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- PDB-8fji: Crystal structure of RalA in a covalent complex with SOF-367 -

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Basic information

Entry
Database: PDB / ID: 8fji
TitleCrystal structure of RalA in a covalent complex with SOF-367
ComponentsRas-related protein Ral-A
KeywordsHYDROLASE / RalA / GTPase
Function / homology
Function and homology information


membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / myosin binding ...membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / myosin binding / exocytosis / cleavage furrow / p38MAPK events / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / G protein activity / synaptic membrane / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / cytoplasmic vesicle membrane / receptor internalization / GDP binding / chemotaxis / ATPase binding / Ras protein signal transduction / cell cycle / cell division / focal adhesion / GTPase activity / ubiquitin protein ligase binding / GTP binding / cell surface / signal transduction / mitochondrion / extracellular exosome / plasma membrane
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Chem-Y0M / Ras-related protein Ral-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLandgraf, A.D. / Yeh, I.-J. / Bum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA197928 United States
CitationJournal: Chemmedchem / Year: 2023
Title: Exploring Covalent Bond Formation at Tyr-82 for Inhibition of Ral GTPase Activation.
Authors: Landgraf, A.D. / Yeh, I.J. / Ghozayel, M.K. / Bum-Erdene, K. / Gonzalez-Gutierrez, G. / Meroueh, S.O.
History
DepositionDec 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Ras-related protein Ral-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2726
Polymers21,3041
Non-polymers9685
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.767, 104.630, 55.823
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-304-

HOH

21B-412-

HOH

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Components

#1: Protein Ras-related protein Ral-A / RalA GTPase


Mass: 21303.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALA, RAL / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P11233, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-Y0M / 8-[fluoro(dihydroxy)-lambda~4~-sulfanyl]-N-(2-methoxypyridin-3-yl)-2,3-dihydro-1,4-benzodioxine-5-sulfonamide


