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- PDB-2f49: Crystal structure of Fus3 in complex with a Ste5 peptide -

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Basic information

Entry
Database: PDB / ID: 2f49
TitleCrystal structure of Fus3 in complex with a Ste5 peptide
Components
  • Mitogen-activated protein kinase FUS3
  • STE5 peptide
KeywordsTRANSFERASE / protein-petide complex
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
THIOCYANATE ION / Mitogen-activated protein kinase FUS3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRemenyi, 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
DepositionNov 22, 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 / 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_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_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_asym_id / _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_asym_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
B: Mitogen-activated protein kinase FUS3
C: STE5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,42312
Polymers84,9683
Non-polymers4559
Water8,611478
1
A: Mitogen-activated protein kinase FUS3
C: STE5 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3576
Polymers44,1592
Non-polymers1994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-30 kcal/mol
Surface area17010 Å2
MethodPISA
2
B: Mitogen-activated protein kinase FUS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0666
Polymers40,8091
Non-polymers2575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-68 kcal/mol
Surface area29910 Å2
MethodPISA
4
A: Mitogen-activated protein kinase FUS3
B: Mitogen-activated protein kinase FUS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,07311
Polymers81,6182
Non-polymers4559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-59 kcal/mol
Surface area29220 Å2
MethodPISA
5
C: STE5 peptide


Theoretical massNumber of molelcules
Total (without water)3,3501
Polymers3,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.622, 95.210, 101.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a protein-peptide complex between chain A and C

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Components

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


Mass: 40809.047 Da / Num. of mol.: 2 / Fragment: Fus3 / 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 STE5 peptide


Mass: 3349.769 Da / Num. of mol.: 1 / Fragment: Fus3 binding region of STE5 / Source method: obtained synthetically
Details: This peptide was chemically synthesized but this sequence naturally occurs in the Ste5 protein from S. cerevisiae
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.1
Details: 18% PEG3350, 0.1M Mes, 10% MPD, 0.2M KSCN, pH 6.1, VAPOR DIFFUSION, 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: 1.9→50 Å / Num. all: 69388 / Num. obs: 69388 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rsym value: 0.07 / Net I/σ(I): 15.3
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.4 / Num. unique all: 5920 / Rsym value: 0.5 / % possible all: 83.2

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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: 1.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 6995 -random
Rwork0.201 ---
all0.201 69316 --
obs0.201 69316 95.1 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 23 478 6063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_bond_d0.011

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