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- PDB-6s6a: Crystal structure of RagA-Q66L/RagC-T90N GTPase heterodimer complex -

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Basic information

Entry
Database: PDB / ID: 6s6a
TitleCrystal structure of RagA-Q66L/RagC-T90N GTPase heterodimer complex
Components(Ras-related GTP-binding protein ...) x 2
KeywordsSIGNALING PROTEIN / small GTPases / mTORC1 activator / roadblock domain / GTPase domain
Function / homology
Function and homology information


Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / regulation of TORC1 signaling / protein localization to lysosome / regulation of TOR signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / enzyme-substrate adaptor activity ...Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / regulation of TORC1 signaling / protein localization to lysosome / regulation of TOR signaling / MTOR signalling / Amino acids regulate mTORC1 / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / enzyme-substrate adaptor activity / Macroautophagy / small GTPase-mediated signal transduction / mTORC1-mediated signalling / cellular response to nutrient levels / positive regulation of TOR signaling / response to amino acid / protein-membrane adaptor activity / positive regulation of TORC1 signaling / tumor necrosis factor-mediated signaling pathway / cellular response to amino acid starvation / cellular response to starvation / negative regulation of autophagy / RNA splicing / Regulation of PTEN gene transcription / cellular response to amino acid stimulus / TP53 Regulates Metabolic Genes / phosphoprotein binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein localization / GDP binding / glucose homeostasis / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / lysosome / molecular adaptor activity / intracellular signal transduction / protein heterodimerization activity / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / GTP binding / magnesium ion binding / protein homodimerization activity / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Beta-Lactamase - #190 / RagA/B / Gtr1/RagA G protein / RagC/D / Gtr1/RagA G protein conserved region / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Beta-Lactamase - #190 / RagA/B / Gtr1/RagA G protein / RagC/D / Gtr1/RagA G protein conserved region / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
pentane-1,5-diol / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Ras-related GTP-binding protein A / Ras-related GTP-binding protein C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.63 Å
AuthorsAnandapadamanaban, M. / Masson, G.R. / Perisic, O. / Kaufman, J. / Williams, R.L.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184308 United Kingdom
Cancer Research UKC14801/A21211 United Kingdom
CitationJournal: Science / Year: 2019
Title: Architecture of human Rag GTPase heterodimers and their complex with mTORC1.
Authors: Madhanagopal Anandapadamanaban / Glenn R Masson / Olga Perisic / Alex Berndt / Jonathan Kaufman / Chris M Johnson / Balaji Santhanam / Kacper B Rogala / David M Sabatini / Roger L Williams /
Abstract: The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag ...The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag heterodimers is critical for their association with mTORC1. Our cryo-electron microscopy structure of RagA/RagC in complex with mTORC1 shows the details of RagA/RagC binding to the RAPTOR subunit of mTORC1 and explains why only the RagA/RagC nucleotide state binds mTORC1. Previous kinetic studies suggested that GTP binding to one Rag locks the heterodimer to prevent GTP binding to the other. Our crystal structures and dynamics of RagA/RagC show the mechanism for this locking and explain how oncogenic hotspot mutations disrupt this process. In contrast to allosteric activation by RHEB, Rag heterodimer binding does not change mTORC1 conformation and activates mTORC1 by targeting it to lysosomes.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related GTP-binding protein A
B: Ras-related GTP-binding protein A
C: Ras-related GTP-binding protein C
D: Ras-related GTP-binding protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,06413
Polymers161,7704
Non-polymers2,2949
Water1,31573
1
A: Ras-related GTP-binding protein A
C: Ras-related GTP-binding protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,9806
Polymers80,8852
Non-polymers1,0954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-38 kcal/mol
Surface area26390 Å2
MethodPISA
2
B: Ras-related GTP-binding protein A
D: Ras-related GTP-binding protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0847
Polymers80,8852
Non-polymers1,1995
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-40 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.103, 81.856, 244.076
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Ras-related GTP-binding protein ... , 2 types, 4 molecules ABCD

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


Mass: 36600.195 Da / Num. of mol.: 2 / Mutation: Q66L
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
#2: Protein Ras-related GTP-binding protein C / RagC / GTPase-interacting protein 2 / TIB929


Mass: 44284.832 Da / Num. of mol.: 2 / Mutation: T90N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RRAGC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HB90

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Non-polymers , 5 types, 82 molecules

#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H16N5O14P3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-9JE / pentane-1,5-diol / Pentane-1,5-diol


