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- PDB-6ehp: The crystal structure of the human LAMTOR complex -

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Basic information

Entry
Database: PDB / ID: 6ehp
TitleThe crystal structure of the human LAMTOR complex
Components(Ragulator complex protein ...) x 5
KeywordsSIGNALING PROTEIN / Scaffolding complex / Rag-GTPase / 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 / 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 / Resolution: 2.3 Å
AuthorsScheffzek, K. / Naschberger, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP 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 1.2Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 20, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.5Sep 18, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.pdbx_Rpim_I_all
Revision 1.6May 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7196
Polymers63,6835
Non-polymers351
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12350 Å2
ΔGint-100 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.896, 133.896, 75.984
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: 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 / Cell line (production host): Sf21 / 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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Non-polymers , 2 types, 72 molecules

#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% [w/v] PEG 3350, 0.1M Tris/HCl pH8.5, 0.2M MgCl2, 3% 2-Methyl-2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 256155 / % possible obs: 99.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 61.3 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.027 / Rsym value: 0.077 / Net I/σ(I): 16.6
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 1.44 / CC1/2: 0.57 / Rpim(I) all: 0.543 / Rsym value: 1.54 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU B: 15.091 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.191 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22758 1539 4.9 %RANDOM
Rwork0.19795 ---
obs0.19942 29683 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.958 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.73 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: 1 / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3738 0 1 71 3810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193799
X-RAY DIFFRACTIONr_bond_other_d0.0010.023608
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9725147
X-RAY DIFFRACTIONr_angle_other_deg0.8838368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6295486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71624.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42915662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8161523
X-RAY DIFFRACTIONr_chiral_restr0.0640.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024199
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
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_it2.6999.0251956
X-RAY DIFFRACTIONr_mcbond_other2.6999.0231955
X-RAY DIFFRACTIONr_mcangle_it4.52516.852435
X-RAY DIFFRACTIONr_mcangle_other4.52416.8542436
X-RAY DIFFRACTIONr_scbond_it3.17410.2391843
X-RAY DIFFRACTIONr_scbond_other3.17110.2331841
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.33618.6842711
X-RAY DIFFRACTIONr_long_range_B_refined7.8360.8823900
X-RAY DIFFRACTIONr_long_range_B_other7.80660.8213893
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 99 -
Rwork0.331 2129 -
obs--99.2 %
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)
11.49480.12840.16590.4315-0.36190.59020.1436-0.4277-0.4135-0.1243-0.0787-0.0172-0.0169-0.0077-0.06490.1718-0.0024-0.05460.2490.11870.13733.243729.595310.1581
22.14010.14440.53090.3928-0.04050.22310.2386-0.3544-0.0555-0.1001-0.1854-0.0430.0736-0.1677-0.05330.0728-0.00770.01420.41730.05450.061210.144638.87018.1126
31.55110.33960.53970.31940.06191.12810.1398-0.04880.14910.0181-0.04590.0995-0.039-0.0467-0.09390.15820.02550.01190.2052-0.06820.081231.387355.7192-0.79
40.51230.65360.07441.59650.55471.18830.056-0.0818-0.00010.0496-0.16640.0898-0.00260.17830.11040.1597-0.03530.01280.2589-0.05820.037451.750357.8785.3932
50.73760.46280.2050.35760.02130.98380.1134-0.12050.01710.0117-0.07440.00540.01390.1895-0.0390.1270.01050.01260.149-0.02240.012839.787743.55812.8229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 122
2X-RAY DIFFRACTION2B4 - 122
3X-RAY DIFFRACTION3C1 - 91
4X-RAY DIFFRACTION4D3 - 94
5X-RAY DIFFRACTION5E80 - 149

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