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- PDB-5x6v: Crystal structure of human heteroheptameric complex -

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Basic information

Entry
Database: PDB / ID: 5x6v
TitleCrystal structure of human heteroheptameric complex
Components
  • (Ragulator complex protein ...) x 5
  • (Ras-related GTP-binding protein ...) x 2
KeywordsPROTEIN BINDING / Ragulator Rag GTPase complex / scaffold / roadblock / lysosome / mTOR signaling / cell growth
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 cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / Gtr1-Gtr2 GTPase complex ...Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of PTEN gene transcription / MTOR signalling / Macroautophagy / Amino acids regulate mTORC1 / regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / Gtr1-Gtr2 GTPase complex / TP53 Regulates Metabolic Genes / FNIP-folliculin RagC/D GAP / mTORC1-mediated signalling / 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 / kinase activator activity / protein localization to membrane / endosomal transport / lysosome organization / azurophil granule membrane / TORC1 signaling / Macroautophagy / regulation of cell size / RHOJ GTPase cycle / RHOQ GTPase cycle / CDC42 GTPase cycle / tertiary granule membrane / RHOH GTPase cycle / mTORC1-mediated signalling / ficolin-1-rich granule membrane / RHOG GTPase cycle / regulation of receptor recycling / RAC2 GTPase cycle / RAC3 GTPase cycle / positive regulation of TOR signaling / enzyme-substrate adaptor activity / response to amino acid / specific granule membrane / protein-membrane adaptor activity / RAC1 GTPase cycle / cellular response to nutrient levels / positive regulation of TORC1 signaling / negative regulation of autophagy / guanyl-nucleotide exchange factor activity / cellular response to amino acid starvation / cholesterol homeostasis / viral genome replication / cellular response to starvation / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / positive regulation of interleukin-8 production / TP53 Regulates Metabolic Genes / regulation of cell growth / cellular response to amino acid stimulus / phosphoprotein binding / MAP2K and MAPK activation / positive regulation of protein localization to nucleus / response to virus / GDP binding / intracellular protein localization / late endosome / late endosome membrane / glucose homeostasis / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / molecular adaptor activity / positive regulation of canonical NF-kappaB signal transduction / lysosome / positive regulation of MAPK cascade / endosome membrane / intracellular signal transduction / membrane raft / protein heterodimerization activity / intracellular membrane-bounded organelle / lysosomal membrane / focal adhesion / GTPase activity / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / GTP binding / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Beta-Lactamase - #190 / 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 ...Beta-Lactamase - #190 / 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 / RagA/B / RagC/D / Gtr1/RagA G protein / Gtr1/RagA G protein conserved region / Ragulator complex protein LAMTOR2-like / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Ragulator complex protein LAMTOR5 / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR1 / Ras-related GTP-binding protein A / Ras-related GTP-binding protein C / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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

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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
F: Ras-related GTP-binding protein A
G: Ras-related GTP-binding protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6759
Polymers92,5937
Non-polymers822
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20820 Å2
ΔGint-167 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.099, 93.476, 125.452
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, 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: S98E
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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Ras-related GTP-binding protein ... , 2 types, 2 molecules FG

#6: Protein Ras-related GTP-binding protein A / RagA / Adenovirus E3 14.7 kDa-interacting protein 1 / FIP-1


Mass: 15661.119 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 183-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRAGA / Production host: Escherichia coli (E. coli) / References: UniProt: Q7L523
#7: Protein Ras-related GTP-binding protein C / RagC / GTPase-interacting protein 2 / TIB929


Mass: 15764.174 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 238-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rragc / Production host: Escherichia coli (E. coli) / References: UniProt: Q99K70

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Non-polymers , 3 types, 350 molecules

#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, ammonium acetate, PEG 4000

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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: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.02→125.45 Å / Num. obs: 57406 / % possible obs: 99.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 40.11 Å2 / Net I/σ(I): 13.6
Reflection shellResolution: 2.02→2.06 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X6U, 4ARZ

5x6u

4arz


Resolution: 2.02→20.36 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU R Cruickshank DPI: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.18 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.164
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2899 5.06 %RANDOM
Rwork0.193 ---
obs0.195 57304 99.2 %-
Displacement parametersBiso mean: 59.92 Å2
Baniso -1Baniso -2Baniso -3
1--11.8732 Å20 Å20 Å2
2--4.7533 Å20 Å2
3---7.1198 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: 1 / Resolution: 2.02→20.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6045 0 5 348 6398
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016161HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.128339HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2174SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes162HARMONIC2
X-RAY DIFFRACTIONt_gen_planes885HARMONIC5
X-RAY DIFFRACTIONt_it6161HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.13
X-RAY DIFFRACTIONt_other_torsion18.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion830SEMIHARMONIC5
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_contact7374SEMIHARMONIC4
LS refinement shellResolution: 2.02→2.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2621 230 5.61 %
Rwork0.2329 3869 -
all0.2346 4099 -
obs--96.74 %
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)
11.0912-0.53650.55572.92970.30843.19570.16680.0438-0.2213-0.5442-0.02640.36060.5317-0.2876-0.14040.304-0.0359-0.0959-0.2091-0.004-0.164413.1121-30.05686.776
20.6342-0.34020.23322.52910.09821.97840.0161-0.03330.0175-0.2371-0.00170.1448-0.1183-0.2214-0.01440.18160.0399-0.022-0.0930.0159-0.133713.0978-6.918415.0475
30.58760.62150.29163.63950.05013.24740.0312-0.0062-0.06980.10610.0464-0.19290.35760.2276-0.07760.06730.0625-0.0024-0.0871-0.0001-0.097326.6708-26.863631.1628
41.7951.01970.12345.6433-0.60812.76610.1382-0.0863-0.54420.2131-0.10690.04680.5442-0.1097-0.03140.28780.03230.0168-0.24670.0565-0.127222.2409-47.861734.8069
50.6972-0.60740.4011.3961-0.97352.03660.20520.0398-0.1379-0.522-0.05920.080.5442-0.0212-0.1460.2076-0.0056-0.0386-0.2524-0.016-0.172319.1721-24.839513.0646
61.9907-1.0151-0.6692.85381.22546.7295-0.0327-0.00080.1660.3490.0847-0.0658-0.5442-0.1735-0.0520.00010.06970.0197-0.12190.0146-0.09873.914422.41088.8756
70.3315-0.1841-0.34731.3465-0.83284.3465-0.0018-0.07820.0025-0.05-0.0038-0.04130.3230.18310.0056-0.01410.0054-0.0072-0.040.0092-0.0913.10269.4834-9.4184
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|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }

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