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- PDB-2gcp: Crystal structure of the human RhoC-GSP complex -

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Basic information

Entry
Database: PDB / ID: 2gcp
TitleCrystal structure of the human RhoC-GSP complex
ComponentsRho-related GTP-binding protein RhoC
KeywordsSIGNALING PROTEIN / GTP-binding protein / GTPase
Function / homology
Function and homology information


positive regulation of lipase activity / skeletal muscle satellite cell migration / RHO GTPases Activate Rhotekin and Rhophilins / stereocilium / apical junction assembly / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / wound healing, spreading of cells / small GTPase-mediated signal transduction ...positive regulation of lipase activity / skeletal muscle satellite cell migration / RHO GTPases Activate Rhotekin and Rhophilins / stereocilium / apical junction assembly / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / wound healing, spreading of cells / small GTPase-mediated signal transduction / RHOC GTPase cycle / cleavage furrow / mitotic cytokinesis / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / actin filament organization / RHO GTPases Activate Formins / positive regulation of protein-containing complex assembly / G alpha (12/13) signalling events / positive regulation of canonical NF-kappaB signal transduction / neuron projection / positive regulation of cell migration / GTPase activity / GTP binding / endoplasmic reticulum membrane / protein kinase 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 / P-loop containing nucleoside triphosphate hydrolase ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Rho-related GTP-binding protein RhoC
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDias, S.M.G. / Cerione, R.A.
CitationJournal: Biochemistry / Year: 2007
Title: X-ray Crystal Structures Reveal Two Activated States for RhoC.
Authors: Dias, S.M.G. / Cerione, R.A.
History
DepositionMar 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 31, 2011Group: Source and taxonomy
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,4617
Polymers22,7251
Non-polymers7366
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.435, 59.435, 138.090
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-related GTP-binding protein RhoC / Rho cDNA clone 9 / h9


Mass: 22724.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARH9, ARHC, RHOC / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) RP / References: UniProt: P08134
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 3M Sodium Chloride, 0.1M Sodium Acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→54.593 Å / Num. all: 14207 / Num. obs: 14205 / % possible obs: 100 % / Observed criterion σ(F): 3.8 / Observed criterion σ(I): 3.8 / Redundancy: 11.8 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 6.1
Reflection shellResolution: 2.15→2.27 Å / % possible obs: 100 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 1.3 / Num. measured all: 24100 / Num. unique obs: 2019 / Rsym value: 0.583 / % possible all: 100

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Phasing

Phasing MRRfactor: 0.332 / Cor.coef. Fo:Fc: 0.729
Highest resolutionLowest resolution
Rotation3 Å27.3 Å
Translation3 Å27.3 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1z2c

1z2c


Resolution: 2.15→54.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.922 / SU B: 6.787 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 3.8 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 710 5 %RANDOM
Rwork0.159 ---
obs0.16229 14152 99.92 %-
all-14205 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.992 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.15→54.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 43 157 1620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221517
X-RAY DIFFRACTIONr_angle_refined_deg1.7332.0042062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0345187
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97624.50771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28315272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1981511
X-RAY DIFFRACTIONr_chiral_restr0.1250.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021135
X-RAY DIFFRACTIONr_nbd_refined0.2060.2710
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21005
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.212
X-RAY DIFFRACTIONr_mcbond_it1.1831.5946
X-RAY DIFFRACTIONr_mcangle_it1.89121476
X-RAY DIFFRACTIONr_scbond_it2.9573669
X-RAY DIFFRACTIONr_scangle_it4.4244.5581
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 57 -
Rwork0.188 967 -
obs-1024 100 %
Refinement TLS params.Method: refined / Origin x: 6.902 Å / Origin y: 17.153 Å / Origin z: 15.37 Å
111213212223313233
T0.0143 Å20.0004 Å20.0021 Å2-0.0206 Å20.0006 Å2---0.0502 Å2
L0.3336 °2-0.0469 °2-0.0383 °2-0.0939 °20.0519 °2--0.2314 °2
S0.0136 Å °0.0022 Å °0.0005 Å °-0.0018 Å °-0.0127 Å °-0.0007 Å °-0.0018 Å °0.0052 Å °-0.0009 Å °
Refinement TLS groupSelection: ALL

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