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- PDB-1sko: MP1-p14 Complex -

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Basic information

Entry
Database: PDB / ID: 1sko
TitleMP1-p14 Complex
Components
  • Late endosomal/lysosomal Mp1 interacting protein
  • Mitogen-activated protein kinase kinase 1 interacting protein 1
KeywordsSIGNALING PROTEIN / MAP kinase pathway / MP1-p14 complex / scaffold proteins
Function / homology
Function and homology information


Energy dependent regulation of mTOR by LKB1-AMPK / Amino acids regulate mTORC1 / MTOR signalling / Regulation of PTEN gene transcription / Macroautophagy / regulation of cell-substrate junction organization / TP53 Regulates Metabolic Genes / mTORC1-mediated signalling / FNIP-folliculin RagC/D GAP / Ragulator complex ...Energy dependent regulation of mTOR by LKB1-AMPK / Amino acids regulate mTORC1 / MTOR signalling / Regulation of PTEN gene transcription / Macroautophagy / regulation of cell-substrate junction organization / TP53 Regulates Metabolic Genes / mTORC1-mediated signalling / FNIP-folliculin RagC/D GAP / Ragulator complex / MAP2K and MAPK activation / protein localization to cell junction / TORC1 signaling / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / Energy dependent regulation of mTOR by LKB1-AMPK / kinase activator activity / Macroautophagy / mTORC1-mediated signalling / tertiary granule membrane / positive regulation of TOR signaling / specific granule membrane / positive regulation of TORC1 signaling / Neutrophil degranulation / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / regulation of cell growth / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / MAP2K and MAPK activation / protein localization / late endosome / late endosome membrane / positive regulation of MAPK cascade / molecular adaptor activity / endosome membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / extracellular exosome / plasma membrane
Similarity search - Function
Ragulator complex protein LAMTOR3 / Mitogen-activated protein kinase kinase 1 interacting / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR2-like / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ragulator complex protein LAMTOR2 / Ragulator complex protein LAMTOR3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLunin, V.V. / Munger, C. / Wagner, J. / Ye, Z. / Cygler, M. / Sacher, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The structure of the MAP kinase scaffold MP1 bound to its partner p14: a complex with a critical role in endosomal MAP kinase signaling
Authors: Lunin, V.V. / Munger, C. / Wagner, J. / Ye, Z. / Cygler, M. / Sacher, M.
History
DepositionMar 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitogen-activated protein kinase kinase 1 interacting protein 1
B: Late endosomal/lysosomal Mp1 interacting protein


Theoretical massNumber of molelcules
Total (without water)30,1452
Polymers30,1452
Non-polymers00
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-19 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.974, 64.193, 73.280
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 kinase 1 interacting protein 1 / MEK binding partner 1 / Mp1 / PRO2783


Mass: 15913.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1IP1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9UHA4
#2: Protein Late endosomal/lysosomal Mp1 interacting protein / p14


Mass: 14232.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: MAPBPIP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9JHS3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 14% PEG 3350, 0.1M Tris-HCl buffer, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X8C11.1
SYNCHROTRONNSLS X8C20.979267, 0.979553, 0.964318
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 22, 2003
ADSC QUANTUM 42CCDNov 22, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.9792671
30.9795531
40.9643181
ReflectionResolution: 2→50 Å / Num. all: 16750 / Num. obs: 16750 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.07 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.07 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→48.22 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.743 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27087 854 5.1 %RANDOM
Rwork0.20106 ---
all0.20472 16750 --
obs0.20472 15937 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.889 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20 Å20 Å2
2---0.04 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 0 230 2032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221830
X-RAY DIFFRACTIONr_angle_refined_deg1.9231.9742478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4665233
X-RAY DIFFRACTIONr_chiral_restr0.1370.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021354
X-RAY DIFFRACTIONr_nbd_refined0.250.2940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2208
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2870.220
X-RAY DIFFRACTIONr_mcbond_it1.1911.51166
X-RAY DIFFRACTIONr_mcangle_it2.1221866
X-RAY DIFFRACTIONr_scbond_it3.0863664
X-RAY DIFFRACTIONr_scangle_it4.724.5612
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.295 49
Rwork0.223 1145

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