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- PDB-2fv8: The crystal structure of RhoB in the GDP-bound state -

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Basic information

Entry
Database: PDB / ID: 2fv8
TitleThe crystal structure of RhoB in the GDP-bound state
ComponentsRho-related GTP-binding protein RhoB
KeywordsSIGNALING PROTEIN / RHOB / GDP/GTP binding / GTP hydrolysis / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


RHO GTPases Activate Rhotekin and Rhophilins / endothelial tube morphogenesis / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / endosome to lysosome transport / cleavage furrow / mitotic cytokinesis ...RHO GTPases Activate Rhotekin and Rhophilins / endothelial tube morphogenesis / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHOB GTPase cycle / endosome to lysosome transport / cleavage furrow / mitotic cytokinesis / negative regulation of cell cycle / Rho protein signal transduction / RHO GTPases activate PKNs / GPVI-mediated activation cascade / positive regulation of endothelial cell migration / regulation of cell migration / negative regulation of cell migration / actin filament organization / cellular response to ionizing radiation / intracellular protein transport / RHO GTPases Activate Formins / Schaffer collateral - CA1 synapse / cellular response to hydrogen peroxide / positive regulation of angiogenesis / GDP binding / late endosome membrane / G alpha (12/13) signalling events / angiogenesis / cell differentiation / early endosome / cell adhesion / endosome membrane / positive regulation of apoptotic process / focal adhesion / GTPase activity / apoptotic process / GTP binding / signal transduction / extracellular exosome / nucleus / plasma membrane / cytosol
Similarity search - Function
Small GTPase Rho / small GTPase Rho family 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 nucleotide triphosphate hydrolases / Rossmann fold ...Small GTPase Rho / small GTPase Rho family 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Rho-related GTP-binding protein RhoB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTurnbull, A.P. / Soundararajan, M. / Smee, C. / Johansson, C. / Schoch, G. / Gorrec, F. / Bray, J. / Papagrigoriou, E. / von Delft, F. / Weigelt, J. ...Turnbull, A.P. / Soundararajan, M. / Smee, C. / Johansson, C. / Schoch, G. / Gorrec, F. / Bray, J. / Papagrigoriou, E. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of RhoB in the GDP-bound state
Authors: Turnbull, A.P. / Soundararajan, M. / Smee, C. / Johansson, C. / Schoch, G. / Gorrec, F. / Bray, J. / Papagrigoriou, E. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D.
History
DepositionJan 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho-related GTP-binding protein RhoB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0762
Polymers23,6331
Non-polymers4431
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.519, 42.233, 33.850
Angle α, β, γ (deg.)90.00, 90.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rho-related GTP-binding protein RhoB / H6


Mass: 23632.775 Da / Num. of mol.: 1 / Fragment: residues 4-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOB, ARH6, ARHB / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)R3 / References: UniProt: P62745
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 30 % PEG 3350, 0.075M ammonium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 14890 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 %
Reflection shellResolution: 1.9→1.97 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swissmodel

Resolution: 1.9→34.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.437 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25324 758 5.1 %RANDOM
Rwork0.21033 ---
all0.21249 14125 --
obs0.21249 14125 96.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.511 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.2 Å2
2--2.37 Å20 Å2
3----2.64 Å2
Refinement stepCycle: LAST / Resolution: 1.9→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 28 112 1527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221440
X-RAY DIFFRACTIONr_bond_other_d0.0020.02963
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9961959
X-RAY DIFFRACTIONr_angle_other_deg0.97632346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.324.12763
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65415236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8831511
X-RAY DIFFRACTIONr_chiral_restr0.090.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02284
X-RAY DIFFRACTIONr_nbd_refined0.2150.2285
X-RAY DIFFRACTIONr_nbd_other0.1970.2998
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2693
X-RAY DIFFRACTIONr_nbtor_other0.0840.2719
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6351.5936
X-RAY DIFFRACTIONr_mcbond_other0.1331.5358
X-RAY DIFFRACTIONr_mcangle_it0.95121447
X-RAY DIFFRACTIONr_scbond_it1.4813601
X-RAY DIFFRACTIONr_scangle_it2.1644.5512
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 41 -
Rwork0.428 961 -
obs--88.44 %
Refinement TLS params.Method: refined / Origin x: 47.9339 Å / Origin y: 37.095 Å / Origin z: 8.3375 Å
111213212223313233
T-0.1429 Å2-0.0209 Å2-0.0011 Å2--0.1278 Å2-0.0415 Å2---0.1547 Å2
L2.3366 °2-0.2866 °2-0.0671 °2-1.7019 °2-0.1192 °2--4.6392 °2
S0.0123 Å °0.0527 Å °-0.1224 Å °0.0298 Å °0.0409 Å °-0.0402 Å °-0.1095 Å °0.6224 Å °-0.0532 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-4 - 019 - 23
2X-RAY DIFFRACTION1AA4 - 3124 - 51
3X-RAY DIFFRACTION1AA39 - 18559 - 205

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