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- PDB-6ehr: The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex -

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Basic information

Entry
Database: PDB / ID: 6ehr
TitleThe crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex
Components
  • (Ragulator complex protein ...) x 5
  • (Ras-related GTP-binding protein ...) x 2
KeywordsSIGNALING PROTEIN / Scaffolding complex / Rag-GTPases / mTOR / Ragulator / mTORC1
Function / homology
Function and homology information


regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / regulation of TORC1 signaling / protein localization to lysosome ...regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / regulation of TORC1 signaling / protein localization to lysosome / regulation of TOR signaling / MTOR signalling / fibroblast migration / Amino acids regulate mTORC1 / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / endosome organization / TORC1 signaling / kinase activator activity / protein localization to membrane / endosomal transport / azurophil granule membrane / lysosome organization / small GTPase-mediated signal transduction / 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 / positive regulation of TOR signaling / RAC3 GTPase cycle / enzyme-substrate adaptor activity / response to amino acid / cellular response to nutrient levels / specific granule membrane / protein-membrane adaptor activity / RAC1 GTPase cycle / positive regulation of TORC1 signaling / negative regulation of autophagy / cellular response to amino acid starvation / RNA splicing / guanyl-nucleotide exchange factor activity / viral genome replication / cholesterol homeostasis / 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 / cellular response to amino acid stimulus / phosphoprotein binding / regulation of cell growth / MAP2K and MAPK activation / positive regulation of protein localization to nucleus / response to virus / GDP binding / late endosome membrane / intracellular protein localization / late endosome / glucose homeostasis / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / molecular adaptor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / endosome membrane / intracellular signal transduction / membrane raft / protein heterodimerization activity / lysosomal membrane / focal adhesion / intracellular membrane-bounded organelle / GTPase activity / apoptotic process / DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / GTP binding / magnesium ion binding / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Beta-Lactamase - #190 / 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 / RagA/B / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 ...Beta-Lactamase - #190 / 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 / RagA/B / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / 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
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.898 Å
AuthorsScheffzek, K. / Naschberger, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
P 26682 Austria
CitationJournal: Science / Year: 2017
Title: Crystal structure of the human lysosomal mTORC1 scaffold complex and its impact on signaling.
Authors: de Araujo, M.E.G. / Naschberger, A. / Furnrohr, B.G. / Stasyk, T. / Dunzendorfer-Matt, T. / Lechner, S. / Welti, S. / Kremser, L. / Shivalingaiah, G. / Offterdinger, M. / Lindner, H.H. / ...Authors: de Araujo, M.E.G. / Naschberger, A. / Furnrohr, B.G. / Stasyk, T. / Dunzendorfer-Matt, T. / Lechner, S. / Welti, S. / Kremser, L. / Shivalingaiah, G. / Offterdinger, M. / Lindner, H.H. / Huber, L.A. / Scheffzek, K.
History
DepositionSep 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4May 8, 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

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


Theoretical massNumber of molelcules
Total (without water)97,1437
Polymers97,1437
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20030 Å2
ΔGint-149 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.090, 92.448, 127.200
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: 13903.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR3, MAP2K1IP1, MAPKSP1, PRO2783 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / 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: 13574.501 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: Spodoptera frugiperda (fall armyworm) / 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 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / 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 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / 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: 15828.839 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR1, C11orf59, PDRO, PP7157 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / 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: 15287.651 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRAGA / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q7L523
#7: Protein Ras-related GTP-binding protein C / RagC / GTPase-interacting protein 2 / TIB929


Mass: 18171.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRAGC / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9HB90

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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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% [w/v] PEG 4000, 0.1M tri-sodium-citrate pH5.5, 5% [v/v] isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.898→46.224 Å / Num. obs: 21957 / % possible obs: 93.8 % / Redundancy: 4.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.078 / Rsym value: 0.176 / Net I/σ(I): 8.2
Reflection shellResolution: 2.9→3.07 Å / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.75 / Rpim(I) all: 0.478 / Rsym value: 1.049 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.898→46.224 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.08
RfactorNum. reflection% reflection
Rfree0.2626 1108 5.05 %
Rwork0.2165 --
obs0.2188 21957 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.898→46.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 0 0 6126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026216
X-RAY DIFFRACTIONf_angle_d0.4198408
X-RAY DIFFRACTIONf_dihedral_angle_d10.0493791
X-RAY DIFFRACTIONf_chiral_restr0.041996
X-RAY DIFFRACTIONf_plane_restr0.0031080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8983-3.03020.3991310.3392512X-RAY DIFFRACTION92
3.0302-3.18990.35731550.30622590X-RAY DIFFRACTION95
3.1899-3.38970.34821340.27982603X-RAY DIFFRACTION95
3.3897-3.65130.31671280.26182633X-RAY DIFFRACTION95
3.6513-4.01850.28441330.22632629X-RAY DIFFRACTION95
4.0185-4.59960.21031600.16952601X-RAY DIFFRACTION94
4.5996-5.79320.22911260.17582622X-RAY DIFFRACTION93
5.7932-46.22990.20991410.18192659X-RAY DIFFRACTION91
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)
11.0319-1.38490.75922.8165-2.27982.950.31760.1798-0.1584-0.8312-0.10540.34570.7022-0.0593-0.06720.4605-0.1084-0.16830.4747-0.09570.407426.2622115.09313.0705
21.5347-0.080.90352.860.57643.49980.89360.5413-0.4348-1.89140.0531.36921.2404-0.43140.0821.31890.0108-0.84980.5906-0.07310.690221.275109.2264-1.3301
33.7575-1.053-0.99287.01070.32138.7139-0.0358-0.1097-0.12790.82130.34050.53110.7456-0.0227-0.24990.49510.0484-0.0280.43860.09830.399533.000692.361626.6582
42.8504-0.55450.21286.00960.92624.59290.0669-0.2462-0.2665-0.04770.08780.1533-0.0713-0.0662-0.14080.23190.0433-0.07010.47820.04730.289333.4532113.186623.819
55.2785-1.24341.42946.1123-0.17336.44330.1893-0.1936-0.111-0.2401-0.0080.3986-0.3024-0.5591-0.14910.61130.0887-0.09930.47170.03120.30118.3404132.07617.4379
63.2095-0.3981-0.54216.3795-0.52065.72130.0059-0.14430.17520.36210.1712-0.4037-0.28040.5284-0.21180.30590.0098-0.00320.4543-0.06980.241416.4278148.8227-17.2074
75.4509-0.4649-0.79415.9291.6477.3825-0.0816-0.88060.63770.84670.34720.2281-1.1716-0.1842-0.20070.91230.13650.04240.637-0.10080.45275.4049159.50121.4701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E'
2X-RAY DIFFRACTION2chain 'A'
3X-RAY DIFFRACTION3chain 'D'
4X-RAY DIFFRACTION4chain 'C'
5X-RAY DIFFRACTION5chain 'B'
6X-RAY DIFFRACTION6chain 'G'
7X-RAY DIFFRACTION7chain 'F'

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