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- PDB-1veu: Crystal structure of the p14/MP1 complex at 2.15 A resolution -

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Basic information

Entry
Database: PDB / ID: 1veu
TitleCrystal structure of the p14/MP1 complex at 2.15 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 / Regulation of PTEN gene transcription / MTOR signalling / Macroautophagy / Amino acids regulate mTORC1 / regulation of cell-substrate junction organization / TP53 Regulates Metabolic Genes / FNIP-folliculin RagC/D GAP / mTORC1-mediated signalling / Ragulator complex ...Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of PTEN gene transcription / MTOR signalling / Macroautophagy / Amino acids regulate mTORC1 / regulation of cell-substrate junction organization / TP53 Regulates Metabolic Genes / FNIP-folliculin RagC/D GAP / mTORC1-mediated signalling / Ragulator complex / protein localization to cell junction / MAP2K and MAPK activation / fibroblast migration / TORC1 signaling / kinase activator activity / positive regulation of TOR signaling / Neutrophil degranulation / positive regulation of TORC1 signaling / guanyl-nucleotide exchange factor activity / cellular response to amino acid stimulus / regulation of cell growth / late endosome membrane / intracellular protein localization / late endosome / molecular adaptor activity / positive regulation of MAPK cascade / 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 / MOLECULAR REPLACEMENT / Resolution: 2.15 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 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)27,3972
Polymers27,3972
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-20 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.416, 62.106, 74.503
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: 13614.563 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: 13781.953 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


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.6 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG4000, Tris, Magnesium Chloride, Sodium/Potassium Phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 16, 2004
RadiationMonochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 33808 / Num. obs: 11596 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.15→2.23 Å / % possible all: 92.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vet

1vet


Resolution: 2.15→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 575 random
Rwork0.201 --
all0.204 33808 -
obs0.204 11596 -
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 0 249 2505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.25

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