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- PDB-1gwn: The crystal structure of the core domain of RhoE/Rnd3 - a constit... -

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Basic information

Entry
Database: PDB / ID: 1gwn
TitleThe crystal structure of the core domain of RhoE/Rnd3 - a constitutively activated small G protein
ComponentsRho-related GTP-binding protein RhoE
KeywordsGTPASE / INACTIVE GTPASE / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


RND3 GTPase cycle / small GTPase-mediated signal transduction / Golgi membrane / GTPase activity / GTP binding
Similarity search - Function
Rho-related GTP-binding protein RhoE / Small GTPase Rho / Small GTPase Rho domain 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 ...Rho-related GTP-binding protein RhoE / Small GTPase Rho / Small GTPase Rho domain 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'-TRIPHOSPHATE / Rho-related GTP-binding protein RhoE
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGaravini, H. / Riento, K. / Phelan, J.P. / McAlister, M.S.B. / Ridley, A.J. / Keep, N.H.
CitationJournal: Biochemistry / Year: 2002
Title: Crystal Structure of the Core Domain of Rhoe/Rnd3: A Constitutively Activated Small G Protein
Authors: Garavini, H. / Riento, K. / Phelan, J.P. / McAlister, M.S.B. / Ridley, A.J. / Keep, N.H.
History
DepositionMar 19, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2002Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation_author.name / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type
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 / pdbx_struct_conn_angle / 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 / _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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 RhoE
C: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8206
Polymers45,7252
Non-polymers1,0954
Water3,549197
1
A: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4103
Polymers22,8631
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: Rho-related GTP-binding protein RhoE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4103
Polymers22,8631
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.454, 59.454, 233.024
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.978372, -0.026484, 0.205153), (-0.01144, -0.999393, -0.027627), (0.20576, 0.022671, -0.978339)
Vector: -6.938, 113.0113, 72.5454)

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Components

#1: Protein Rho-related GTP-binding protein RhoE / Rho family GTPase 3 / Rnd3


Mass: 22862.746 Da / Num. of mol.: 2 / Fragment: CORE DOMAIN, RESIDUES 16-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rnd3, Arhe, Rhoe / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61588
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES 1-15 AND 201 ONWARDS HAVE BEEN DELETED. THE N-TERMINUS INCLUDES AN UNCLEAVED HIS-TAG.

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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: 2.25 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5 / Details: 0.1M HEPES PH 7.5, 10% PROPAN-2-OL, 20% PEG 4000
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
20.1 MHEPES1reservoirpH7.5
310 %propanol-di-ol1reservoir
420 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→18.8 Å / Num. obs: 25276 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
Num. measured all: 115552
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 3592 / Num. measured obs: 15240 / Mean I/σ(I) obs: 3.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CXZ CHAIN A

1cxz


Resolution: 2.1→18.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.871 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ELECTRON DENSITY IN THE REGION OF RESIDUE 23 IS AMBIGUOUS AND THE CIS-CONFORMATION OF LYS23 MAY BE DUE TO THE POOR DEFINITION OF THE ENCLOSING DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1260 4.9 %RANDOM
Rwork0.183 ---
obs0.185 24265 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.1→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 66 197 3043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0212933
X-RAY DIFFRACTIONr_bond_other_d0.0010.022536
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.9281.984013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.90635941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1370.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023219
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02557
X-RAY DIFFRACTIONr_nbd_refined0.2410.3728
X-RAY DIFFRACTIONr_nbd_other0.2120.32622
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.5239
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.37703
X-RAY DIFFRACTIONr_metal_ion_refined0.06201
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.320
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.352
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9651.51799
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.79322935
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.91131134
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6664.51078
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.254 81
Rwork0.218 1758
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)
11.2102-0.1609-0.19793.32541.04672.4926-0.1093-0.0587-0.01350.30190.07990.07360.1908-0.030.02940.1959-0.01550.0220.00630.02960.197734.57247.1451.517
21.3152-0.14460.15282.2910.40772.3641-0.0234-0.1628-0.0211-0.11480.0313-0.00770.0023-0.1093-0.00790.072-0.0028-0.00530.01990.03950.21146.70522.83930.348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 200
2X-RAY DIFFRACTION2C23 - 200
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 22.3 Å / Rfactor obs: 0.183 / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.92
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.15 Å / Rfactor obs: 0.218

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