Mass: 104.148 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O2
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.36 Å3/Da / Density % sol: 47.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MOPSO, Bis-Tris pH 6.5, 40mM polyamines ( mixture of spermine tetrahydrochloride, spermidine trihydrochloride, 1,4. diaminobutane dihydrochloride, 0.1 M D/L-ornithine monohydrochloride) ...Details: 100mM MOPSO, Bis-Tris pH 6.5, 40mM polyamines ( mixture of spermine tetrahydrochloride, spermidine trihydrochloride, 1,4. diaminobutane dihydrochloride, 0.1 M D/L-ornithine monohydrochloride), 10% (w/v) PEG 8000. 20% (v/v) 1,5 - Pentanediol and 24 % (v/v) glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.63→46.62 Å / Num. obs: 43123 / % possible obs: 98 % / Redundancy: 6.787 % / Biso Wilson estimate: 83.533 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.07 / Χ2: 1.166 / Net I/σ(I): 17.91 / Num. measured all: 292679
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.63-2.796.8861.261.2446895697968100.5871.36297.6
2.79-2.986.8380.7112.3744904657765670.8180.7799.8
2.98-3.226.5150.3774.739869613761200.9360.4199.7
3.22-3.526.1560.16210.1831684570851470.9840.17890.2
3.52-3.937.1690.08421.4436618514351080.9970.09199.3
3.93-4.547.1810.05135.6132988460245940.9980.05599.8
4.54-5.557.0340.04141.9827445390939020.9990.04599.8
5.55-7.796.8960.03743.2321197308330740.9990.0499.7
7.79-46.626.1520.02854.0611079186118010.9990.0396.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→46.62 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.929 / SU B: 34.282 / SU ML: 0.327 / SU R Cruickshank DPI: 0.9608 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.961 / ESU R Free: 0.356
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 2105 4.9 %RANDOM
Rwork0.1954 ---
obs0.1992 41018 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 204.94 Å2 / Biso mean: 89.865 Å2 / Biso min: 52.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å2-0 Å2
2---2.32 Å20 Å2
3---3.15 Å2
Refinement stepCycle: final / Resolution: 2.63→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9314 0 143 73 9530
Biso mean--92.43 82.27 -
Num. residues----1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0139646
X-RAY DIFFRACTIONr_bond_other_d0.0050.0178977
X-RAY DIFFRACTIONr_angle_refined_deg1.851.64413018
X-RAY DIFFRACTIONr_angle_other_deg1.2831.58520794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.64351138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51622.308533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.657151766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1651564
X-RAY DIFFRACTIONr_chiral_restr0.080.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0210557
X-RAY DIFFRACTIONr_gen_planes_other0.0080.022095
LS refinement shellResolution: 2.63→2.696 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.396 160 -
Rwork0.367 2851 -
obs--95.04 %
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)
10.7682-1.73080.94584.0517-1.88282.4947-0.2115-0.16790.13490.18130.3709-0.4403-0.2982-0.2047-0.15930.8045-0.0230.02470.699-0.09470.601440.644245.7544-17.3197
20.86610.4744-0.32592.48090.00831.8016-0.0147-0.043-0.0332-0.3448-0.00870.1692-0.0681-0.24330.02340.7665-0.00770.01020.6865-0.0710.513639.137442.3101-19.3666
30.4769-0.09720.47511.47520.08540.7419-0.0038-0.16730.1131-0.14470.2351-0.2885-0.060.0755-0.23130.6803-0.06140.05980.7057-0.13470.690955.632744.3311-14.6301
40.663-0.6957-1.25292.36891.17442.49530.2472-0.08620.0343-0.0226-0.1042-0.0373-0.21960.1906-0.1430.7803-0.06720.02620.7636-0.20060.519640.480150.97683.0802
51.04920.9062-1.05871.106-0.94781.07780.01360.15230.11870.15150.04660.0031-0.0088-0.1424-0.06020.7263-0.0695-0.00770.788-0.15580.512630.153443.72568.9541
