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- PDB-5x6u: Crystal structure of human heteropentameric complex -

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Basic information

Entry
Database: PDB / ID: 5x6u
TitleCrystal structure of human heteropentameric complex
Components(Ragulator complex protein ...) x 5
KeywordsPROTEIN BINDING / Ragulator complex / scaffold / roadblock / lysosome / mTOR signaling / cell growth
Function / homology
Function and homology information


regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / protein localization to lysosome / TORC1 signaling ...regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / protein localization to lysosome / TORC1 signaling / endosome organization / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / kinase activator activity / azurophil granule membrane / endosomal transport / regulation of cell size / Macroautophagy / lysosome organization / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / cellular response to nutrient levels / tertiary granule membrane / CDC42 GTPase cycle / RHOH GTPase cycle / ficolin-1-rich granule membrane / RHOG GTPase cycle / regulation of receptor recycling / positive regulation of TOR signaling / RAC2 GTPase cycle / RAC3 GTPase cycle / specific granule membrane / protein-membrane adaptor activity / positive regulation of TORC1 signaling / RAC1 GTPase cycle / viral genome replication / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / cholesterol homeostasis / regulation of cell growth / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / response to virus / MAP2K and MAPK activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein localization / positive regulation of protein localization to nucleus / late endosome / GTPase binding / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / molecular adaptor activity / lysosome / endosome membrane / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / Neutrophil degranulation / positive regulation of gene expression / protein-containing complex / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR2-like ...LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 / 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 LAMTOR5 / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR1 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYonehara, R. / Nada, S. / Nakai, T. / Nakai, M. / Kitamura, A. / Ogawa, A. / Nakatsumi, H. / Nakayama, K.I. / Li, S. / Standley, D.M. ...Yonehara, R. / Nada, S. / Nakai, T. / Nakai, M. / Kitamura, A. / Ogawa, A. / Nakatsumi, H. / Nakayama, K.I. / Li, S. / Standley, D.M. / Yamashita, E. / Nakagawa, A. / Okada, M.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for the assembly of the Ragulator-Rag GTPase complex.
Authors: Yonehara, R. / Nada, S. / Nakai, T. / Nakai, M. / Kitamura, A. / Ogawa, A. / Nakatsumi, H. / Nakayama, K.I. / Li, S. / Standley, D.M. / Yamashita, E. / Nakagawa, A. / Okada, M.
History
DepositionFeb 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ragulator complex protein LAMTOR3
B: Ragulator complex protein LAMTOR2
C: Ragulator complex protein LAMTOR5
D: Ragulator complex protein LAMTOR4
E: Ragulator complex protein LAMTOR1


Theoretical massNumber of molelcules
Total (without water)61,1685
Polymers61,1685
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint-92 kcal/mol
Surface area21930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.038, 133.038, 75.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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Ragulator complex protein ... , 5 types, 5 molecules ABCDE

#1: Protein Ragulator complex protein LAMTOR3 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 3 / MEK-binding partner 1 / Mp1 / ...Late endosomal/lysosomal adaptor and MAPK and MTOR activator 3 / MEK-binding partner 1 / Mp1 / Mitogen-activated protein kinase kinase 1-interacting protein 1 / Mitogen-activated protein kinase scaffold protein 1


Mass: 13868.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR3, MAP2K1IP1, MAPKSP1, PRO2783 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHA4
#2: Protein Ragulator complex protein LAMTOR2 / Endosomal adaptor protein p14 / Late endosomal/lysosomal Mp1-interacting protein / Late ...Endosomal adaptor protein p14 / Late endosomal/lysosomal Mp1-interacting protein / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 2 / Mitogen-activated protein-binding protein-interacting protein / MAPBP-interacting protein / Roadblock domain-containing protein 3


Mass: 13517.450 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR2, MAPBPIP, ROBLD3, HSPC003 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2Q5
#3: Protein Ragulator complex protein LAMTOR5 / Hepatitis B virus X-interacting protein / HBX-interacting protein / Late endosomal/lysosomal ...Hepatitis B virus X-interacting protein / HBX-interacting protein / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 5


Mass: 9622.900 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR5, HBXIP, XIP / Production host: Escherichia coli (E. coli) / References: UniProt: O43504
#4: Protein Ragulator complex protein LAMTOR4 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 4


Mass: 10753.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR4, C7orf59 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VGL1
#5: Protein Ragulator complex protein LAMTOR1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1 / Lipid raft adaptor protein p18 / ...Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1 / Lipid raft adaptor protein p18 / Protein associated with DRMs and endosomes / p27Kip1-releasing factor from RhoA / p27RF-Rho


Mass: 13405.055 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 42-161 / Mutation: S98D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR1, C11orf59, PDRO, PP7157 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IAA8

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Non-polymers , 1 types, 130 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Tris-HCl, 2-propanol, 1,6-hexandiol, 1,4-butandiol, 1-butanol, 1,3-propanediol, PEG 100, PEG 3350, 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAR scanner 300 mm plate / Detector: CCD / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→133.04 Å / Num. obs: 26934 / % possible obs: 100 % / Redundancy: 10.9 % / Biso Wilson estimate: 70.59 Å2 / Net I/σ(I): 23.9
Reflection shellResolution: 2.4→2.44 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VET, 3MSH

1vet

3msh


Resolution: 2.4→133.04 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.273 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1291 4.8 %RANDOM
Rwork0.186 ---
obs0.188 26910 99.8 %-
Displacement parametersBiso mean: 76.24 Å2
Baniso -1Baniso -2Baniso -3
1-4.0789 Å20 Å20 Å2
2--4.0789 Å20 Å2
3----8.1577 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.4→133.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 0 130 3929
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013854HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.185223HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1344SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes556HARMONIC5
X-RAY DIFFRACTIONt_it3854HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion20.02
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion514SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4485SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2649 142 5.19 %
Rwork0.2161 2596 -
all0.2186 2738 -
obs--98.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.83770.52580.0842.533-0.22061.30810.01710.5421-0.5426-0.15060.10660.0360.31660.1036-0.1237-0.0974-0.0032-0.03810.0566-0.073-0.05633.5388-37.4134-9.9337
23.9935-0.0573-0.42931.39390.07050.73180.04910.5118-0.2108-0.1692-0.0396-0.07890.11020.1312-0.0095-0.17530.01710.02190.2423-0.0232-0.113856.6925-28.1699-8.1802
33.1617-0.030.75212.22730.33832.04850.03290.35820.36190.0060.09570.0037-0.09180.3235-0.1286-0.1017-0.05480.07410.01730.1520.027635.2658-11.15540.6442
43.4951-0.14780.70693.3556-1.42682.9073-0.15730.30180.4258-0.07540.00370.3613-0.163-0.13360.1536-0.1727-0.04010.0274-0.04570.1520.115715.0581-8.7939-5.6929
52.343-0.10760.04422.16120.59440.99230.0290.320.098-0.00910.05960.2530.1154-0.0143-0.0886-0.06-0.0230.0186-0.0590.152-0.232727.6917-24.041-3.2524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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