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- PDB-8zla: Crystal Structure of monomeric Rag-like small GTPase from Asgard ... -

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Basic information

Entry
Database: PDB / ID: 8zla
TitleCrystal Structure of monomeric Rag-like small GTPase from Asgard Lokiarchaeota (LokiRagM) in complex with GDP
ComponentsGTP-binding protein
KeywordsHYDROLASE / RAG / Small GTPase / Asgard / Monomer / GDP Binding protein
Function / homology
Function and homology information


Gtr1-Gtr2 GTPase complex / positive regulation of TORC1 signaling / cellular response to starvation / lysosome / GTPase activity / GTP binding
Similarity search - Function
Gtr1/RagA G protein / Gtr1/RagA G protein conserved region / Small GTPase Arf domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTP-binding protein
Similarity search - Component
Biological speciesCandidatus Prometheoarchaeum syntrophicum (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAlsheikh, F.B. / Robinson, R.C.
Funding support Thailand, United Kingdom, United States, 3items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
Moore Foundation grantGBMF9743 United Kingdom
Simons FoundationGBMF9743 United States
CitationJournal: To Be Published
Title: Crystal Structure of monomeric Rag-like small GTPase from Asgard Lokiarchaeota (LokiRagM) in complex with GDP
Authors: Alsheikh, F.B. / Robinson, R.C.
History
DepositionMay 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9453
Polymers45,4771
Non-polymers4682
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-17 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.040, 85.040, 153.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

21A-701-

HOH

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Components

#1: Protein GTP-binding protein


Mass: 45477.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Prometheoarchaeum syntrophicum (archaea)
Gene: DSAG12_01154 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B9D832
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.05 Å3/Da / Density % sol: 59.66 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: PEG 8000, ethylene glycol, magnesium chloride, calcium chloride
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1.000032 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000032 Å / Relative weight: 1
ReflectionResolution: 1.73→85.04 Å / Num. obs: 57509 / % possible obs: 97.6 % / Redundancy: 26.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.021 / Net I/σ(I): 25
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 19.4 % / Rmerge(I) obs: 1.266 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 49830 / CC1/2: 0.683 / Rpim(I) all: 0.405 / % possible all: 81.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
DIALS3.18.0data reduction
DIALS3.18.0data scaling
PHENIX1.20.1refinement
PHASER2.8.3phasing
PDB_EXTRACT4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.5 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2083 2766 4.93 %
Rwork0.1735 --
obs0.1752 56078 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 29 240 2926
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172774
X-RAY DIFFRACTIONf_angle_d1.3823763
X-RAY DIFFRACTIONf_dihedral_angle_d12.4661018
X-RAY DIFFRACTIONf_chiral_restr0.099407
X-RAY DIFFRACTIONf_plane_restr0.01478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.28221200.24762323X-RAY DIFFRACTION87
1.78-1.810.20751370.20592486X-RAY DIFFRACTION93
1.81-1.850.23161220.19552556X-RAY DIFFRACTION94
1.85-1.890.21681430.18372566X-RAY DIFFRACTION97
1.89-1.930.22311400.18922628X-RAY DIFFRACTION98
1.93-1.970.21121430.19152646X-RAY DIFFRACTION99
1.97-2.020.15921330.16532639X-RAY DIFFRACTION99
2.02-2.070.20121560.15712649X-RAY DIFFRACTION99
2.07-2.140.18011420.15852656X-RAY DIFFRACTION99
2.14-2.20.19061370.16082653X-RAY DIFFRACTION99
2.2-2.280.19981330.16182671X-RAY DIFFRACTION99
2.28-2.370.18791370.17182700X-RAY DIFFRACTION99
2.37-2.480.19181340.16682697X-RAY DIFFRACTION99
2.48-2.610.2121410.1652708X-RAY DIFFRACTION99
2.61-2.780.19921240.16392717X-RAY DIFFRACTION99
2.78-2.990.19071310.17122746X-RAY DIFFRACTION100
2.99-3.290.19891630.16382721X-RAY DIFFRACTION100
3.29-3.770.19381270.16642796X-RAY DIFFRACTION100
3.77-4.740.18631570.16042804X-RAY DIFFRACTION100
4.74-29.50.28911460.20612950X-RAY DIFFRACTION99
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)
12.14631.115-1.08631.4435-1.22262.99090.01680.09970.1572-0.06110.0197-0.1128-0.13450.1069-0.03330.2863-0.010.02850.24690.01790.23828.30437.433-19.476
25.5779-1.6773-3.89982.13731.00635.8976-0.01680.9477-0.148-0.48-0.22390.02150.4116-0.62340.2190.3706-0.1358-0.00990.3415-0.03140.2955-6.21324.333-16.903
32.64340.4515-0.13311.3532-0.11061.8745-0.0070.20290.8473-0.10040.03520.2642-0.4232-0.2411-0.04410.39860.04730.00730.37410.06690.4934-16.98441.878-8.094
43.64810.28120.96562.7724-0.09972.7579-0.06240.36870.3738-0.19110.09810.3089-0.1527-0.2378-0.0520.189-0.0264-0.01880.3520.03280.2737-24.65131.31-9.006
52.38030.4024-0.34040.69030.12260.0995-0.0330.2632-0.0092-0.09380.06190.11530.0799-0.3267-0.03190.2477-0.0558-0.02230.3587-0.00150.2379-20.32424.25-8.975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 188:308 )A188 - 308
2X-RAY DIFFRACTION2( CHAIN A AND RESID 309:326 )A309 - 326
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1:77 )A1 - 77
4X-RAY DIFFRACTION4( CHAIN A AND RESID 78:135 )A78 - 135
5X-RAY DIFFRACTION5( CHAIN A AND RESID 136:187 )A136 - 187

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