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- PDB-1mh1: SMALL G-PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1mh1
TitleSMALL G-PROTEIN
ComponentsRAC1
KeywordsGTP-BINDING / GTPASE / SMALL G-PROTEIN / RHO FAMILY / RAS SUPER FAMILY
Function / homology
Function and homology information


regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / regulation of hydrogen peroxide metabolic process / negative regulation of receptor-mediated endocytosis / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex ...regulation of respiratory burst / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / regulation of hydrogen peroxide metabolic process / negative regulation of receptor-mediated endocytosis / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / respiratory burst / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / hepatocyte growth factor receptor signaling pathway / ruffle organization / cell projection assembly / positive regulation of bicellular tight junction assembly / thioesterase binding / regulation of stress fiber assembly / regulation of lamellipodium assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / regulation of nitric oxide biosynthetic process / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / motor neuron axon guidance / PCP/CE pathway / Activation of RAC1 / RHO GTPases activate KTN1 / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / Azathioprine ADME / positive regulation of neutrophil chemotaxis / Sema4D mediated inhibition of cell attachment and migration / Ephrin signaling / CD28 dependent Vav1 pathway / superoxide anion generation / lamellipodium assembly / Wnt signaling pathway, planar cell polarity pathway / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / NRAGE signals death through JNK / regulation of cell size / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / Rho GDP-dissociation inhibitor binding / Rac protein signal transduction / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / positive regulation of focal adhesion assembly / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / RHO GTPases activate PKNs / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / positive regulation of microtubule polymerization / actin filament polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / regulation of cell migration / secretory granule membrane / small monomeric GTPase / actin filament organization / cell-matrix adhesion / Signal transduction by L1 / VEGFR2 mediated vascular permeability / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / cell chemotaxis / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / cell motility / RHO GTPases Activate Formins / trans-Golgi network / Signaling by SCF-KIT / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / response to wounding / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / ruffle membrane / recycling endosome membrane / neuron migration / Constitutive Signaling by Aberrant PI3K in Cancer / melanosome / DAP12 signaling
Similarity search - Function
Small GTPase Rho / small GTPase Rho family 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 family 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsHirshberg, M. / Stockley, R.W. / Dodson, G. / Webb, M.R.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: The crystal structure of human rac1, a member of the rho-family complexed with a GTP analogue.
Authors: Hirshberg, M. / Stockley, R.W. / Dodson, G. / Webb, M.R.
History
DepositionJan 21, 1997Processing site: BNL
Revision 1.0Jan 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0593
Polymers20,5131
Non-polymers5472
Water4,612256
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.440, 103.050, 43.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RAC1


Mass: 20512.697 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 184 / Mutation: M1P, F78S
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH GUANOSINE-5'-(BETA,GAMMA-IMIDO) TRIPHOSPHATE (GPPNP)
Source: (gene. exp.) Homo sapiens (human) / Gene: RHO / Gene (production host): RHO / Production host: Escherichia coli (E. coli) / References: UniProt: P63000
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.49 Å3/Da / Density % sol: 51.68 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13-4 mg/mlprotein1drop
220 mMTris-HCl1drop
31 mM1dropMgCl2
41 mMdithiothreitol1drop
518-20 %PEG80001reservoir
625 mMTris-HCl1reservoir
710 mM1reservoirMgCl2
85 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 101 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Date: Dec 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.38→51.3 Å / Num. obs: 42134 / % possible obs: 99.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 9.8
Reflection shellResolution: 1.38→1.44 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.6 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 312780
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 821P

821p


Resolution: 1.38→10 Å /
Rfactor% reflection
Rfree0.205 5 %
Rwork0.175 -
Refinement stepCycle: LAST / Resolution: 1.38→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1395 0 33 256 1684
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_deg1.543

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