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- PDB-1foe: CRYSTAL STRUCTURE OF RAC1 IN COMPLEX WITH THE GUANINE NUCLEOTIDE ... -

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Basic information

Entry
Database: PDB / ID: 1foe
TitleCRYSTAL STRUCTURE OF RAC1 IN COMPLEX WITH THE GUANINE NUCLEOTIDE EXCHANGE REGION OF TIAM1
Components
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
  • T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
Keywordssignaling protein / immune system/signaling protein / DBL HOMOLOGY DOMAIN / PLECKSTRIN HOMOLOGY DOMAIN / GTPASE / GUANINE NUCLEOTIDE EXCHANGE FACTOR / immune system-signaling protein COMPLEX
Function / homology
Function and homology information


brain-derived neurotrophic factor receptor signaling pathway / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / RAC3 GTPase cycle / CDC42 GTPase cycle / RAC2 GTPase cycle / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / NRAGE signals death through JNK / RAC1 GTPase cycle ...brain-derived neurotrophic factor receptor signaling pathway / regulation of non-canonical Wnt signaling pathway / regulation of dopaminergic neuron differentiation / RAC3 GTPase cycle / CDC42 GTPase cycle / RAC2 GTPase cycle / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / NRAGE signals death through JNK / RAC1 GTPase cycle / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / auditory receptor cell morphogenesis / G alpha (12/13) signalling events / cerebral cortex radially oriented cell migration / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / RHOA GTPase cycle / interneuron migration / kinocilium / regulation of hydrogen peroxide metabolic process / regulation of cell adhesion involved in heart morphogenesis / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / cochlea morphogenesis / regulation of neuron maturation / respiratory burst / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / positive regulation of skeletal muscle acetylcholine-gated channel clustering / cell-cell contact zone / hepatocyte growth factor receptor signaling pathway / GTP-dependent protein binding / activation of GTPase activity / midbrain dopaminergic neuron differentiation / epithelial cell morphogenesis / cell projection assembly / positive regulation of bicellular tight junction assembly / ruffle organization / regulation of lamellipodium assembly / thioesterase binding / regulation of neuron migration / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / cell-cell junction organization / motor neuron axon guidance / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / RHO GTPases activate KTN1 / positive regulation of axonogenesis / Activation of RAC1 / MET activates RAP1 and RAC1 / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / DCC mediated attractive signaling / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / Azathioprine ADME / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of ruffle assembly / positive regulation of cell-substrate adhesion / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / regulation of GTPase activity / lamellipodium assembly / regulation of receptor signaling pathway via JAK-STAT / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Activation of RAC1 downstream of NMDARs / dendrite morphogenesis / Rho GDP-dissociation inhibitor binding / regulation of cell size / positive regulation of Rho protein signal transduction / synaptic transmission, GABAergic / positive regulation of dendritic spine development / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / pericentriolar material / Rac protein signal transduction / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / regulation of postsynapse assembly / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion
Similarity search - Function
TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / : / T-lymphoma invasion and metastasis CC-Ex domain / Tiam1 second PH domain-like / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Raf-like Ras-binding domain ...TIAM1, CC-Ex domain / Tiam1/Tiam2/Protein still life / : / T-lymphoma invasion and metastasis CC-Ex domain / Tiam1 second PH domain-like / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Small GTPase Rho / Small GTPase Rho domain profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / PDZ domain / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rho (Ras homology) subfamily of Ras-like small GTPases / PDZ superfamily / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ras-related C3 botulinum toxin substrate 1 / Rho guanine nucleotide exchange factor TIAM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsWorthylake, D.K. / Rossman, K.L. / Sondek, J.
CitationJournal: Nature / Year: 2000
Title: Crystal structure of Rac1 in complex with the guanine nucleotide exchange region of Tiam1.
Authors: Worthylake, D.K. / Rossman, K.L. / Sondek, J.
History
DepositionAug 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
C: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
D: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
E: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
F: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
G: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
H: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,53712
Polymers254,1538
Non-polymers3844
Water1,67593
1
A: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6343
Polymers63,5382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-29 kcal/mol
Surface area27510 Å2
MethodPISA
2
C: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
D: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6343
Polymers63,5382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-29 kcal/mol
Surface area27390 Å2
MethodPISA
3
E: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
F: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6343
Polymers63,5382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-30 kcal/mol
Surface area27010 Å2
MethodPISA
4
G: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
H: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6343
Polymers63,5382
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-30 kcal/mol
Surface area27030 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21680 Å2
ΔGint-175 kcal/mol
Surface area99880 Å2
MethodPISA
6
A: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
G: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
H: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,2696
Polymers127,0774
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-71 kcal/mol
Surface area52470 Å2
MethodPISA
7
C: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
D: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
E: T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1
F: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,2696
Polymers127,0774
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-71 kcal/mol
Surface area52340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.95, 149.27, 149.21
Angle α, β, γ (deg.)90, 121, 90
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe biological assembly is a heterodimer composed of a Tiam1 Dbl/pleckstrin element (chains A,C,E,G) in complex with a Rac1 molecule (Chains B,D,F,H). There are 4 heterodimers in the crystal asymmetric unit

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Components

#1: Protein
T-LYMPHOMA INVASION AND METASTASIS INDUCING PROTEIN 1 / TIAM1 PROTEIN / T-CELL LYMPHOMA INVASION AND METASTASIS 1


Mass: 43827.539 Da / Num. of mol.: 4
Fragment: RESIDUES 1033 TO 1406 FROM MURINE T-LYMPHOMA INVASION AND METASTASIS FACTOR 1, PLECKSTRIN HOMOLOGY DOMAIN
Mutation: ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS
Source method: isolated from a genetically manipulated source
Details: ALA-MET-GLY CLONING ARTIFACT ADDED TO N-TERMINUS / Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PPROEXHTA / Production host: Escherichia coli (E. coli) / References: UniProt: Q60610
#2: Protein
RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE / P21-RAC1 / RAS-LIKE PROTEIN TC25 / RAC1 P21(SMALL) GTP-BINDING PROTEIN


Mass: 19710.764 Da / Num. of mol.: 4 / Fragment: RESIDUES 1 TO 177 FROM HUMAN RAC1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / References: UniProt: P63000
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.51 Å3/Da / Density % sol: 64.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: PEG 3350, Li2SO4, MES, glycerol, pH 6.0, VAPOR DIFFUSION, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMMES1reservoir
218 %PEG33501reservoir
3400 mM1reservoirLi2SO4
45 %glycerol1reservoir
520 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9729,0.9787,0.9724
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97291
20.97871
30.97241
ReflectionResolution: 2.8→15 Å / Num. all: 80441 / Num. obs: 80441 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 27.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.392 / Num. unique all: 5874 / % possible all: 68.9
Reflection
*PLUS
% possible obs: 94.2 % / Num. measured all: 382085
Reflection shell
*PLUS
% possible obs: 68.9 % / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: Used maximum likelihood target function in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.293 4051 5 %RANDOM
Rwork0.262 ---
all-85778 --
obs-80511 93.8 %-
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17461 0 20 93 17574
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.262
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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