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- PDB-2j1l: Crystal Structure of Human Rho-related GTP-binding protein RhoD -

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Basic information

Entry
Database: PDB / ID: 2j1l
TitleCrystal Structure of Human Rho-related GTP-binding protein RhoD
ComponentsRHO-RELATED GTP-BINDING PROTEIN RHOD
KeywordsHYDROLASE / GTPASE / MEMBRANE / GTP-BINDING / PRENYLATION / NUCLEOTIDE-BINDING / METHYLATION / LIPOPROTEIN / ENDOSOME DYNAMICS
Function / homology
Function and homology information


focal adhesion assembly / RHOD GTPase cycle / regulation of small GTPase mediated signal transduction / lamellipodium assembly / actin filament bundle assembly / Rho protein signal transduction / positive regulation of cell adhesion / guanyl-nucleotide exchange factor activity / actin filament organization / RHO GTPases Activate Formins ...focal adhesion assembly / RHOD GTPase cycle / regulation of small GTPase mediated signal transduction / lamellipodium assembly / actin filament bundle assembly / Rho protein signal transduction / positive regulation of cell adhesion / guanyl-nucleotide exchange factor activity / actin filament organization / RHO GTPases Activate Formins / cell migration / mitochondrial outer membrane / early endosome / endosome membrane / positive regulation of cell migration / Golgi membrane / GTPase activity / GTP binding / protein kinase binding / signal transduction / plasma membrane / cytosol
Similarity search - Function
Small GTPase Rho / small GTPase Rho family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 ...Small GTPase Rho / small GTPase Rho family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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
GUANOSINE-5'-DIPHOSPHATE / Rho-related GTP-binding protein RhoD
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPike, A.C.W. / Johansson, C. / Gileadi, C. / Niesen, F.H. / Sobott, F. / Schoch, G. / Elkins, J. / Smee, C. / Gorrec, F. / Watt, S. ...Pike, A.C.W. / Johansson, C. / Gileadi, C. / Niesen, F.H. / Sobott, F. / Schoch, G. / Elkins, J. / Smee, C. / Gorrec, F. / Watt, S. / Bray, J. / Turnbull, A.P. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Doyle, D.
CitationJournal: To be Published
Title: Crystal Structure of Human Rho-Related GTP-Binding Protein Rhod
Authors: Pike, A.C.W. / Johansson, C. / Gileadi, C. / Niesen, F.H. / Sobott, F. / Schoch, G. / Elkins, J. / Smee, C. / Gorrec, F. / Watt, S. / Bray, J. / Turnbull, A.P. / von Delft, F. / Arrowsmith, ...Authors: Pike, A.C.W. / Johansson, C. / Gileadi, C. / Niesen, F.H. / Sobott, F. / Schoch, G. / Elkins, J. / Smee, C. / Gorrec, F. / Watt, S. / Bray, J. / Turnbull, A.P. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Doyle, D.
History
DepositionAug 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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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 RHOD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4843
Polymers24,0161
Non-polymers4682
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.811, 66.810, 103.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein RHO-RELATED GTP-BINDING PROTEIN RHOD / RHO-RELATED PROTEIN HP1 / RHOHP1 / RHOD


Mass: 24016.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MGC / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00212, small monomeric GTPase
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.79 Å3/Da / Density % sol: 56 %
Crystal growpH: 6
Details: 19% PEG6K, 0.4M NH4CL, 15% ETG, 0.05M MES PH6.0, pH 6.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: May 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50.6 Å / Num. obs: 9805 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 82.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.8
Reflection shellResolution: 2.5→2.62 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MH1

1mh1


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 17.082 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ELECTRON DENSITY SUGGESTS HIGH LIKELIHOOD OF A DOMAIN SWAP. IN THE CRYSTAL, THE AMINO TERMINAL RESIDUES 15- 39 APPEAR TO BE EXCHANGED WITH ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ELECTRON DENSITY SUGGESTS HIGH LIKELIHOOD OF A DOMAIN SWAP. IN THE CRYSTAL, THE AMINO TERMINAL RESIDUES 15- 39 APPEAR TO BE EXCHANGED WITH AN ADJACENT MOLECULE. HOWEVER THE INTERVENING 'SWITCH 1' REGION BETWEEN RESIDUES 39 AND 47 IS DISORDERED. CONSEQUENTLY THE COMPACT FORM OF THE MOLECULE IS PRESENTED IN THIS ENTRY AS THE DOMAIN SWAP CANNOT BE CONFIRMED UNAMBIGUOUSLY. MASS SPECTROMETRIC ANALYSIS OF THE CRYSTALS CONFIRM THAT THE MOLECULE IS INTACT.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 467 4.8 %RANDOM
Rwork0.217 ---
obs0.219 9279 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.5 Å21.75 Å20 Å2
2--3.5 Å20 Å2
3----5.25 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 29 8 1197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211214
X-RAY DIFFRACTIONr_bond_other_d0.0020.02757
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9671659
X-RAY DIFFRACTIONr_angle_other_deg0.89431847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3895154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85623.61747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43115171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.31156
X-RAY DIFFRACTIONr_chiral_restr0.0740.2195
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021350
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02246
X-RAY DIFFRACTIONr_nbd_refined0.230.2231
X-RAY DIFFRACTIONr_nbd_other0.1850.2728
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2580
X-RAY DIFFRACTIONr_nbtor_other0.0860.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0970.212
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4991.5792
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92321244
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3533487
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1284.5415
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.438 41
Rwork0.384 676
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)
111.46990.62572.00256.63-1.3859.17970.06950.48110.6235-0.0719-0.09390.3939-0.7586-0.77040.0244-0.0130.01670.1196-0.07640.042-0.0881-38.287124.4599-5.4356
26.5086-0.76042.05414.5666-1.522610.52210.25880.0513-0.25140.3723-0.2599-0.01770.08280.01490.00110.0098-0.02670.057-0.11210.0431-0.1551-33.192718.7363-1.2702
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 39
2X-RAY DIFFRACTION2A47 - 193

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