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- PDB-2q3h: The crystal structure of RhouA in the GDP-bound state. -

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Basic information

Entry
Database: PDB / ID: 2q3h
TitleThe crystal structure of RhouA in the GDP-bound state.
ComponentsRas homolog gene family, member U
KeywordsSTRUCTURAL GENOMICS / GTPase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / Cdc42 protein signal transduction / cell projection assembly / podosome / regulation of small GTPase mediated signal transduction / positive regulation of protein targeting to mitochondrion / Rac protein signal transduction / cytoskeleton organization / cell projection / G1/S transition of mitotic cell cycle ...: / Cdc42 protein signal transduction / cell projection assembly / podosome / regulation of small GTPase mediated signal transduction / positive regulation of protein targeting to mitochondrion / Rac protein signal transduction / cytoskeleton organization / cell projection / G1/S transition of mitotic cell cycle / endocytosis / cytokine-mediated signaling pathway / cell migration / regulation of cell shape / actin cytoskeleton organization / Interleukin-4 and Interleukin-13 signaling / Golgi membrane / focal adhesion / GTPase activity / GTP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Small GTPase Rho / small GTPase Rho family profile. / Small GTPase / Ras family / 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
GUANOSINE-5'-DIPHOSPHATE / Rho-related GTP-binding protein RhoU / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsGileadi, C. / Yang, X. / Papagrigoriou, E. / Elkins, J. / Zhao, Y. / Bray, J. / Gileadi, O. / Umeano, C. / Ugochukwu, E. / Uppenberg, J. ...Gileadi, C. / Yang, X. / Papagrigoriou, E. / Elkins, J. / Zhao, Y. / Bray, J. / Gileadi, O. / Umeano, C. / Ugochukwu, E. / Uppenberg, J. / Bunkoczi, G. / von Delft, F. / Pike, A.C.W. / Phillips, C. / Savitsky, P. / Fedorov, O. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The crystal structure of RhouA in the GDP-bound state.
Authors: Gileadi, C. / Yang, X. / Papagrigoriou, E. / Elkins, J. / Zhao, Y. / Bray, J. / Gileadi, O. / Umeano, C. / Ugochukwu, E. / Uppenberg, J. / Bunkoczi, G. / von Delft, F. / Pike, A.C.W. / ...Authors: Gileadi, C. / Yang, X. / Papagrigoriou, E. / Elkins, J. / Zhao, Y. / Bray, J. / Gileadi, O. / Umeano, C. / Ugochukwu, E. / Uppenberg, J. / Bunkoczi, G. / von Delft, F. / Pike, A.C.W. / Phillips, C. / Savitsky, P. / Fedorov, O. / Edwards, A. / Weigelt, J. / Arrowsmith, C.H. / Sundstrom, M. / Doyle, D.A.
History
DepositionMay 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 3, 2024Group: 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.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: Ras homolog gene family, member U
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1543
Polymers21,6871
Non-polymers4682
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.068, 53.600, 54.128
Angle α, β, γ (deg.)90.00, 118.80, 90.00
Int Tables number5
Space group name H-MC121
Detailsthe monomer in the asu represents a biological unit

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Components

#1: Protein Ras homolog gene family, member U / Ras-like gene family member U / Wrch-1 / Ryu GTPase / CDC42-like GTPase / Rho GTPase-like protein ...Ras-like gene family member U / Wrch-1 / Ryu GTPase / CDC42-like GTPase / Rho GTPase-like protein ARHU / GTP-binding protein like 1


Mass: 21686.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOU / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3) with with pRARE plasmid encoding rare codon tRNAs,(chloramphenicol-resistant)
References: UniProt: Q9NPY5, UniProt: Q7L0Q8*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


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


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M MgCl2; 0.1M TRIS; 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.03315 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2007 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03315 Å / Relative weight: 1
ReflectionResolution: 1.73→47.46 Å / Num. all: 21616 / Num. obs: 21530 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.033 / Rsym value: 0.049
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Num. unique all: 2077 / Rsym value: 0.387 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology based model

Resolution: 1.73→47.46 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.621 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.101 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22198 1107 5.1 %RANDOM
Rwork0.18276 ---
all0.18276 21616 --
obs0.18474 20423 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.051 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å2-2.01 Å2
2--1.5 Å20 Å2
3----1.82 Å2
Refinement stepCycle: LAST / Resolution: 1.73→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 29 124 1429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221336
X-RAY DIFFRACTIONr_bond_other_d0.0030.02861
X-RAY DIFFRACTIONr_angle_refined_deg1.6862.0011828
X-RAY DIFFRACTIONr_angle_other_deg0.97732131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4765171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69925.30649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93415213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.968155
X-RAY DIFFRACTIONr_chiral_restr0.1020.2224
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
X-RAY DIFFRACTIONr_nbd_refined0.2280.2280
X-RAY DIFFRACTIONr_nbd_other0.1970.2913
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2669
X-RAY DIFFRACTIONr_nbtor_other0.0870.2682
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3350.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5330.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.423879
X-RAY DIFFRACTIONr_mcbond_other1.0453341
X-RAY DIFFRACTIONr_mcangle_it4.29951398
X-RAY DIFFRACTIONr_scbond_it6.7528521
X-RAY DIFFRACTIONr_scangle_it8.10611429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 84 -
Rwork0.238 1441 -
obs--97.13 %
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)
15.2441-4.0615-0.57199.68580.46152.17110.58620.6493-0.16-0.3367-0.55960.5989-0.2604-0.523-0.0266-0.16790.1276-0.0609-0.0132-0.0479-0.10449.0861-3.230314.6322
24.3903-3.4276-0.73494.98590.94442.66070.78730.9580.2871-0.8143-0.83360.1182-0.3171-0.42680.0463-0.04470.19770.01470.00130.0535-0.112214.28950.004110.8588
35.7783-1.6892-1.55866.9632-0.04124.99180.22590.62-0.5824-0.3066-0.2541-0.01710.62670.00640.0282-0.14130.0241-0.0693-0.2069-0.0543-0.118426.5595-18.647617.144
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA49 - 7120 - 42
2X-RAY DIFFRACTION2AA80 - 16351 - 134
3X-RAY DIFFRACTION2AA164 - 184135 - 155
4X-RAY DIFFRACTION3AA185 - 227156 - 198

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