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- PDB-5y39: Crystal structure of Ragulator complex (p18 76-145) -

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Basic information

Entry
Database: PDB / ID: 5y39
TitleCrystal structure of Ragulator complex (p18 76-145)
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 / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / protein localization to lysosome / MTOR signalling / fibroblast migration ...regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / protein localization to lysosome / MTOR signalling / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / endosome organization / Amino acids regulate mTORC1 / TORC1 signaling / kinase activator activity / protein localization to membrane / endosomal transport / lysosome organization / azurophil granule membrane / Macroautophagy / regulation of cell size / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / CDC42 GTPase cycle / tertiary granule membrane / RHOH GTPase cycle / ficolin-1-rich granule membrane / RHOG GTPase cycle / regulation of receptor recycling / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of TOR signaling / cellular response to nutrient levels / specific granule membrane / protein-membrane adaptor activity / RAC1 GTPase cycle / positive regulation of TORC1 signaling / viral genome replication / cholesterol homeostasis / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / regulation of cell growth / MAP2K and MAPK activation / positive regulation of protein localization to nucleus / response to virus / late endosome membrane / intracellular protein localization / late endosome / GTPase binding / molecular adaptor activity / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / endosome membrane / membrane raft / lysosomal membrane / focal adhesion / intracellular membrane-bounded organelle / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / protein-containing complex / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
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 / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Ragulator complex protein LAMTOR2-like ...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 / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / 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 / Resolution: 2.65 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 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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: 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


Theoretical massNumber of molelcules
Total (without water)111,19710
Polymers111,19710
Non-polymers00
Water1,04558
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


Theoretical massNumber of molelcules
Total (without water)55,5985
Polymers55,5985
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11720 Å2
ΔGint-84 kcal/mol
Surface area21760 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


Theoretical massNumber of molelcules
Total (without water)55,5985
Polymers55,5985
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-66 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.659, 117.854, 157.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 7966.005 Da / Num. of mol.: 2 / Fragment: coiled coil, UNP residues 76-145
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: 13517.450 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: 9535.823 Da / Num. of mol.: 2 / Fragment: Roadblock domain, UNP residues 1-90
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 , 1 types, 58 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
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: 0.9792 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→50.01 Å / Num. obs: 29802 / % possible obs: 98.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.023 / Rrim(I) all: 0.052 / Χ2: 0.915 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.744.60.50929710.8010.2620.5760.94798.6
2.74-2.854.60.34129740.8910.1760.3860.88799.3
2.85-2.984.60.23229820.9410.1190.2620.88499
2.98-3.144.70.1529580.9770.0760.1690.85898.9
3.14-3.344.60.08729720.9910.0440.0980.84198.7
3.34-3.64.60.05629590.9950.0280.0630.87398.4
3.6-3.964.60.04329840.9910.0210.0480.83698.2
3.96-4.534.60.03229920.9980.0150.0350.83898
4.53-5.714.50.03429820.9980.0170.0381.33397.5
5.71-504.40.02230280.9970.0110.0250.86794.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
PHENIXphasing
RefinementResolution: 2.65→50.01 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.885 / SU B: 33.87 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.383 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 1365 5.1 %RANDOM
Rwork0.21551 ---
obs0.21799 25354 88.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.279 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2---4.26 Å2-0 Å2
3---3.18 Å2
Refinement stepCycle: 1 / Resolution: 2.65→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6750 0 0 58 6808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196836
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.9719265
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64424.945273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.255151143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.51533
X-RAY DIFFRACTIONr_chiral_restr0.0660.21123
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215016
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_it1.9914.1033594
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4466.0984461
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2134.3233241
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.20691.01910066
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.07736835
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded52.54356749
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 61 -
Rwork0.284 1126 -
obs--53.3 %
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)
10.34160.34370.11580.78060.13660.30710.0259-0.0294-0.02990.0756-0.03340.04160.0545-0.03080.00750.14870.02820.00690.2640.03450.0747-17.697-26.0235-5.9171
20.02570.0627-0.08010.2682-0.36320.5111-0.0106-0.0072-0.04540.0006-0.0046-0.0236-0.05050.03690.01520.17430.00350.00730.2841-0.0060.15519.3641-15.8763-16.5813
30.2340.09640.05690.63830.11650.66840.0051-0.0032-0.03780.0757-0.04210.0006-0.0492-0.0650.0370.17680.00390.00660.29020.00110.1247-6.41-15.54350.6644
40.4322-0.0872-0.12480.3607-0.03460.4508-0.01990.0076-0.0185-0.0870.0236-0.01030.0398-0.0183-0.00380.1741-0.00940.00620.2921-0.01110.1477-25.075-44.0338-8.593
50.89780.27320.29690.2335-0.25030.8927-0.01730.0325-0.0124-0.0537-0.0181-0.03850.06660.04210.03540.19140.01450.0180.2796-0.00580.1448-13.299-32.0563-21.2133
66.8278-1.8407-1.27250.52510.33930.25410.0885-0.31410.11790.0194-0.0156-0.0269-0.01460.0883-0.07290.1937-0.08820.09270.3593-0.01920.2165-42.2666-22.032-21.4745
70.6021-0.2744-0.17840.56110.13560.0810.0109-0.062-0.06720.0039-0.02170.0374-0.06710.02950.01080.2065-0.00010.01620.31790.00910.0938-16.8514-2.5504-39.5333
80.8518-0.3734-0.32261.55690.52050.3528-0.0403-0.0525-0.0224-0.10550.02460.222-0.17540.06890.01570.218-0.00330.03270.3302-0.01360.0871-33.384710.736-30.6216
92.9805-2.3944-0.28682.0767-0.20523.0505-0.28820.2383-0.08570.3679-0.33920.14330.10190.09250.62730.2797-0.16250.29540.4295-0.18520.4306-50.4314-10.0743-10.7071
100.36580.6998-0.43251.8516-0.37130.93850.04330.03920.08790.16050.04480.1540.0242-0.004-0.08810.14280.02120.05510.32350.01230.153-37.5878-15.591-26.7027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A79 - 145
2X-RAY DIFFRACTION2B5 - 120
3X-RAY DIFFRACTION3C3 - 123
4X-RAY DIFFRACTION4D0 - 98
5X-RAY DIFFRACTION5E83 - 172
6X-RAY DIFFRACTION6F114 - 145
7X-RAY DIFFRACTION7G6 - 122
8X-RAY DIFFRACTION8H3 - 119
9X-RAY DIFFRACTION9I4 - 88
10X-RAY DIFFRACTION10J83 - 171

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