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- PDB-9t3f: RACB with GSP and the fragment of RIPb protein bound (parallel) -

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Basic information

Entry
Database: PDB / ID: 9t3f
TitleRACB with GSP and the fragment of RIPb protein bound (parallel)
Components
  • RACB protein
  • RIPb from Hordeum vulgare
KeywordsPLANT PROTEIN / RACB / Hordeum vulgare / GSP / RIPb
Function / homology
Function and homology information


small GTPase-mediated signal transduction / small monomeric GTPase / GTPase activity / GTP binding / plasma membrane / cytoplasm
Similarity search - Function
Interactor of constitutive active ROPs / : / Interactor of constitutive active ROPs 5 C-terminal domain / 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 ...Interactor of constitutive active ROPs / : / Interactor of constitutive active ROPs 5 C-terminal domain / 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 / small monomeric GTPase
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 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 from Hordeum vulgare
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6034
Polymers25,0402
Non-polymers5642
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-27 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.000, 64.000, 243.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-323-

HOH

21A-347-

HOH

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Components

#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/peptide RIPb from Hordeum vulgare


Mass: 3230.571 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
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % w/v PEG 6,000, 100 mM HEPES pH 7.0, 200 mM Sodium Chloride

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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: 2.07→50 Å / Num. obs: 18023 / % possible obs: 99.9 % / Redundancy: 19.1 % / CC1/2: 0.999 / Net I/σ(I): 24.5
Reflection shellResolution: 2.07→2.12 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1279 / CC1/2: 0.637 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→45.8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 11.2 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24691 949 5 %RANDOM
Rwork0.20548 ---
obs0.20752 18023 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.415 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0.6 Å2-0 Å2
2---1.21 Å2-0 Å2
3---3.91 Å2
Refinement stepCycle: 1 / Resolution: 2.07→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1604 0 33 51 1688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121683
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161600
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.8182296
X-RAY DIFFRACTIONr_angle_other_deg0.5671.7573679
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0355208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.901510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89610271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02381
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0854.395835
X-RAY DIFFRACTIONr_mcbond_other4.0874.392834
X-RAY DIFFRACTIONr_mcangle_it5.7127.8491042
X-RAY DIFFRACTIONr_mcangle_other5.717.8521043
X-RAY DIFFRACTIONr_scbond_it4.6534.822848
X-RAY DIFFRACTIONr_scbond_other4.654.824849
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0448.6461255
X-RAY DIFFRACTIONr_long_range_B_refined9.57540.771895
X-RAY DIFFRACTIONr_long_range_B_other9.5840.751892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.124 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 67 -
Rwork0.329 1279 -
obs--99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.21631.32271.34262.58360.76451.7591-0.21160.18620.5607-0.3711-0.07240.2159-0.53930.050.2840.4114-0.0122-0.03490.02290.03230.11315.71916.1575-0.6091
23.92583.28422.11993.24512.59082.69530.4303-0.6778-0.25360.3908-0.5264-0.0640.5438-0.3620.09610.383-0.189-0.0390.33310.09450.06754.02212.562816.0663
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 201
2X-RAY DIFFRACTION2B525 - 554

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