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- PDB-8b69: Heterotetramer of K-Ras4B(G12V) and Rgl2(RBD) -

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Basic information

Entry
Database: PDB / ID: 8b69
TitleHeterotetramer of K-Ras4B(G12V) and Rgl2(RBD)
Components
  • Isoform 2B of GTPase KRas
  • Ral guanine nucleotide dissociation stimulator-like 2
KeywordsONCOPROTEIN / KRas / RalGEF / Rgl2 / Ral pathway / Ras signalling / small G-protein / Ras binding domain
Function / homology
Function and homology information


regulation of Ral protein signal transduction / negative regulation of cardiac muscle cell apoptotic process / guanyl-nucleotide exchange factor activity / small monomeric GTPase / RAF/MAP kinase cascade / Ca2+ pathway / Ras protein signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytosol
Similarity search - Function
Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor ...Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ral guanine nucleotide dissociation stimulator-like 2 / Isoform 2B of GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsTariq, M. / Fairall, L. / Romartinez-Alonso, B. / Dominguez, C. / Schwabe, J.W.R. / Tanaka, K.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust204801/Z/16/Z United Kingdom
Other government
Citation
Journal: Life Sci Alliance / Year: 2024
Title: Structural insights into the complex of oncogenic KRas4B G12V and Rgl2, a RalA/B activator.
Authors: Tariq, M. / Ikeya, T. / Togashi, N. / Fairall, L. / Kamei, S. / Mayooramurugan, S. / Abbott, L.R. / Hasan, A. / Bueno-Alejo, C. / Sukegawa, S. / Romartinez-Alonso, B. / Muro Campillo, M.A. / ...Authors: Tariq, M. / Ikeya, T. / Togashi, N. / Fairall, L. / Kamei, S. / Mayooramurugan, S. / Abbott, L.R. / Hasan, A. / Bueno-Alejo, C. / Sukegawa, S. / Romartinez-Alonso, B. / Muro Campillo, M.A. / Hudson, A.J. / Ito, Y. / Schwabe, J.W. / Dominguez, C. / Tanaka, K.
#1: Journal: Biorxiv / Year: 2023
Title: Structural insights into the complex of oncogenic K-Ras4BG12V and Rgl2, a RalA/B activator
Authors: Tariq, M. / Ikeya, T. / Togashi, N. / Fairall, L. / Bueno-Alejo, C. / Kamei, S. / Romartinez-Alonso, B. / Campillo, M.A.M. / Hudson, A.J. / Ito, Y. / Schwabe, J.W.R. / Dominguez, C. / Tanaka, K.
History
DepositionSep 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ral guanine nucleotide dissociation stimulator-like 2
B: Isoform 2B of GTPase KRas
C: Ral guanine nucleotide dissociation stimulator-like 2
D: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8408
Polymers60,7474
Non-polymers1,0934
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-41 kcal/mol
Surface area23570 Å2
Unit cell
Length a, b, c (Å)77.843, 77.843, 163.728
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 647 through 734)
d_2ens_1(chain "C" and (resid 647 through 655 or resid 658 through 734))
d_1ens_2(chain "B" and (resid 0 through 102 or (resid 104...
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERARGARGAA647 - 7347 - 94
d_21ens_1SERSERGLNGLNCC647 - 6557 - 15
d_22ens_1LEULEUARGARGCC658 - 73418 - 94
d_11ens_2SERSERARGARGBB0 - 1021 - 103
d_12ens_2LYSLYSLYSLYSBB104 - 167105 - 168
d_13ens_2MGMGMGMGBE201
d_14ens_2GNPGNPGNPGNPBF202
d_21ens_2SERSERLYSLYSDD0 - 1671 - 168
d_22ens_2MGMGMGMGDG201
d_23ens_2GNPGNPGNPGNPDH202

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein Ral guanine nucleotide dissociation stimulator-like 2 / RalGDS-like 2 / RalGDS-like factor / Ras-associated protein RAB2L


Mass: 10972.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RGL2, RAB2L / Plasmid: Novagen pET-49b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15211
#2: Protein Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19400.916 Da / Num. of mol.: 2 / Mutation: G12V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Plasmid: Novagen pET-43.1a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01116-2, small monomeric GTPase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
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: 2.39 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium/potassium phosphate pH 7.5, 0.1M HEPES 7.5, 22.5% v/v PEG (16.67%w/v PEG 8000, 16.67%w/v PEG 10000, 16.67% w/v PEG 6000), 10% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.07→29.472 Å / Num. obs: 11107 / % possible obs: 98.22 % / Redundancy: 2 % / Biso Wilson estimate: 95.59 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02682 / Rpim(I) all: 0.02682 / Rrim(I) all: 0.03794 / Net I/σ(I): 10.15
Reflection shellResolution: 3.071→3.18 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.1774 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 949 / CC1/2: 0.973 / CC star: 0.993 / Rrim(I) all: 0.2509 / % possible all: 86.51

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
REFMAC5. 8. 0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LFD

1lfd


Resolution: 3.07→29.45 Å / SU ML: 0.4432 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.7498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.317 581 5.25 %Random
Rwork0.2367 10484 --
obs0.2401 11107 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.5 Å2
Refinement stepCycle: LAST / Resolution: 3.07→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4050 0 66 0 4116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744175
X-RAY DIFFRACTIONf_angle_d1.40215647
X-RAY DIFFRACTIONf_chiral_restr0.0982639
X-RAY DIFFRACTIONf_plane_restr0.0042724
X-RAY DIFFRACTIONf_dihedral_angle_d7.5344572
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS2.12338583251
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.17479722379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.07-3.380.36851180.31222477X-RAY DIFFRACTION94.19
3.38-3.870.33911300.24372622X-RAY DIFFRACTION99.71
3.87-4.870.31131850.23852601X-RAY DIFFRACTION99.75
4.87-29.450.29881480.21832784X-RAY DIFFRACTION99.8

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