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- PDB-2c2h: CRYSTAL STRUCTURE OF THE HUMAN RAC3 IN COMPLEX WITH GDP -

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Basic information

Entry
Database: PDB / ID: 2c2h
TitleCRYSTAL STRUCTURE OF THE HUMAN RAC3 IN COMPLEX WITH GDP
ComponentsRAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
KeywordsSIGNALING PROTEIN / GTPASE RAC3 / SMALL GTP BINDING PROTEIN / P21 RAC / RAS- RELATED C3 BUTULINUM TOXIN SUBSTRATE 3
Function / homology
Function and homology information


postsynaptic actin cytoskeleton organization / cerebral cortex GABAergic interneuron development / regulation of neutrophil migration / NADPH oxidase complex / regulation of neuron maturation / respiratory burst / cortical cytoskeleton organization / cell projection assembly / motor neuron axon guidance / PCP/CE pathway ...postsynaptic actin cytoskeleton organization / cerebral cortex GABAergic interneuron development / regulation of neutrophil migration / NADPH oxidase complex / regulation of neuron maturation / respiratory burst / cortical cytoskeleton organization / cell projection assembly / motor neuron axon guidance / PCP/CE pathway / positive regulation of cell adhesion mediated by integrin / establishment or maintenance of cell polarity / synaptic transmission, GABAergic / Rac protein signal transduction / filamentous actin / neuromuscular process controlling balance / regulation of postsynapse assembly / RAC3 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / endomembrane system / homeostasis of number of cells within a tissue / actin filament organization / small monomeric GTPase / cell periphery / cell chemotaxis / regulation of actin cytoskeleton organization / Wnt signaling pathway / calcium-dependent protein binding / lamellipodium / regulation of cell shape / G protein activity / actin cytoskeleton organization / growth cone / cytoplasmic vesicle / cytoskeleton / postsynapse / neuron projection / intracellular signal transduction / neuronal cell body / GTPase activity / endoplasmic reticulum membrane / protein kinase binding / GTP binding / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / 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'-DIPHOSPHATE / Ras-related C3 botulinum toxin substrate 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDebreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. ...Debreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / von Delft, F. / Doyle, D. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A.
CitationJournal: To be Published
Title: Crystal Structure of the Human Rac3 in Complex with Gdp
Authors: Debreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / von Delft, F. / Doyle, D. / Sundstrom, M. / ...Authors: Debreczeni, J.E. / Yang, X. / Zao, Y. / Elkins, J. / Gileadi, C. / Burgess, N. / Colebrook, S. / Gileadi, O. / Fedorov, O. / Bunkoczi, G. / von Delft, F. / Doyle, D. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A.
History
DepositionSep 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.3Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Dec 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
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,69532
Polymers42,7202
Non-polymers4,97630
Water2,990166
1
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,08117
Polymers21,3601
Non-polymers2,72216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,61415
Polymers21,3601
Non-polymers2,25414
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.320, 110.320, 81.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-1187-

CA

21B-1186-

CA

31A-2097-

HOH

41A-2104-

HOH

51A-2105-

HOH

61B-2057-

HOH

71B-2059-

HOH

81B-2060-

HOH

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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 3 - 177 / Label seq-ID: 3 - 177

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (0.16319, 0.9865, 0.0136), (0.98658, -0.16325, 0.00333), (0.00551, 0.01287, -0.9999)
Vector: 54.62536, -32.00429, 89.00022)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 3 / GTPASE RAC3 / P21-RAC3


Mass: 21359.770 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P60763

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Non-polymers , 5 types, 196 molecules

#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 178 TO GLY ENGINEERED RESIDUE IN CHAIN B, CYS 178 TO GLY

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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: 2.2 Å3/Da / Density % sol: 44.6 %
Crystal growpH: 7.5
Details: 30% MPD, 0.5 M AMMONIUM SULFATE, 0.1 M HEPES PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0038
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 3, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0038 Å / Relative weight: 1
ReflectionResolution: 1.85→27.07 Å / Num. obs: 28734 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.99
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.76 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G4U

1g4u


Resolution: 1.85→62.14 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.301 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1461 5.1 %RANDOM
Rwork0.194 ---
obs0.195 27267 90.5 %-
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: 23.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.85→62.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 289 166 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222917
X-RAY DIFFRACTIONr_bond_other_d0.0010.022538
X-RAY DIFFRACTIONr_angle_refined_deg1.7732.0934052
X-RAY DIFFRACTIONr_angle_other_deg0.8435859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.595344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.04723.54893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63515403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.6211513
X-RAY DIFFRACTIONr_chiral_restr0.0840.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
X-RAY DIFFRACTIONr_nbd_refined0.2230.2630
X-RAY DIFFRACTIONr_nbd_other0.1810.22607
X-RAY DIFFRACTIONr_nbtor_refined0.1960.21401
X-RAY DIFFRACTIONr_nbtor_other0.0850.21628
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2890.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6561.51754
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04622758
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.68431445
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4284.51289
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
978medium positional0.110.5
1396loose positional0.315
978medium thermal0.62
1396loose thermal0.9810
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 109
Rwork0.291 1988
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)
11.5823-1.0786-0.60732.48180.57612.0716-0.00890.1193-0.0066-0.0102-0.0385-0.04070.0933-0.03360.0474-0.08490.00380.0049-0.08260.0211-0.10313.7864-19.103332.5224
22.413-0.8352-0.35172.32270.12681.79240.04440.00620.3054-0.0033-0.05790.1854-0.0635-0.07380.01360.0095-0.0219-0.035-0.00880.01920.046238.4781-15.046956.5043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 177
2X-RAY DIFFRACTION2B3 - 177

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