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- PDB-2cls: The crystal structure of the human RND1 GTPase in the active GTP ... -

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Basic information

Entry
Database: PDB / ID: 2cls
TitleThe crystal structure of the human RND1 GTPase in the active GTP bound state
ComponentsRHO-RELATED GTP-BINDING PROTEIN RHO6
KeywordsNUCLEOTIDE BINDING PROTEIN / NUCLEOTIDE-BINDING / GTP-BINDING PROTEIN RHO6 / MEMBRANE / PRENYLATION / LIPOPROTEIN / GTP-BINDING / CYTOSKELETON / SMALL GTPASE
Function / homology
Function and homology information


SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / negative regulation of cell adhesion / Sema4D induced cell migration and growth-cone collapse / Sema4D mediated inhibition of cell attachment and migration / RND1 GTPase cycle / small GTPase-mediated signal transduction / neuron remodeling / actin filament organization / adherens junction / regulation of actin cytoskeleton organization ...SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / negative regulation of cell adhesion / Sema4D induced cell migration and growth-cone collapse / Sema4D mediated inhibition of cell attachment and migration / RND1 GTPase cycle / small GTPase-mediated signal transduction / neuron remodeling / actin filament organization / adherens junction / regulation of actin cytoskeleton organization / actin cytoskeleton / signaling receptor binding / intracellular membrane-bounded organelle / GTPase activity / protein kinase binding / GTP binding / signal transduction / plasma membrane / cytosol
Similarity search - Function
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 ...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 Rho6
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsPike, A.C.W. / Yang, X. / Colebrook, S. / Gileadi, O. / Sobott, F. / Bray, J. / Wen Hwa, L. / Marsden, B. / Zhao, Y. / Schoch, G. ...Pike, A.C.W. / Yang, X. / Colebrook, S. / Gileadi, O. / Sobott, F. / Bray, J. / Wen Hwa, L. / Marsden, B. / Zhao, Y. / Schoch, G. / Elkins, J. / Debreczeni, J.E. / Turnbull, A.P. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Doyle, D.
CitationJournal: To be Published
Title: The Crystal Structure of the Human Rnd1 Gtpase in the Active GTP Bound State
Authors: Pike, A.C.W. / Yang, X. / Colebrook, S. / Gileadi, O. / Sobott, F. / Bray, J. / Wen Hwa, L. / Marsden, B. / Zhao, Y. / Schoch, G. / Elkins, J. / Debreczeni, J.E. / Turnbull, A.P. / von ...Authors: Pike, A.C.W. / Yang, X. / Colebrook, S. / Gileadi, O. / Sobott, F. / Bray, J. / Wen Hwa, L. / Marsden, B. / Zhao, Y. / Schoch, G. / Elkins, J. / Debreczeni, J.E. / Turnbull, A.P. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / Sundstrom, M. / Doyle, D.
History
DepositionApr 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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 RHO6
B: RHO-RELATED GTP-BINDING PROTEIN RHO6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3106
Polymers44,2152
Non-polymers1,0954
Water2,324129
1
A: RHO-RELATED GTP-BINDING PROTEIN RHO6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6553
Polymers22,1071
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RHO-RELATED GTP-BINDING PROTEIN RHO6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6553
Polymers22,1071
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.168, 67.762, 206.409
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-2038-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CYSCYSLEULEUAA14 - 5412 - 52
21CYSCYSLEULEUBB14 - 5412 - 52
12GLUGLUSERSERAA62 - 9560 - 93
22GLUGLUSERSERBB62 - 9560 - 93
13LYSLYSCYSCYSAA105 - 187103 - 185
23LYSLYSCYSCYSBB105 - 187103 - 185

NCS oper: (Code: given
Matrix: (0.002, -1, -0.001), (-0.999, -0.002, 0.039), (-0.039, -0.999)
Vector: -0.25917, -4.62606, 51.9663)

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Components

#1: Protein RHO-RELATED GTP-BINDING PROTEIN RHO6 / RHO FAMILY GTPASE 1 / RND1


Mass: 22107.387 Da / Num. of mol.: 2 / Fragment: RESIDUES 5-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION(MGC) / Plasmid: PLIC-SGC1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92730
#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.: 129 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONTROL REARRANGEMENTS OF THE ACTIN CYTOSKELETON

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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: 2.66 Å3/Da / Density % sol: 54 %
Crystal growpH: 8.5
Details: 0.2M NAI, 20%(W/V)PEG3350, 0.1M BISTRISPROPANE PH8.5, 10% (V/V) ETHYLENE GLYCOL, 0.5% (V/V) DIMETHYLSULPHOXIDE, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 20279 / % possible obs: 95.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 7 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M7B

1m7b


Resolution: 2.31→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 10.588 / SU ML: 0.151 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1021 5 %RANDOM
Rwork0.205 ---
obs0.207 19213 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2--2.39 Å20 Å2
3----3.65 Å2
Refinement stepCycle: LAST / Resolution: 2.31→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2708 0 66 129 2903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222841
X-RAY DIFFRACTIONr_bond_other_d0.0030.021823
X-RAY DIFFRACTIONr_angle_refined_deg1.6012.0113881
X-RAY DIFFRACTIONr_angle_other_deg1.523.0014472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.71624.175103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.36915468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4261513
X-RAY DIFFRACTIONr_chiral_restr0.1280.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023076
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02535
X-RAY DIFFRACTIONr_nbd_refined0.2020.2554
X-RAY DIFFRACTIONr_nbd_other0.1960.21836
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21336
X-RAY DIFFRACTIONr_nbtor_other0.0920.21475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6091.51831
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03522881
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5631186
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3084.51000
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
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
933tight positional0.050.05
1068medium positional0.540.5
933tight thermal0.110.5
1068medium thermal0.52
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 84
Rwork0.23 1335
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)
12.56251.06831.22183.81562.53995.5587-0.0414-0.24280.03280.2786-0.13460.10210.0609-0.02810.176-0.2290.00390.011-0.15080.0031-0.15555.3687-24.391811.5976
23.3703-0.12071.82483.16380.3017.2812-0.13550.0236-0.0035-0.0462-0.00640.01360.13970.35030.142-0.0955-0.0315-0.045-0.10410.017-0.140824.1611-9.362240.2939
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 188
2X-RAY DIFFRACTION2B11 - 188

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