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- PDB-9x54: Crystal structure of RhoGDI2 in complex with Compound 3054b -

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Basic information

Entry
Database: PDB / ID: 9x54
TitleCrystal structure of RhoGDI2 in complex with Compound 3054b
ComponentsRho GDP-dissociation inhibitor 2
KeywordsSIGNALING PROTEIN / Inhibitor / Complex / Rho GDP-dissociation inhibitor 2
Function / homology
Function and homology information


cellular response to redox state / Rho GDP-dissociation inhibitor activity / negative regulation of trophoblast cell migration / regulation of Rho protein signal transduction / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / Rho protein signal transduction ...cellular response to redox state / Rho GDP-dissociation inhibitor activity / negative regulation of trophoblast cell migration / regulation of Rho protein signal transduction / CDC42 GTPase cycle / RHOH GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / Rho protein signal transduction / RAC1 GTPase cycle / GTPase activator activity / small GTPase binding / cytoplasmic vesicle / cytoskeleton / GTPase activity / extracellular exosome / membrane / cytoplasm / cytosol
Similarity search - Function
Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Immunoglobulin E-set
Similarity search - Domain/homology
: / Rho GDP-dissociation inhibitor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsLiu, M. / Ruan, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22377119 China
CitationJournal: Acs Chem.Biol. / Year: 2025
Title: Fragment-Based Discovery of a Small-Molecule RhoGDI2 Ligand, HR3119, that Inhibits Cancer Cell Migration.
Authors: Liu, M. / Wan, S. / Guo, S. / Liu, J. / Li, W. / Wang, L. / Li, F. / Zhang, J. / Liu, X. / Liu, D. / Yao, X. / Gao, J. / Ruan, K. / He, W.
History
DepositionOct 12, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho GDP-dissociation inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7624
Polymers16,1581
Non-polymers6043
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-1 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.313, 55.313, 95.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Rho GDP-dissociation inhibitor 2 / Rho GDI 2 / Ly-GDI / Rho-GDI beta


Mass: 16158.364 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGDIB, GDIA2, GDID4, RAP1GN1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P52566
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-A1EY5 / (3~{R})-~{N}-[2-oxidanylidene-2-[[(~{R})-(4-phenylphenyl)-thiophen-2-yl-methyl]amino]ethyl]pyrrolidine-3-carboxamide


Mass: 419.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C24H25N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 8604 / % possible obs: 97.5 % / Redundancy: 24.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.09 / Net I/σ(I): 39.1
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 20.4 % / Rmerge(I) obs: 0.732 / Num. unique obs: 411 / CC1/2: 0.948 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(1.19rc3_4028: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→36.18 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 418 4.87 %
Rwork0.1926 --
obs0.1946 8576 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 42 36 1181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081173
X-RAY DIFFRACTIONf_angle_d0.9261586
X-RAY DIFFRACTIONf_dihedral_angle_d9.372159
X-RAY DIFFRACTIONf_chiral_restr0.062172
X-RAY DIFFRACTIONf_plane_restr0.007198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.440.31531360.23882638X-RAY DIFFRACTION98
2.44-3.070.3111430.25132681X-RAY DIFFRACTION98
3.07-36.180.19261390.16792839X-RAY DIFFRACTION98
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)
14.68450.01720.1785.6413-3.80934.89530.0731-0.06530.04540.08680.30940.59860.0527-0.747-0.3360.2177-0.0438-0.03240.3955-0.03080.2699-13.455614.00331.6302
21.61721.2505-0.91333.9354-2.6945.06020.01690.0811-0.0606-0.16540.07560.07550.1694-0.1762-0.10160.230.03220.00770.294-0.02780.3059-5.158313.89235.5516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 64 through 96 )
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 201 )

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