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- PDB-1e96: Structure of the Rac/p67phox complex -

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Basic information

Entry
Database: PDB / ID: 1.0E+96
TitleStructure of the Rac/p67phox complex
Components
  • NEUTROPHIL CYTOSOL FACTOR 2 (NCF-2) TPR DOMAIN, RESIDUES 1-203
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
KeywordsSIGNALING PROTEIN / SIGNALLING COMPLEX / GTPASE / NADPH OXIDASE / PROTEIN-PROTEIN COMPLEX / TPR MOTIF
Function / homology
Function and homology information


superoxide-generating NADPH oxidase activator activity / phagolysosome / engulfment of apoptotic cell / 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 / superoxide-generating NAD(P)H oxidase activity ...superoxide-generating NADPH oxidase activator activity / phagolysosome / engulfment of apoptotic cell / 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 / superoxide-generating NAD(P)H oxidase activity / negative regulation of receptor-mediated endocytosis / Cross-presentation of particulate exogenous antigens (phagosomes) / 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 / ROS and RNS production in phagocytes / regulation of lamellipodium assembly / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / regulation of nitric oxide biosynthetic process / motor neuron axon guidance / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / 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 / Sema4D mediated inhibition of cell attachment and migration / positive regulation of neutrophil chemotaxis / Ephrin signaling / CD28 dependent Vav1 pathway / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / Activation of RAC1 downstream of NMDARs / small GTPase-mediated signal transduction / NRAGE signals death through JNK / superoxide metabolic process / regulation of cell size / positive regulation of Rho protein signal transduction / Rho GDP-dissociation inhibitor binding / establishment or maintenance of cell polarity / Detoxification of Reactive Oxygen Species / 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 / RAC2 GTPase cycle / RAC3 GTPase cycle / phagocytosis / RHO GTPases activate IQGAPs / cellular defense response / 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 endothelial cell migration / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / acrosomal vesicle / regulation of cell migration / secretory granule membrane / small monomeric GTPase / cell-matrix adhesion / actin filament organization / Signal transduction by L1 / VEGFR2 mediated vascular permeability / cell projection / cell chemotaxis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / cell motility / trans-Golgi network
Similarity search - Function
Neutrophil cytosol factor 2, PB1 domain / Neutrophil cytosol factor 2 / Neutrophil cytosol factor 2, SH3 domain 1 / : / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Small GTPase Rho ...Neutrophil cytosol factor 2, PB1 domain / Neutrophil cytosol factor 2 / Neutrophil cytosol factor 2, SH3 domain 1 / : / PB1 domain / PB1 domain / PB1 domain / : / PB1 domain profile. / Small GTPase Rho / Small GTPase Rho domain profile. / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / SH3 domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Small GTP-binding protein domain / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related C3 botulinum toxin substrate 1 / Neutrophil cytosol factor 2 / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLapouge, K. / Smith, S.J.M. / Walker, P.A. / Gamblin, S.J. / Smerdon, S.J. / Rittinger, K.
CitationJournal: Mol.Cell / Year: 2000
Title: Structure of the TPR domain of p67phox in complex with Rac.GTP.
Authors: Lapouge, K. / Smith, S.J. / Walker, P.A. / Gamblin, S.J. / Smerdon, S.J. / Rittinger, K.
History
DepositionOct 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
B: NEUTROPHIL CYTOSOL FACTOR 2 (NCF-2) TPR DOMAIN, RESIDUES 1-203
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4674
Polymers44,9202
Non-polymers5472
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.220, 83.220, 138.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 / RAC1


Mass: 21429.062 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P15154, UniProt: P63000*PLUS
#2: Protein NEUTROPHIL CYTOSOL FACTOR 2 (NCF-2) TPR DOMAIN, RESIDUES 1-203 / P67PHOX


Mass: 23490.471 Da / Num. of mol.: 1 / Fragment: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P19878
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION MET1PRO, GLN61LEU RAC1 ARE GTP-BINDING PROTEINS ASSOCIATED WITH PLASMA ...CHAIN A ENGINEERED MUTATION MET1PRO, GLN61LEU RAC1 ARE GTP-BINDING PROTEINS ASSOCIATED WITH PLASMA MEMBRANE WHICH COULD REGULATE SECRETORY PROCESSES. THE NCF2 IS INVOLVED IN ACTIVATION OF THE LATENT NADPH OXIDASE IN ASSOCIATION WITH NCF1, AND A MEMBRANE BOUND CYTOCHROME B558

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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: 3.08 Å3/Da / Density % sol: 54.6 %
Crystal growpH: 10.5
Details: 0.1 M CAPS PH 10.5, 0.2 M LI ACETATE, 0.8 M NAH2PO4, 1.2 M K2HPO4
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
250 mMTris1drop
350 mM1dropNaCl
42 mMdithiothreitol1drop
55 mM1dropMgCl2
60.1 MCaps1reservoir
70.2 Mlithium acetate1reservoir
80.8 Msodium phophate1reservoir
91.2 Mpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 123873 / % possible obs: 94 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 16.9
Reflection shellResolution: 2.4→2.45 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.2 / % possible all: 100
Reflection
*PLUS
Num. obs: 20975 / Num. measured all: 123873

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MH1, 1A17

1mh1

1a17


Resolution: 2.4→15 Å / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.411 / ESU R Free: 0.288
RfactorNum. reflection% reflectionSelection details
Rfree0.284 -10 %RANDOM
Rwork0.244 ---
obs0.248 18798 94.2 %-
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 33 77 2998
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.022
X-RAY DIFFRACTIONp_angle_d1.391.98
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7361.5
X-RAY DIFFRACTIONp_mcangle_it1.4062
X-RAY DIFFRACTIONp_scbond_it1.9233
X-RAY DIFFRACTIONp_scangle_it3.2694.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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