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- PDB-6p0i: Crystal structure of GDP-bound human RalA in a covalent complex w... -

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Basic information

Entry
Database: PDB / ID: 6p0i
TitleCrystal structure of GDP-bound human RalA in a covalent complex with aryl sulfonyl fluoride compounds.
ComponentsRas-related protein Ral-A
Keywordssignaling protein/inhibitor / Ral GTPase / RalA / covalent inhibitor / sulfonyl fluoride / SIGNALING PROTEIN / signaling protein-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 nucleotide triphosphate hydrolases ...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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GUANOSINE-5'-DIPHOSPHATE / Chem-NL7 / Ras-related protein Ral-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsBum-Erdene, K. / Gonzalez-Gutierrez, G. / Liu, D. / Ghozayel, M.K. / Xu, D. / Meroueh, S.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA197928 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Small-molecule covalent bond formation at tyrosine creates a binding site and inhibits activation of Ral GTPases.
Authors: Bum-Erdene, K. / Liu, D. / Gonzalez-Gutierrez, G. / Ghozayel, M.K. / Xu, D. / Meroueh, S.O.
History
DepositionMay 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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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)22,47411
Polymers21,3041
Non-polymers1,17010
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.850, 104.330, 55.240
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-527-

HOH

21B-634-

HOH

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Ras-related protein Ral-A


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 (E. coli) / References: UniProt: P11233

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Non-polymers , 9 types, 204 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NL7 / 4-[(5-methoxypyridin-3-yl)sulfamoyl]benzene-1-sulfonic acid


Mass: 344.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N2O6S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.39 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M Calcium Acetate pH 5.5, 18-22% PEG3350.

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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: Feb 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.18→39 Å / Num. obs: 61827 / % possible obs: 100 % / Redundancy: 8.1 % / Biso Wilson estimate: 10.69 Å2 / CC1/2: 1 / Rpim(I) all: 0.015 / Rrim(I) all: 0.048 / Rsym value: 0.045 / Net I/σ(I): 22.7
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2645 / CC1/2: 0.681 / Rpim(I) all: 0.419 / Rrim(I) all: 0.909 / Rsym value: 0.807 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.15_3459model building
PHENIX1.15_3459refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u8z

1u8z


Resolution: 1.18→39 Å / SU ML: 0.0808 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.45
RfactorNum. reflection% reflection
Rfree0.1472 3013 4.88 %
Rwork0.1253 --
obs0.1265 61802 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.82 Å2
Refinement stepCycle: LAST / Resolution: 1.18→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1378 0 47 194 1619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01271516
X-RAY DIFFRACTIONf_angle_d1.18072056
X-RAY DIFFRACTIONf_chiral_restr0.0896216
X-RAY DIFFRACTIONf_plane_restr0.007271
X-RAY DIFFRACTIONf_dihedral_angle_d11.1044883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.20.20791270.21292645X-RAY DIFFRACTION99.96
1.2-1.220.19181290.18922642X-RAY DIFFRACTION100
1.22-1.240.19891360.17442609X-RAY DIFFRACTION99.96
1.24-1.260.1681340.15482660X-RAY DIFFRACTION100
1.26-1.290.1881350.15172651X-RAY DIFFRACTION100
1.29-1.310.18961570.14972642X-RAY DIFFRACTION100
1.31-1.340.20461190.13592651X-RAY DIFFRACTION100
1.34-1.370.15121260.12582668X-RAY DIFFRACTION100
1.37-1.410.14941470.11512638X-RAY DIFFRACTION100
1.41-1.440.14031250.11152655X-RAY DIFFRACTION100
1.44-1.490.12361450.10482651X-RAY DIFFRACTION100
1.49-1.530.10651180.09662701X-RAY DIFFRACTION100
1.53-1.590.12521200.09372643X-RAY DIFFRACTION100
1.59-1.650.11761200.09262699X-RAY DIFFRACTION100
1.65-1.730.11921320.09442663X-RAY DIFFRACTION100
1.73-1.820.12831410.09642666X-RAY DIFFRACTION100
1.82-1.930.111290.1022690X-RAY DIFFRACTION100
1.93-2.080.12551510.10122685X-RAY DIFFRACTION99.96
2.08-2.290.12181710.10652664X-RAY DIFFRACTION100
2.29-2.620.12141320.11682710X-RAY DIFFRACTION100
2.62-3.310.14941620.13592719X-RAY DIFFRACTION100
3.31-39.020.18711570.15652837X-RAY DIFFRACTION99.87

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