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- PDB-6p0j: Crystal structure of GDP-bound human RalA -

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Basic information

Entry
Database: PDB / ID: 6p0j
TitleCrystal structure of GDP-bound human RalA
ComponentsRas-related protein Ral-A
KeywordsSIGNALING PROTEIN / HYDROLASE / Ral GTPase / RalA / covalent inhibitor / sulfonyl fluoride
Function / homology
Function and homology information


membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / : / 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 / : / 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 / synaptic membrane / cytoplasmic vesicle 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 / ATPase binding / G protein activity / 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 / Ras-related protein Ral-A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsBum-Erdene, K. / Gonzalez-Gutierrez, G. / Liu, D. / Meroueh, S.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA197928 United States
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
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
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.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)21,7873
Polymers21,3041
Non-polymers4832
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-22 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.948, 104.809, 55.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

21B-339-

HOH

31B-415-

HOH

41B-496-

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 (E. coli)
References: UniProt: P11233, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
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: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Mar 22, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.31→30.78 Å / Num. obs: 45413 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 10.86 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Rrim(I) all: 0.078 / Rsym value: 0.072 / Net I/σ(I): 17.3
Reflection shellResolution: 1.31→1.34 Å / Num. unique obs: 2587 / CC1/2: 0.684 / Rpim(I) all: 0.429 / Rrim(I) all: 1.094 / Rsym value: 1.004

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Processing

Software
NameVersionClassification
PHENIX1.14_3260model building
PHENIX1.14_3260refinement
PHENIX1.14_3260model building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1U8Z

1u8z


Resolution: 1.31→30.77 Å / SU ML: 0.1313 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.789
RfactorNum. reflection% reflection
Rfree0.156 2290 5.04 %
Rwork0.1201 --
obs0.1219 45413 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.76 Å2
Refinement stepCycle: LAST / Resolution: 1.31→30.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 1 257 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00851499
X-RAY DIFFRACTIONf_angle_d1.07462036
X-RAY DIFFRACTIONf_chiral_restr0.0819219
X-RAY DIFFRACTIONf_plane_restr0.0064271
X-RAY DIFFRACTIONf_dihedral_angle_d0.5445678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.340.28541770.22732587X-RAY DIFFRACTION98.96
1.34-1.370.21861420.18162648X-RAY DIFFRACTION99.01
1.37-1.40.21611410.16512665X-RAY DIFFRACTION99.12
1.4-1.440.23551270.14752651X-RAY DIFFRACTION99.14
1.44-1.480.17381400.13452675X-RAY DIFFRACTION99.43
1.48-1.530.15971430.11882678X-RAY DIFFRACTION99.68
1.53-1.590.15971500.11222662X-RAY DIFFRACTION99.5
1.59-1.650.15121230.09962695X-RAY DIFFRACTION99.82
1.65-1.730.13151360.09332710X-RAY DIFFRACTION99.79
1.73-1.820.13931690.08692659X-RAY DIFFRACTION99.96
1.82-1.930.15261410.08992717X-RAY DIFFRACTION99.93
1.93-2.080.12461250.0942717X-RAY DIFFRACTION99.96
2.08-2.290.13431310.09822742X-RAY DIFFRACTION99.86
2.29-2.620.13351220.1032733X-RAY DIFFRACTION99.86
2.62-3.30.14121640.12372735X-RAY DIFFRACTION99.69
3.3-30.780.1641590.14792849X-RAY DIFFRACTION99.24

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