 18.7

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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: 2.5→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1347 -random
Rwork0.202 ---
all-13321 --
obs-13095 98.3 %-
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 28 94 2944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.6

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