60.37560.90531.57493.10855.22478.89220.1491-0.2221-0.0472-0.1592-0.06060.0807-0.3204-0.2786-0.08850.706-0.02340.07670.72120.10.620425.481657.665312.3288
70.86270.87990.3731.75-0.47972.72670.2478-0.07930.47650.5101-0.31730.9964-0.0666-0.15360.06950.70530.02920.40580.6675-0.22720.723-3.581532.41338.8907
81.33950.7130.76581.40440.0171.57210.2970.11850.14490.2563-0.23140.280.18810.1675-0.06560.7058-0.01510.09310.6926-0.09350.60322.064919.319231.5719
90.98370.92440.31172.1412-0.70431.92810.18050.00080.18590.1027-0.18860.2274-0.0738-0.0520.00810.85440.0130.18960.6796-0.07470.486312.381842.190234.5895
103.7347-1.0131-3.72910.5591.44274.71350.1994-0.1243-0.09550.1607-0.18080.0743-0.26280.0536-0.01860.9789-0.09750.17270.7626-0.14840.323914.269641.50745.5096
111.14390.90211.27792.1111-0.50163.12710.04550.10450.03420.697-0.02580.2153-0.80210.2776-0.01971.0461-0.15870.03760.6281-0.14980.413219.311953.477243.6504
1212.03674.77584.0552.22430.54295.4560.00250.27170.20550.20430.05690.2205-0.4564-0.177-0.05940.72830.01240.08430.5727-0.01720.67098.511857.479232.2604
133.2539-3.2171-0.75866.82384.43713.92540.19860.1090.0803-0.2180.0423-0.3847-0.04510.0335-0.24090.33250.00370.04710.8118-0.26490.733947.83615.117411.8481
140.3587-0.7854-1.39541.76743.11555.53640.1244-0.09790.064-0.13620.2151-0.2385-0.32520.2285-0.33950.50810.0361-0.06360.756-0.16470.83646.770818.858718.4908
152.0087-0.7551-0.3871.1079-0.73362.6128-0.34550.4192-0.56760.23550.0618-0.4192-0.25430.03550.28370.34660.02940.05870.7022-0.43890.847543.27024.357.1761
161.9051-0.2614-0.80741.86121.1490.9792-0.03580.2349-0.35330.26010.1233-0.25720.0217-0.1022-0.08760.6770.06840.01410.8466-0.23230.608431.704313.738616.1571
171.460.97790.35412.3833-0.55530.5056-0.05270.09580.0090.1393-0.0167-0.07290.05830.06020.06940.7071-0.0308-0.00020.8617-0.14690.478232.114532.661217.3662
184.4832-1.891.91291.79280.211.98270.0907-0.1866-0.02230.13280.00690.0915-0.0063-0.0232-0.09760.7244-0.03040.07220.805-0.07260.522622.917831.796627.8503
190.73510.88751.58743.07641.24493.68370.007-0.1572-0.1989-0.08520.3164-0.6031-0.0489-0.393-0.32340.7620.04830.26680.9164-0.13440.38120.092427.219770.7558
200.2823-1.49190.43528.4752-2.34420.6888-0.0240.09450.04990.6439-0.0379-0.0550.01980.06550.06191.09930.13040.0970.7343-0.12710.625326.489219.218281.6107
211.25140.45440.19651.7717-1.14760.9877-0.4685-0.3675-0.1645-0.20290.2415-0.33150.1084-0.36430.2270.95450.00790.28761.0560.12950.16818.739825.290981.2114
220.3299-0.894-0.65336.87733.82182.4550.1059-0.458-0.1118-0.6202-0.81440.7873-0.373-0.21110.70850.98720.0609-0.08211.7219-0.27710.41217.710846.900875.7435
230.5487-0.25420.34522.1422-2.19122.26720.1180.0088-0.11090.8607-0.3579-0.2111-0.84010.27730.23991.382-0.31130.08490.8529-0.24370.19417.883947.607260.6654
240.55131.462-0.38525.6076-1.24790.30890.3039-0.08130.17290.7102-0.365-0.5954-0.27520.05990.06110.8904-0.1738-0.08790.4864-0.14830.932623.593759.510265.3713
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 24
2X-RAY DIFFRACTION2A25 - 85
3X-RAY DIFFRACTION3A86 - 159
4X-RAY DIFFRACTION4A160 - 235
5X-RAY DIFFRACTION5A236 - 277
6X-RAY DIFFRACTION6A278 - 301
7X-RAY DIFFRACTION7B5 - 60
8X-RAY DIFFRACTION8B61 - 162
9X-RAY DIFFRACTION9B163 - 216
10X-RAY DIFFRACTION10B217 - 250
11X-RAY DIFFRACTION11B251 - 290
12X-RAY DIFFRACTION12B291 - 303
13X-RAY DIFFRACTION13C60 - 81
14X-RAY DIFFRACTION14C82 - 115
15X-RAY DIFFRACTION15C131 - 199
16X-RAY DIFFRACTION16C200 - 263
17X-RAY DIFFRACTION17C264 - 341
18X-RAY DIFFRACTION18C342 - 369
19X-RAY DIFFRACTION19D60 - 114
20X-RAY DIFFRACTION20D115 - 134
21X-RAY DIFFRACTION21D135 - 225
22X-RAY DIFFRACTION22D226 - 253
23X-RAY DIFFRACTION23D254 - 342
24X-RAY DIFFRACTION24D343 - 367

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