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- PDB-5y3a: Crystal structure of Ragulator complex (p18 49-161) -

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Basic information

Entry
Database: PDB / ID: 5y3a
TitleCrystal structure of Ragulator complex (p18 49-161)
Components(Ragulator complex protein ...) x 5
KeywordsSIGNALING PROTEIN / Ragulator complex / LAMTOR
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 / kinase activator activity / protein localization to membrane / azurophil granule membrane / endosomal transport / Macroautophagy / regulation of cell size / lysosome organization / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / cellular response to nutrient levels / tertiary granule membrane / RHOH GTPase cycle / CDC42 GTPase cycle / ficolin-1-rich granule membrane / RHOG GTPase cycle / positive regulation of TOR signaling / regulation of receptor recycling / 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 / cholesterol homeostasis / regulation of cell growth / positive regulation of interleukin-8 production / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / 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 / lysosome / molecular adaptor activity / endosome membrane / membrane raft / lysosomal membrane / focal adhesion / intracellular membrane-bounded organelle / 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: 2.9 Å
AuthorsZhang, T. / Ding, J.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1.
Authors: Zhang, T. / Wang, R. / Wang, Z. / Wang, X. / Wang, F. / Ding, J.
History
DepositionJul 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ragulator complex protein LAMTOR1
B: Ragulator complex protein LAMTOR2
C: Ragulator complex protein LAMTOR3
D: Ragulator complex protein LAMTOR4
E: Ragulator complex protein LAMTOR5
F: Ragulator complex protein LAMTOR1
G: Ragulator complex protein LAMTOR2
H: Ragulator complex protein LAMTOR3
I: Ragulator complex protein LAMTOR4
J: Ragulator complex protein LAMTOR5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,71518
Polymers120,94610
Non-polymers7698
Water21612
1
A: Ragulator complex protein LAMTOR1
B: Ragulator complex protein LAMTOR2
C: Ragulator complex protein LAMTOR3
D: Ragulator complex protein LAMTOR4
E: Ragulator complex protein LAMTOR5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,95310
Polymers60,4735
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13420 Å2
ΔGint-161 kcal/mol
Surface area21820 Å2
MethodPISA
2
F: Ragulator complex protein LAMTOR1
G: Ragulator complex protein LAMTOR2
H: Ragulator complex protein LAMTOR3
I: Ragulator complex protein LAMTOR4
J: Ragulator complex protein LAMTOR5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7618
Polymers60,4735
Non-polymers2883
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12840 Å2
ΔGint-141 kcal/mol
Surface area21600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.341, 89.626, 232.173
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Ragulator complex protein ... , 5 types, 10 molecules AFBGCHDIEJ

#1: 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: 12348.945 Da / Num. of mol.: 2 / Fragment: coiled coil, UNP residues 50-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR1, C11orf59, PDRO, PP7157 / Plasmid: pET28SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q6IAA8
#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: 13719.723 Da / Num. of mol.: 2 / Fragment: Roadblock domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR2, MAPBPIP, ROBLD3, HSPC003 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9Y2Q5
#3: 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: 13637.678 Da / Num. of mol.: 2 / Fragment: Roadblock domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR3, MAP2K1IP1, MAPKSP1, PRO2783 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q9UHA4
#4: Protein Ragulator complex protein LAMTOR4 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 4


Mass: 10941.483 Da / Num. of mol.: 2 / Fragment: Roadblock domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR4, C7orf59 / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q0VGL1
#5: 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: 9825.174 Da / Num. of mol.: 2 / Fragment: Roadblock domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR5, HBXIP, XIP / Plasmid: pETDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: O43504

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Non-polymers , 2 types, 20 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris (pH 5.5), and 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50.01 Å / Num. obs: 30426 / % possible obs: 90 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.056 / Rrim(I) all: 0.12 / Χ2: 2.205 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-34.20.540.8410.2910.6161.50588.4
3-3.124.20.3790.9110.2040.4321.55987.9
3.12-3.274.20.2840.9480.1520.3231.64286.8
3.27-3.444.20.20.9670.1070.2281.99686.2
3.44-3.654.10.1590.980.0850.1812.32687.1
3.65-3.9440.1470.9830.0790.1682.82287.3
3.94-4.3340.0960.9940.0510.1092.7790.5
4.33-4.963.90.0750.9960.0380.0842.96791.9
4.96-6.2440.0810.9920.0430.0922.33595.7
6.24-50.014.40.0420.9980.0220.0482.1897.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MS6, 1VET

