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- PDB-1vet: Crystal Structure of p14/MP1 at 1.9 A resolution -

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Basic information

Entry
Database: PDB / ID: 1vet
TitleCrystal Structure of p14/MP1 at 1.9 A resolution
Components
  • Late endosomal/lysosomal Mp1 interacting protein
  • Mitogen-activated protein kinase kinase 1 interacting protein 1
KeywordsSIGNALING PROTEIN/PROTEIN BINDING / profilin / scaffold / adaptor / SIGNALING PROTEIN-PROTEIN BINDING COMPLEX
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 / fibroblast migration / kinase activator activity / positive regulation of TOR signaling / positive regulation of TORC1 signaling / Neutrophil degranulation / guanyl-nucleotide exchange factor activity / regulation of cell growth / cellular response to amino acid stimulus / protein localization / late endosome / late endosome membrane / positive regulation of MAPK cascade / molecular adaptor activity / lysosomal 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 LAMTOR3 / Ragulator complex protein LAMTOR2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsKurzbauer, R. / Teis, D. / Maurer-Stroh, S. / Eisenhaber, F. / Hekman, M. / Bourenkov, G.P. / Bartunik, H.D. / Huber, L.A. / Clausen, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of the p14/MP1 scaffolding complex: How a twin couple attaches mitogen- activated protein kinase signaling to late endosomes
Authors: Kurzbauer, R. / Teis, D. / De Araujo, M.E. / Maurer-Stroh, S. / Eisenhaber, F. / Bourenkov, G.P. / Bartunik, H.D. / Hekman, M. / Rapp, U.R. / Huber, L.A. / Clausen, T.
History
DepositionApr 5, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Mitogen-activated protein kinase kinase 1 interacting protein 1
B: Late endosomal/lysosomal Mp1 interacting protein


Theoretical massNumber of molelcules
Total (without water)27,0582
Polymers27,0582
Non-polymers00
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-19 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.078, 63.289, 72.383
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 / Mp1 / MEK binding partner 1


Mass: 13567.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: O88653
#2: Protein Late endosomal/lysosomal Mp1 interacting protein / p14


Mass: 13490.425 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9JHS3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 1.6 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG4000, Tris, Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9791 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 18, 2003
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 58360 / Num. obs: 18402 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.042 / Net I/σ(I): 23
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 1.59 / Rsym value: 0.419 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 912 -random
Rwork0.213 ---
all0.215 58360 --
obs0.215 18402 99.5 %-
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 0 258 2064
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6

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