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- PDB-2gco: Crystal structure of the human RhoC-GppNHp complex -

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Basic information

Entry
Database: PDB / ID: 2gco
TitleCrystal structure of the human RhoC-GppNHp complex
Components(Rho-related GTP-binding protein RhoC) x 2
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 / regulation of actin cytoskeleton organization / positive regulation of protein-containing complex assembly / G alpha (12/13) signalling events / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / GTPase activity / endoplasmic reticulum membrane / GTP binding / 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Rho-related GTP-binding protein RhoC
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 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.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,5596
Polymers45,4662
Non-polymers1,0934
Water9,044502
1
A: Rho-related GTP-binding protein RhoC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2873
Polymers22,7411
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rho-related GTP-binding protein RhoC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2713
Polymers22,7251
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.092, 75.645, 82.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1068-

HOH

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Components

#1: Protein Rho-related GTP-binding protein RhoC / H9


Mass: 22740.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residue 107 in this chain is modified to S-OXY CYSTEINE
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOC, ARH9, ARHC / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) RP / References: UniProt: P08134
#2: Protein Rho-related GTP-binding protein RhoC / H9


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 30% PEG 8000, 0.2M Sodium Acetate,1.2% Inositol, 0.1M Sodium Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.4→82.903 Å / Num. all: 77234 / Num. obs: 75377 / % possible obs: 95 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 4.3
Reflection shellResolution: 1.4→1.48 Å / % possible obs: 96.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 1.2 / Num. measured all: 52822 / Num. unique obs: 11027 / Rsym value: 0.508 / % possible all: 95

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Phasing

Phasing MRRfactor: 0.521 / Cor.coef. Fo:Fc: 0.552
Highest resolutionLowest resolution
Rotation3 Å30.32 Å
Translation3 Å30.32 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: 1.4→8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.871 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3768 5 %RANDOM
Rwork0.197 ---
all0.198 ---
obs0.19804 75014 94.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.087 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 66 502 3503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223144
X-RAY DIFFRACTIONr_angle_refined_deg1.3624283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1285392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99623.973146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7215563
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3181526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022358
X-RAY DIFFRACTIONr_nbd_refined0.2040.21640
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22138
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2469
X-RAY DIFFRACTIONr_metal_ion_refined0.040.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.248
X-RAY DIFFRACTIONr_mcbond_it0.6951.51937
X-RAY DIFFRACTIONr_mcangle_it1.10123078
X-RAY DIFFRACTIONr_scbond_it1.62631360
X-RAY DIFFRACTIONr_scangle_it2.4114.51191
LS refinement shellResolution: 1.4→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 276 -
Rwork0.27 5139 -
obs-5415 95.47 %
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)
10.5196-0.1407-0.01560.44310.08241.48330.0072-0.0242-0.0491-0.00170.02620.00150.0508-0.068-0.0335-0.0398-0.00660.0032-0.01370.0108-0.023215.827-6.37230.946
20.50990.0430.28460.42180.0051.41020.0102-0.01170.03430.02890.0206-0.0018-0.0443-0.0696-0.0309-0.03910.0048-0.0012-0.0160.0061-0.018815.82221.96510.274
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 18022 - 200
21AA-12 - -48 - 16
32BB4 - 18024 - 200
42BB-11 - -49 - 16

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