Mass: 404.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13FN2O7S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Ca(Ac)2 0.1 M pH 5.5 PEG3350 18-22%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.44→55.07 Å / Num. obs: 32302 / % possible obs: 92.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.99 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Rsym value: 0.084 / Net I/σ(I): 14.3
Reflection shellResolution: 1.44→1.46 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1559 / CC1/2: 0.596 / Rpim(I) all: 0.465 / Rrim(I) all: 1.085 / Rsym value: 0.976 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→55.07 Å / SU ML: 0.1485 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.4316
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2087 1531 4.86 %
Rwork0.1833 29959 -
obs0.1845 31490 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.29 Å2
Refinement stepCycle: LAST / Resolution: 1.48→55.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 56 195 1616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951534
X-RAY DIFFRACTIONf_angle_d1.12192091
X-RAY DIFFRACTIONf_chiral_restr0.0752221
X-RAY DIFFRACTIONf_plane_restr0.0071277
X-RAY DIFFRACTIONf_dihedral_angle_d13.7153224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.530.27411380.23122706X-RAY DIFFRACTION99.23
1.53-1.580.23781390.20712716X-RAY DIFFRACTION99.55
1.58-1.650.24541360.19172735X-RAY DIFFRACTION99.72
1.65-1.720.18841350.18012734X-RAY DIFFRACTION99.76
1.72-1.810.19781880.16492697X-RAY DIFFRACTION99.97
1.81-1.930.30441410.26062491X-RAY DIFFRACTION91.14
1.93-2.070.20381530.17632716X-RAY DIFFRACTION99.27
2.07-2.280.24371340.23682615X-RAY DIFFRACTION94.66
2.28-2.610.18381370.15582771X-RAY DIFFRACTION100
2.61-3.290.16221100.16372845X-RAY DIFFRACTION100
3.29-55.070.18971200.1642933X-RAY DIFFRACTION99.32
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)
12.25018862450.1826198300841.466114091851.052157113950.7695428906212.064810214440.07008300140670.364064434614-0.152669149381-0.3381836933190.01249379625450.1035023079520.349011357387-0.137076397517-0.1002653141250.199019112601-0.00110414108259-0.02799144663470.146787658288-0.02515347197520.101661450768-18.50126311428.59122044471-22.4977627776
21.02184745597-0.5429565531511.456540414980.901354038328-0.8303662154033.04630658812-0.0496249796266-0.04529576291090.101927639381-0.0350455513537-0.0510380078627-0.024336357038-0.0306997460204-0.2425630277160.08343358006280.08913086935720.000481579472892-0.009792656875730.133536744107-0.007568585381320.120905248954-23.991707815715.4969992611-9.19271182719
30.934011366006-0.2484027151020.2092906059467.69233319519-2.665976399452.34668999353-0.0305865580515-0.1832005145360.134981957060.02533474536850.1531724367460.715928537540.133039891807-0.646754220135-0.1202087642690.101861496692-0.01322413517670.006198903241210.285657388343-0.02486634490080.195454611247-30.538634278715.5743420809-6.25314910562
42.122404386111.88283881255-1.686412240263.38957001134-3.052451596945.43252114711-0.06337284761090.265401870810.0232291793671-0.2792804169350.1664746066860.1520635439170.228681522388-0.666605698228-0.1045710710640.1278887932650.0105741709803-0.03213020141290.16747980286-0.005970987717280.130879258854-21.763837598513.4306879245-22.4541331898
52.81112927512-1.244293400261.621733593317.584011516980.3522066612071.10057913828-0.0463446868951-0.241871528754-0.1522640280490.0282423958440.1079111195550.37167325597-0.0130760712071-0.0851745808533-0.06295639342310.141815515557-0.007911913106410.008956371475960.1152482313950.01736982131150.123795891486-20.388377598-3.17691384574-8.57805817021
60.975173421076-0.1542973157230.0371163880661.625589574510.01574374636941.64882629165-0.0414714494732-0.030565483936-0.03732334386360.0042227103954-0.00926814478697-0.04967414950040.1006806115820.01137072650170.03405233101790.07500819474060.005333877438610.007221761227770.07139046295830.003911277370360.089440097196-12.12378088297.62700643647-3.92406944749
71.690728623380.4223862502641.031121555051.07771986745-0.4428214567251.14013321964-0.1010666307010.0629379395878-0.296500246339-0.0825003014999-0.013025069313-0.05742565267850.1929067681760.2029008010460.09339308368140.1264510598710.01764372029370.02576064142730.06714139898820.01939552739960.126172259109-7.055498060638.06639028657-11.7466659414
82.345846185920.03686644134212.441914342753.69823525909-0.2404106564012.640610976710.0891533825968-0.0582993587518-0.008405981187670.0831373739802-0.03355980477440.00943025838391-0.0312274456739-0.0530195457139-0.05027495134130.1162394824950.02868026878350.005681047733420.0862545441354-0.02140178012990.110977240267-15.118988937323.22612834053.91546882897
95.87807220361-3.21344559709-2.455301050094.646366559443.857538262957.38863213463-0.0591250484637-0.4841733905740.2155084188550.02072728467210.220870753638-0.238216058064-0.2456234564550.406591900532-0.1276507899640.0949311304726-0.0106307712637-0.01779409176240.131707338359-0.01412830928530.13522539309-1.9017126030616.0639353183-1.3167439059
106.78025911971-4.587592756280.2309852255335.844554943830.0730376201051.731752262550.02285085910740.05212497237790.121942134896-0.104650122276-0.0544366142324-0.0151928959753-0.169859746661-0.06143656380670.01983258377050.0742205500437-0.0079689056463-0.01012092870060.0465506052436-0.001830194811480.058149371223-12.713319562119.8984489677-7.74523433157
115.8253394867-0.376325712748-1.756896325840.9650887993820.222387274125.69849708319-0.03712234653830.136755999269-0.108080883438-0.082982183329-0.0529116646445-0.09071751285780.0971703618139-0.009371864888370.08831720932120.08874056572830.00571012566024-0.0142167893610.05809806614980.01973104819350.0936791104053-11.808119156515.4273194493-19.2436148254
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 10 through 20 )10 - 201 - 11
22chain 'B' and (resid 21 through 36 )21 - 3612 - 27
33chain 'B' and (resid 37 through 48 )37 - 4828 - 39
44chain 'B' and (resid 49 through 68 )49 - 6840 - 59
55chain 'B' and (resid 69 through 85 )69 - 8560 - 76
66chain 'B' and (resid 86 through 115 )86 - 11577 - 106
77chain 'B' and (resid 116 through 127 )116 - 127107 - 118
88chain 'B' and (resid 128 through 138 )128 - 138119 - 129
99chain 'B' and (resid 139 through 148 )139 - 148130 - 139
1010chain 'B' and (resid 149 through 163 )149 - 163140 - 154
1111chain 'B' and (resid 164 through 179 )164 - 179155 - 170

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