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- PDB-1i4d: CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21) -

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Basic information

Entry
Database: PDB / ID: 1i4d
TitleCRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21)
Components
  • ARFAPTIN 2
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
KeywordsSIGNALING PROTEIN / coiled coil / G-protein / complex
Function / homology
Function and homology information


membrane curvature sensor activity / Retrograde transport at the Trans-Golgi-Network / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / localization within membrane / ruffle assembly / regulation of Arp2/3 complex-mediated actin nucleation ...membrane curvature sensor activity / Retrograde transport at the Trans-Golgi-Network / regulation of respiratory burst / positive regulation of ovarian follicle development / regulation of neutrophil migration / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / localization within membrane / ruffle assembly / regulation of Arp2/3 complex-mediated actin nucleation / kinocilium / regulation of cell adhesion involved in heart morphogenesis / protein localization to phagophore assembly site / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / engulfment of apoptotic cell / regulation of hydrogen peroxide metabolic process / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / cell projection assembly / respiratory burst / motor neuron axon guidance / ruffle organization / midbrain dopaminergic neuron differentiation / positive regulation of bicellular tight junction assembly / GTP-dependent protein binding / negative regulation of fibroblast migration / thioesterase binding / regulation of lamellipodium assembly / regulation of stress fiber assembly / RHO GTPases activate CIT / phosphatidylinositol-4-phosphate binding / Nef and signal transduction / Activation of RAC1 / PCP/CE pathway / hepatocyte growth factor receptor signaling pathway / sphingosine-1-phosphate receptor signaling pathway / RHO GTPases activate KTN1 / DCC mediated attractive signaling / MET activates RAP1 and RAC1 / superoxide anion generation / regulation of nitric oxide biosynthetic process / Azathioprine ADME / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / positive regulation of neutrophil chemotaxis / positive regulation of ruffle assembly / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / forebrain development / regulation of receptor signaling pathway via JAK-STAT / NRAGE signals death through JNK / small GTPase-mediated signal transduction / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / positive regulation of Rho protein signal transduction / pericentriolar material / Rac protein signal transduction / establishment or maintenance of cell polarity / semaphorin-plexin signaling pathway / RHO GTPases activate PAKs / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / ficolin-1-rich granule membrane / positive regulation of focal adhesion assembly / regulation of postsynapse assembly / RHO GTPases Activate NADPH Oxidases / anatomical structure morphogenesis / regulation of synaptic vesicle endocytosis / RHO GTPases Activate WASPs and WAVEs / positive regulation of lamellipodium assembly / mitophagy / RHO GTPases activate IQGAPs / positive regulation of stress fiber assembly / RHO GTPases activate PKNs / GPVI-mediated activation cascade / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / phagocytic cup / substrate adhesion-dependent cell spreading / ruffle / cell projection / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / RAC1 GTPase cycle / EPHB-mediated forward signaling / cell-matrix adhesion / regulation of cell migration / positive regulation of endothelial cell migration / secretory granule membrane / positive regulation of insulin secretion involved in cellular response to glucose stimulus / actin filament organization / trans-Golgi network membrane / Signal transduction by L1 / VEGFR2 mediated vascular permeability / regulation of actin cytoskeleton organization / small monomeric GTPase / cell motility
Similarity search - Function
Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Small GTPase Rho / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Small GTPase Rho domain profile. ...Arfaptin homology (AH) domain / Arfaptin family / Arfaptin-like domain / Arfaptin homology (AH) domain profile. / Arfaptin-like domain / Arfaptin homology (AH) domain/BAR domain / AH/BAR domain superfamily / Small GTPase Rho / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / 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 / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Arfaptin-2 / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / molecular replacement / Resolution: 2.5 Å
AuthorsTarricone, C. / Xiao, B. / Justin, N. / Gamblin, S.J. / Smerdon, S.J.
CitationJournal: Nature / Year: 2001
Title: The structural basis of Arfaptin-mediated cross-talk between Rac and Arf signalling pathways.
Authors: Tarricone, C. / Xiao, B. / Justin, N. / Walker, P.A. / Rittinger, K. / Gamblin, S.J. / Smerdon, S.J.
History
DepositionFeb 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_atoms / reflns_shell
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: ARFAPTIN 2
B: ARFAPTIN 2
D: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1745
Polymers72,7063
Non-polymers4682
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-65 kcal/mol
Surface area27550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.566, 47.462, 125.311
Angle α, β, γ (deg.)90.00, 97.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ARFAPTIN 2 / PARTNER OF RAC1


Mass: 25614.057 Da / Num. of mol.: 2 / Fragment: RESIDUES 118-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P53365
#2: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 / P21-RAC1


Mass: 21478.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P63000
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Tris, Peg20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 MTris1reservoir
310 %PEG200001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 22993 / Num. obs: 21742 / % possible obs: 94.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.65 / Num. unique all: 2334

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / molecular replacement / Resolution: 2.5→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.298 1086 random
Rwork0.238 --
all-22993 -
obs-21742 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4385 0 29 147 4561
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.0074
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

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