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- PDB-9t3e: RACB with GSP and the fragment of RIPb protein bound (antiparallel) -

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Basic information

Entry
Database: PDB / ID: 9t3e
TitleRACB with GSP and the fragment of RIPb protein bound (antiparallel)
Components
  • RACB protein
  • RIPb
KeywordsPLANT PROTEIN / RACB / Hordeum vulgare / GSP / RIPb
Function / homology
Function and homology information


small GTPase-mediated signal transduction / GTPase activity / GTP binding / plasma membrane / cytoplasm
Similarity search - Function
Interactor of constitutive active ROPs / Small GTPase Rho / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase Ras domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases ...Interactor of constitutive active ROPs / Small GTPase Rho / Small GTPase Rab domain profile. / Small GTPase Rho domain profile. / Small GTPase Ras domain profile. / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Predicted protein / RACB protein
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJanowski, R. / Mohamadi, M. / Hagn, F. / Niessing, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2026
Title: Nucleotide-dependent switching and RIPb effector recognition of the barley susceptibility factor RACB.
Authors: Mohamadi, M. / Bradai, M. / Janowski, R. / Gunsel, U. / Tran, M. / Kahl, S.M. / McCollum, C. / Niessing, D. / Huckelhoven, R. / Hagn, F.
History
DepositionOct 27, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2026Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RACB protein
B: RIPb
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5187
Polymers28,7382
Non-polymers7805
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-50 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.510, 139.450, 60.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein RACB protein


Mass: 21809.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Gene: pRacB / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RW50
#2: Protein RIPb


Mass: 6928.614 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Production host: Escherichia coli (E. coli) / References: UniProt: F2D8Y4

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Non-polymers , 4 types, 19 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.06 Å3/Da / Density % sol: 59.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10 mM Magnesium Chloride, 50 mM MES pH 5.6, 1.8 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 14643 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 1 / Net I/σ(I): 19.5
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1063 / CC1/2: 0.67 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.53 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 42.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3175 748 5.11 %
Rwork0.2585 --
obs0.2618 14643 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→45.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 44 14 1899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081916
X-RAY DIFFRACTIONf_angle_d1.0922607
X-RAY DIFFRACTIONf_dihedral_angle_d19.713696
X-RAY DIFFRACTIONf_chiral_restr0.056295
X-RAY DIFFRACTIONf_plane_restr0.009329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.41821490.40772721X-RAY DIFFRACTION100
2.48-2.730.41011290.36092766X-RAY DIFFRACTION100
2.73-3.120.35061490.34492751X-RAY DIFFRACTION100
3.12-3.930.37941650.28312754X-RAY DIFFRACTION100
3.93-45.530.26661560.21012903X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.3091 Å / Origin y: -16.8622 Å / Origin z: -8.4739 Å
111213212223313233
T0.8717 Å20.0799 Å20.2369 Å2-0.7097 Å2-0.0075 Å2--0.5556 Å2
L0.229 °2-0.3911 °21.2749 °2-1.5175 °2-2.1051 °2--0.4921 °2
S0.1458 Å °0.1206 Å °-0.0362 Å °-0.0001 Å °0.1072 Å °0.1036 Å °-0.5812 Å °-0.3628 Å °0.0013 Å °
Refinement TLS groupSelection details: all

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