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- PDB-8be3: Crystal structure of KRasG12V-Nanobody84 -

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Basic information

Entry
Database: PDB / ID: 8be3
TitleCrystal structure of KRasG12V-Nanobody84
Components
  • Isoform 2B of GTPase KRas
  • Nanobody84
KeywordsSIGNALING PROTEIN / Complex / Stabilizer
Function / homologysmall monomeric GTPase / Ca2+ pathway / GUANOSINE-5'-DIPHOSPHATE / Isoform 2B of GTPase KRas
Function and homology information
Biological speciesLama glama (llama)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFischer, B. / Wohlkonig, A. / Steyaert, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Nat Commun / Year: 2024
Title: Allosteric nanobodies to study the interactions between SOS1 and RAS.
Authors: Fischer, B. / Uchanski, T. / Sheryazdanova, A. / Gonzalez, S. / Volkov, A.N. / Brosens, E. / Zogg, T. / Kalichuk, V. / Ballet, S. / Versees, W. / Sablina, A.A. / Pardon, E. / Wohlkonig, A. / Steyaert, J.
History
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA0A: Nanobody84
R: Isoform 2B of GTPase KRas
A: Isoform 2B of GTPase KRas
A00A: Nanobody84
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3248
Polymers70,3894
Non-polymers9354
Water6,305350
1
AA0A: Nanobody84
R: Isoform 2B of GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6624
Polymers35,1942
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Isoform 2B of GTPase KRas
A00A: Nanobody84
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6624
Polymers35,1942
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.850, 130.500, 55.600
Angle α, β, γ (deg.)90.000, 116.250, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody Nanobody84


Mass: 13519.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21675.314 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 / Production host: Escherichia coli (E. coli) / 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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 21%, MES 0.1 M pH 6.0, NaCl 150mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.84→42.3 Å / Num. obs: 54015 / % possible obs: 98.6 % / Redundancy: 4.7 % / Biso Wilson estimate: 33.43 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.7
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 38376 / CC1/2: 0.66

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L9S

4l9s


Resolution: 1.85→42.3 Å / SU ML: 0.232 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.8998
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2303 2698 5 %
Rwork0.2008 51280 -
obs0.2023 53978 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.19 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4263 0 58 350 4671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00584453
X-RAY DIFFRACTIONf_angle_d0.75446036
X-RAY DIFFRACTIONf_chiral_restr0.0603672
X-RAY DIFFRACTIONf_plane_restr0.0044774
X-RAY DIFFRACTIONf_dihedral_angle_d16.57811650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.35171170.33662251X-RAY DIFFRACTION84.75
1.88-1.910.30781460.29382765X-RAY DIFFRACTION99.11
1.91-1.950.32181410.28322667X-RAY DIFFRACTION99.19
1.95-20.28241450.2682752X-RAY DIFFRACTION99.38
2-2.040.30081380.24942636X-RAY DIFFRACTION99.25
2.04-2.090.29521440.2522726X-RAY DIFFRACTION99.48
2.09-2.150.26731440.23812746X-RAY DIFFRACTION99.66
2.15-2.210.25141420.22232693X-RAY DIFFRACTION99.68
2.21-2.290.30781430.22392722X-RAY DIFFRACTION99.69
2.29-2.370.2681450.2152747X-RAY DIFFRACTION99.9
2.37-2.460.24661420.21432693X-RAY DIFFRACTION99.89
2.46-2.570.25781440.21572735X-RAY DIFFRACTION99.97
2.57-2.710.29691430.21672718X-RAY DIFFRACTION99.9
2.71-2.880.26611440.22092734X-RAY DIFFRACTION99.69
2.88-3.10.22641450.20712772X-RAY DIFFRACTION99.62
3.1-3.410.24991410.19682678X-RAY DIFFRACTION99.72
3.41-3.910.20371450.17612748X-RAY DIFFRACTION99.59
3.91-4.920.17641440.15532728X-RAY DIFFRACTION99.55
4.92-42.30.17991450.18622769X-RAY DIFFRACTION99.32

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