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- PDB-8fjh: Crystal structure of RalA in a covalent complex with SOF-531 -

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Basic information

Entry
Database: PDB / ID: 8fjh
TitleCrystal structure of RalA in a covalent complex with SOF-531
ComponentsRas-related protein Ral-A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / RalA / GTPase / inhibitor / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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-Y0P / Ras-related protein Ral-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,2896
Polymers21,3041
Non-polymers9855
Water4,396244
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)64.754, 104.813, 55.347
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-301-

HOH

21B-315-

HOH

31B-423-

HOH

41B-483-

HOH

51B-526-

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-Y0P / 8-[bis(oxidanyl)-$l^{3}-sulfanyl]-~{N}-(3-fluoranyl-5-methoxy-phenyl)-2,3-dihydro-1,4-benzodioxine-5-sulfonamide


Mass: 421.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13F2NO7S2 / 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.: 244 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: Ca(Ac)2 0.2 M pH 5.5 PEG 3350 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: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.54→55.09 Å / Num. obs: 27863 / % possible obs: 98.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 12.64 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.037 / Rrim(I) all: 0.096 / Rsym value: 0.088 / Net I/σ(I): 14.7
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1153 / CC1/2: 0.567 / Rpim(I) all: 0.353 / Rrim(I) all: 0.78 / Rsym value: 0.69 / % possible all: 84.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→55.09 Å / SU ML: 0.1199 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.388
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1841 1402 5.04 %
Rwork0.1494 26391 -
obs0.1512 27793 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.14 Å2
Refinement stepCycle: LAST / Resolution: 1.54→55.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 57 244 1666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00891541
X-RAY DIFFRACTIONf_angle_d1.09632101
X-RAY DIFFRACTIONf_chiral_restr0.0579220
X-RAY DIFFRACTIONf_plane_restr0.0079278
X-RAY DIFFRACTIONf_dihedral_angle_d16.7857225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.590.22751300.20522246X-RAY DIFFRACTION86.21
1.59-1.660.18631380.18162610X-RAY DIFFRACTION98.14
1.66-1.730.1831450.15592646X-RAY DIFFRACTION99.93
1.73-1.820.17711380.15182658X-RAY DIFFRACTION100
1.83-1.940.2171380.16722656X-RAY DIFFRACTION99.68
1.94-2.090.19951310.14482684X-RAY DIFFRACTION99.96
2.09-2.30.19841570.15312660X-RAY DIFFRACTION99.26
2.3-2.630.19231390.13652692X-RAY DIFFRACTION100
2.63-3.320.17561390.13672720X-RAY DIFFRACTION99.76
3.32-55.090.16041470.14492819X-RAY DIFFRACTION99.33
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)
11.28494129758-0.07796648946640.525221305471.20983748992-0.3117253848851.47366963277-0.0365877107521-0.0432638045054-0.02624020131240.0112309673837-0.05115960556550.1622078000230.0641164309708-0.4123186514350.07013628881020.065197674496-0.00951320075777-0.008042132800660.142371066604-0.01223988299080.0988648296692-24.885962919513.5108367191-11.5457651598
21.737640798361.5491712836-1.865851466642.85658805985-2.377633109643.45491731274-0.01445407933740.31815445936-0.0435319024183-0.264000392054-0.004795000287420.1741047936670.143543239301-0.468213180789-0.04895288030520.09320068561770.017671092916-0.0357881909640.1507332688690.000697104099840.0948075628614-21.675247087613.4746702577-22.2698643573
31.579524881030.07339524229490.6600244426784.6641189013-0.6416911761630.37617558449-0.13146005688-0.219218734960.06725686462950.03559003386960.1230152012210.26826398115-0.0107586668183-0.09852157310620.02289243060770.162045675173-0.00651260752328-0.01952520127390.1566758584210.03355447389760.1629028285-20.7162676942-3.18228427807-8.1432148041
40.809851234657-0.1646209968090.1205549188640.957819980201-0.0004812137847141.25253666587-0.0707439180157-0.070838694554-0.09446038752530.05166505569740.0241992931346-0.007240870658330.133068794315-0.02346143718820.04433276059950.09096579480840.0070520632890.01063424136040.05890318068030.01741205668760.090003818862-12.07480135267.65122288199-3.81896363705
51.67738784842-0.646247655542-0.374156853121.577828319430.6151129274181.98043350352-0.0605844704506-0.07473238503570.05704448469330.05259316403550.0481499930955-0.0728822614527-0.03718727133910.04603429944020.002416588939270.05455146998610.000772596767568-0.008191407589380.0424762176050.006848172707640.069781266278-9.2091060100416.6260405303-4.63140736568
64.56059107884-0.290497000114-1.278144060490.983519512384-0.1553377422393.854218240910.01505905149890.173926065865-0.108411097832-0.0772169131414-0.056934254917-0.0697045836511-0.0173261163323-0.01262613451350.04951818445750.07554852566030.00630735588455-0.01145735927120.059348784540.023459745610.091367197596-11.751697271815.5494226684-19.0992965358
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 48 )10 - 481 - 39
22chain 'B' and (resid 49 through 68 )49 - 6840 - 59
33chain 'B' and (resid 69 through 85 )69 - 8560 - 76
44chain 'B' and (resid 86 through 115 )86 - 11577 - 106
55chain 'B' and (resid 116 through 163 )116 - 163107 - 154
66chain 'B' and (resid 164 through 179 )164 - 179155 - 170

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