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- PDB-3cpt: MP1-p14 Scaffolding complex -

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Basic information

Entry
Database: PDB / ID: 3cpt
TitleMP1-p14 Scaffolding complex
Components
  • Mitogen-activated protein kinase kinase 1-interacting protein 1
  • Mitogen-activated protein-binding protein-interacting protein
KeywordsPROTEIN BINDING / scaffold / complex / alpha/beta / Endosome / Membrane / Lysosome
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 / mTORC1-mediated signalling / FNIP-folliculin RagC/D GAP / 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 / mTORC1-mediated signalling / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / MAP2K and MAPK activation / TORC1 signaling / fibroblast migration / Amino acids regulate mTORC1 / MTOR signalling / 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 / late endosome / protein localization / 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 / Resolution: 1.9 Å
AuthorsSchrag, J.D. / Cygler, M. / Munger, C. / Magloire, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Molecular dynamics-solvated interaction energy studies of protein-protein interactions: the MP1-p14 scaffolding complex.
Authors: Cui, Q. / Sulea, T. / Schrag, J.D. / Munger, C. / Hung, M.N. / Naim, M. / Cygler, M. / Purisima, E.O.
History
DepositionApr 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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: Mitogen-activated protein-binding protein-interacting protein


Theoretical massNumber of molelcules
Total (without water)30,1402
Polymers30,1402
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-20.3 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.950, 63.140, 75.780
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


Mass: 15913.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K1IP1 / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UHA4
#2: Protein Mitogen-activated protein-binding protein-interacting protein / Late endosomal/lysosomal Mp1-interacting protein / p14


Mass: 14227.210 Da / Num. of mol.: 1 / Mutation: Y56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mapbpip / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JHS3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1.78 Å3/Da / Density % sol: 31.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10%(w/v) PEG 3350, 0.1 M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.9→48.51 Å / Num. obs: 17610 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.056 / Χ2: 0.97 / Net I/σ(I): 13.4 / Scaling rejects: 665
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.9-1.975.080.2884.5883117251.36100
1.97-2.055.10.2135.8892117401.24100
2.05-2.145.090.1666.7880117171.1100
2.14-2.255.080.1337.6886617301.01100
2.25-2.395.060.1049.7888517350.98100
2.39-2.585.070.08112.7897917540.93100
2.58-2.845.020.06315892017600.78100
2.84-3.255.010.05118.8883717530.7799.9
3.25-4.094.850.04224.2877417960.76100
4.09-26.334.640.03629.3882919000.77100

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Processing

Software
NameVersionClassificationNB
d*TREK9.5Ldata scaling
REFMAC5.2.0003refinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 1.9→48.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.896 / SU B: 3.917 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27718 856 4.9 %RANDOM
Rwork0.20107 ---
obs0.20454 16707 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.955 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 0 154 1963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221837
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9752491
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5595237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29424.93779
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36115321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1291510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211363
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8391.51171
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60721877
X-RAY DIFFRACTIONr_scbond_it2.5583666
X-RAY DIFFRACTIONr_scangle_it4.2834.5612
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 65 -
Rwork0.227 1202 -
all-1267 -
obs--100 %

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