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- PDB-1upk: Crystal structure of MO25 in complex with a C-terminal peptide of... -

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Basic information

Entry
Database: PDB / ID: 1upk
TitleCrystal structure of MO25 in complex with a C-terminal peptide of STRAD
Components
  • MO25 PROTEIN
  • STE-20 RELATED ADAPTOR
KeywordsTRANSFERASE / MO25 / STRAD / STE-20 RELATED ADAPTOR / ARMADILLO
Function / homology
Function and homology information


intracellular protein-containing complex / negative regulation of potassium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / cellular hypotonic response / activation of protein kinase activity / response to thyroid hormone / Energy dependent regulation of mTOR by LKB1-AMPK / serine/threonine protein kinase complex / G1 to G0 transition / positive regulation of peptidyl-threonine phosphorylation ...intracellular protein-containing complex / negative regulation of potassium ion transmembrane transport / negative regulation of potassium ion transmembrane transporter activity / cellular hypotonic response / activation of protein kinase activity / response to thyroid hormone / Energy dependent regulation of mTOR by LKB1-AMPK / serine/threonine protein kinase complex / G1 to G0 transition / positive regulation of peptidyl-threonine phosphorylation / protein kinase activator activity / positive regulation of protein serine/threonine kinase activity / protein export from nucleus / protein serine/threonine kinase activator activity / response to activity / Z disc / kinase binding / peptidyl-serine phosphorylation / secretory granule lumen / ficolin-1-rich granule lumen / intracellular signal transduction / Neutrophil degranulation / signal transduction / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Mo25-like / Mo25-like / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Protein kinase domain / Protein kinase domain profile. ...: / Mo25-like / Mo25-like / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Alpha
Similarity search - Domain/homology
STE20-related kinase adapter protein alpha / Calcium-binding protein 39
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.85 Å
AuthorsMilburn, C.C. / Boudeau, J. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Crystal Structure of Mo25 Alpha in Complex with the C-Terminus of the Pseudo Kinase Ste-20 Related Adaptor (Strad)
Authors: Milburn, C.C. / Boudeau, J. / Deak, M. / Alessi, D.R. / Van Aalten, D.M.F.
History
DepositionOct 7, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn / struct_ref_seq
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MO25 PROTEIN
B: STE-20 RELATED ADAPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0783
Polymers41,8832
Non-polymers1951
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)77.650, 134.033, 40.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2120-

HOH

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Components

#1: Protein MO25 PROTEIN / MO25 ALPHA / CGI 66


Mass: 40344.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6T-1 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): B834 / References: UniProt: Q9Y376
#2: Protein/peptide STE-20 RELATED ADAPTOR / STRAD ALPHA


Mass: 1537.579 Da / Num. of mol.: 1 / Fragment: C-TERMINAL 12 AMINO ACIDS, RESIDUES 1-12 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q7RTN6*PLUS
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 52.6 %
Crystal growpH: 5
Details: 15% PEG 20000, 0.1 M MES PH 5.0, 3.3% W/V D-GLUCOSE MONOHYDRATE.
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114.5 mg/mlprotein1drop
215 %(w/v)PEG200001reservoir
30.1 MMES1reservoirpH5.0
430 %(w/v)D-glucose monohydrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979355,0.979333
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9793551
20.9793331
ReflectionResolution: 1.85→25 Å / Num. obs: 36794 / % possible obs: 99.6 % / Redundancy: 8.8 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 41.7
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 4.9 / % possible all: 99
Reflection
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 25 Å / Redundancy: 8.8 % / Num. measured all: 324698 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 99 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1.85→24.15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1411659.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 744 2 %RANDOM
Rwork0.202 ---
obs0.202 36515 99.4 %-
Solvent computationSolvent model: FLAT MODEL / ksol: 0.314326 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2---7.92 Å20 Å2
3---9.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.85→24.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 7 307 2984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it2.532
X-RAY DIFFRACTIONc_scangle_it3.62.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 112 1.9 %
Rwork0.291 5843 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION3MES.PARPROTEIN.LINK
X-RAY DIFFRACTION4WATER.TOP
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection Rfree: 745 / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96

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