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- PDB-6p0l: Crystal structure of GDP-bound human RalA in a covalent complex w... -

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Basic information

Entry
Database: PDB / ID: 6p0l
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 / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / regulation of postsynaptic neurotransmitter receptor internalization / myosin binding ...membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / regulation of postsynaptic neurotransmitter receptor internalization / myosin binding / exocytosis / cleavage furrow / p38MAPK events / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoplasmic vesicle membrane / synaptic membrane / small monomeric GTPase / regulation of actin cytoskeleton organization / Translocation of SLC2A4 (GLUT4) to the plasma membrane / neural tube closure / receptor internalization / Schaffer collateral - CA1 synapse / chemotaxis / GDP binding / G protein activity / ATPase binding / Ras protein signal transduction / 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 domain 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 domain 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Chem-NLJ / Ras-related protein Ral-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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.ptnr3_auth_seq_id / _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_type.id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)22,1314
Polymers21,3041
Non-polymers8283
Water4,234235
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)65.115, 104.375, 55.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-607-

HOH

21B-638-

HOH

31B-733-

HOH

41B-804-

HOH

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Components

#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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NLJ / 4-[(2-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
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2 M Calcium Acetate pH 5.5 18-20% 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: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.3→38.05 Å / Num. obs: 46861 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Rsym value: 0.086 / Net I/σ(I): 15.2
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2521 / CC1/2: 0.658 / Rpim(I) all: 0.519 / Rrim(I) all: 1.331 / Rsym value: 1.224 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u8z

1u8z


Resolution: 1.3→38.049 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.65
RfactorNum. reflection% reflection
Rfree0.1671 2316 4.95 %
Rwork0.1341 --
obs0.1357 46822 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.3→38.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 0 50 235 1635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011423
X-RAY DIFFRACTIONf_angle_d1.0551922
X-RAY DIFFRACTIONf_dihedral_angle_d14.569529
X-RAY DIFFRACTIONf_chiral_restr0.078207
X-RAY DIFFRACTIONf_plane_restr0.005246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.32650.28591650.23862521X-RAY DIFFRACTION99
1.3265-1.35540.23231410.212590X-RAY DIFFRACTION100
1.3554-1.38690.21621540.17792555X-RAY DIFFRACTION100
1.3869-1.42160.19291530.16072574X-RAY DIFFRACTION100
1.4216-1.460.18461330.14972591X-RAY DIFFRACTION100
1.46-1.5030.19171370.14062594X-RAY DIFFRACTION100
1.503-1.55150.18281250.12482597X-RAY DIFFRACTION100
1.5515-1.6070.15831200.10822607X-RAY DIFFRACTION100
1.607-1.67130.16311270.10722633X-RAY DIFFRACTION100
1.6713-1.74740.19821350.11162591X-RAY DIFFRACTION100
1.7474-1.83950.14461170.10682640X-RAY DIFFRACTION100
1.8395-1.95470.1621380.11062607X-RAY DIFFRACTION100
1.9547-2.10570.13591190.10792640X-RAY DIFFRACTION100
2.1057-2.31750.17271340.11212665X-RAY DIFFRACTION100
2.3175-2.65280.15321430.11882633X-RAY DIFFRACTION100
2.6528-3.3420.14591310.13662684X-RAY DIFFRACTION100
3.342-38.06540.15881440.16182784X-RAY DIFFRACTION100

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