3ms6

1vet


Resolution: 2.9→50.01 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.828 / SU B: 48.309 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28849 1457 5.1 %RANDOM
Rwork0.24563 ---
obs0.24788 27052 84.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.125 Å2
Baniso -1Baniso -2Baniso -3
1--5.1 Å20 Å2-0 Å2
2--0.72 Å20 Å2
3---4.38 Å2
Refinement stepCycle: 1 / Resolution: 2.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7411 0 40 12 7463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197549
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.97610234
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5575962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39524.713314
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.011151296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3431543
X-RAY DIFFRACTIONr_chiral_restr0.0790.21224
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215542
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_it1.1761.9733884
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3072.944834
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5513.0073665
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined2.11810639
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.73237515
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded23.59657408
LS refinement shellResolution: 2.902→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 48 -
Rwork0.311 872 -
obs--37.6 %
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)
10.01670.0337-0.040.1971-0.13390.30890.0435-0.0233-0.01150.0689-0.01060.0056-0.00980.0369-0.0330.36350.00040.01190.2862-0.01080.063217.4839-9.7756154.5265
20.23720.19220.03280.49220.22710.8942-0.0380.0161-0.0243-0.04850.05190.0284-0.02430.0303-0.01390.37560.00390.00290.31310.01030.019623.0416-7.7664126.4212
30.084-0.04950.1630.7963-0.04160.37320.01840.0250.03010.0017-0.04550.00840.00080.00570.02710.3765-0.0088-0.01260.3125-0.00840.045124.02361.7653147.9436
40.4178-0.12090.230.6038-0.03050.2737-0.0213-0.0370.04820.0238-0.00680.01130.06090.02570.02820.3805-0.0054-0.01250.28850.00780.031416.9931-24.6133168.9046
50.56890.2163-0.09280.22170.00590.5453-0.01020.0411-0.0344-0.0460.0256-0.055-0.0070.0573-0.01530.3808-0.0004-0.00650.27510.0070.034112.9657-23.8636147.2471
60.09340.1536-0.02550.2733-0.07780.15060.01270.01560.01880.00930.0040.02270.02070.0088-0.01670.3590.0171-0.02290.28090.0010.070952.9418-32.6584156.799
70.18560.230.30731.0365-0.12410.8507-0.028-0.01040.0044-0.04010.0132-0.0065-0.0135-0.02090.01480.37290.0047-0.00130.33040.00380.000444.6567-36.977128.4719
80.2093-0.02180.23161.31420.12331.34510.00930.04810.02080.01570.0026-0.04290.088-0.0706-0.01190.3452-0.01120.00110.30140.01560.026144.9003-46.1548150.5132
90.04040.1085-0.05420.6576-0.10810.37290.0225-0.0448-0.00040.0636-0.00460.0771-0.05090.0117-0.01790.3856-0.00090.00430.3-0.02060.058853.3649-19.6328170.2839
100.66730.3942-0.14590.40270.20480.5634-0.01640.03510.08470.00540.02340.0674-0.0536-0.0494-0.0070.38820.0094-0.00540.27770.01770.045655.3015-20.3575148.7339
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A76 - 149
2X-RAY DIFFRACTION2B6 - 120
3X-RAY DIFFRACTION3C3 - 122
4X-RAY DIFFRACTION4D0 - 93
5X-RAY DIFFRACTION5E83 - 172
6X-RAY DIFFRACTION6F80 - 149
7X-RAY DIFFRACTION7G6 - 120
8X-RAY DIFFRACTION8H3 - 122
9X-RAY DIFFRACTION9I1 - 93
10X-RAY DIFFRACTION10J83 - 172

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