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- PDB-5yyz: Crystal structure of the MEK1 FHA domain in complex with the HOP1... -

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Basic information

Entry
Database: PDB / ID: 5yyz
TitleCrystal structure of the MEK1 FHA domain in complex with the HOP1 pThr318 peptide.
Components
  • Meiosis-specific protein HOP1
  • Meiosis-specific serine/threonine-protein kinase MEK1
KeywordsTRANSFERASE / MEK1 / HOP1 / Meiosis
Function / homology
Function and homology information


meiotic recombination checkpoint signaling / HSF1-dependent transactivation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / lateral element / calmodulin-dependent protein kinase activity / four-way junction DNA binding / meiotic cell cycle / condensed nuclear chromosome / cellular response to oxidative stress ...meiotic recombination checkpoint signaling / HSF1-dependent transactivation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / lateral element / calmodulin-dependent protein kinase activity / four-way junction DNA binding / meiotic cell cycle / condensed nuclear chromosome / cellular response to oxidative stress / non-specific serine/threonine protein kinase / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / nucleus
Similarity search - Function
Meiosis-specific protein Hop1 / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily ...Meiosis-specific protein Hop1 / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / 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
Similarity search - Domain/homology
Meiosis-specific protein HOP1 / Meiosis-specific serine/threonine-protein kinase MEK1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å
AuthorsXie, C. / Li, F. / Jiang, Y. / Wu, J. / Shi, Y.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Structural insights into the recognition of phosphorylated Hop1 by Mek1
Authors: Xie, C. / He, C. / Jiang, Y. / Yu, H. / Cheng, L. / Nshogoza, G. / Ala, M.S. / Tian, C. / Wu, J. / Shi, Y. / Li, F.
History
DepositionDec 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Meiosis-specific serine/threonine-protein kinase MEK1
B: Meiosis-specific protein HOP1


Theoretical massNumber of molelcules
Total (without water)17,6212
Polymers17,6212
Non-polymers00
Water1,928107
1
A: Meiosis-specific serine/threonine-protein kinase MEK1


Theoretical massNumber of molelcules
Total (without water)16,1071
Polymers16,1071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Meiosis-specific protein HOP1


Theoretical massNumber of molelcules
Total (without water)1,5141
Polymers1,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.640, 38.183, 54.418
Angle α, β, γ (deg.)90.000, 94.970, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Meiosis-specific serine/threonine-protein kinase MEK1


Mass: 16107.298 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: MEK1, MRE4, YOR351C, O6357
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P24719, non-specific serine/threonine protein kinase
#2: Protein/peptide Meiosis-specific protein HOP1


Mass: 1513.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288c (yeast) / References: UniProt: P20050
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium Citrate tribasic tetrahydrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.798→40 Å / Num. obs: 15415 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.38 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.025 / Rrim(I) all: 0.066 / Χ2: 0.525 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.866.20.54715220.8770.2340.5960.44698.6
1.86-1.946.80.42115330.9370.1720.4550.45299.9
1.94-2.036.70.28515420.970.1180.3090.45999.5
2.03-2.136.60.19815220.9830.0830.2150.46599.3
2.13-2.276.50.14515210.9890.0610.1580.50198.4
2.27-2.446.90.11615270.9930.0470.1250.49799.5
2.44-2.696.80.08615550.9960.0350.0930.49999.7
2.69-3.086.70.05815360.9980.0240.0630.57598.7
3.08-3.886.80.04215710.9990.0170.0450.62199.6
3.88-406.50.0415860.9980.0160.0430.72198.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G6G

1g6g


Resolution: 1.798→33.701 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 693 4.5 %
Rwork0.1882 14714 -
obs0.1897 15407 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.76 Å2 / Biso mean: 36.3355 Å2 / Biso min: 14.97 Å2
Refinement stepCycle: final / Resolution: 1.798→33.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 0 107 989
Biso mean---48.7 -
Num. residues----109
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006898
X-RAY DIFFRACTIONf_angle_d0.7941217
X-RAY DIFFRACTIONf_chiral_restr0.062145
X-RAY DIFFRACTIONf_plane_restr0.005150
X-RAY DIFFRACTIONf_dihedral_angle_d13.868538
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7976-1.93640.24431390.20862900303998
1.9364-2.13120.27021340.19372932306699
2.1312-2.43960.22671190.19192930304999
2.4396-3.07330.23041510.21092944309599
3.0733-33.70710.20851500.17383008315899
Refinement TLS params.Method: refined / Origin x: 27.1255 Å / Origin y: 12.7781 Å / Origin z: 33.1246 Å
111213212223313233
T0.1435 Å2-0.0106 Å20.028 Å2-0.11 Å2-0.0047 Å2--0.2188 Å2
L4.1115 °2-0.1166 °21.1532 °2-1.2826 °2-0.2657 °2--5.3485 °2
S0.0149 Å °-0.1105 Å °0.061 Å °0.0119 Å °0.0236 Å °-0.0325 Å °-0.0555 Å °0.0617 Å °-0.0448 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA21 - 138
2X-RAY DIFFRACTION1allS1 - 153
3X-RAY DIFFRACTION1allS156 - 185
4X-RAY DIFFRACTION1allB315 - 321

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