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- PDB-1lb1: Crystal Structure of the Dbl and Pleckstrin homology domains of D... -

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Basic information

Entry
Database: PDB / ID: 1lb1
TitleCrystal Structure of the Dbl and Pleckstrin homology domains of Dbs in complex with RhoA
Components
  • Guanine nucleotide exchange factor DBS
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN / GUANINE NUCLEOTIDE EXCHANGE FACTOR / SMALL G-PROTEIN / RHOA / DBS / DH domain / PH domain
Function / homology
Function and homology information


RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / 1-phosphatidylinositol binding / NRAGE signals death through JNK / RAC1 GTPase cycle / RHOG GTPase cycle / G alpha (12/13) signalling events / aortic valve formation ...RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / 1-phosphatidylinositol binding / NRAGE signals death through JNK / RAC1 GTPase cycle / RHOG GTPase cycle / G alpha (12/13) signalling events / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / negative regulation of cell size / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / odontogenesis / motor neuron apoptotic process / wound healing, spreading of cells / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / positive regulation of Rho protein signal transduction / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / extrinsic component of membrane / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / endomembrane system / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cytoplasmic microtubule organization / regulation of microtubule cytoskeleton organization / skeletal muscle tissue development / negative regulation of reactive oxygen species biosynthetic process / regulation of cell migration / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / extrinsic component of cytoplasmic side of plasma membrane / phosphatidylinositol binding / cell-matrix adhesion / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity
Similarity search - Function
DBS, SH3 domain / DBS, PH domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain ...DBS, SH3 domain / DBS, PH domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Small GTPase Rho / small GTPase Rho family 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. / Pleckstrin homology 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 / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transforming protein RhoA / Guanine nucleotide exchange factor DBS
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsSnyder, J.T. / Worthylake, D.K. / Rossman, K.L. / Betts, L. / Pruitt, W.M. / Siderovski, D.P. / Der, C.J. / Sondek, J.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structural basis for the selective activation of Rho GTPases by Dbl exchange factors.
Authors: Snyder, J.T. / Worthylake, D.K. / Rossman, K.L. / Betts, L. / Pruitt, W.M. / Siderovski, D.P. / Der, C.J. / Sondek, J.
History
DepositionApr 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide exchange factor DBS
B: Transforming protein RhoA
C: Guanine nucleotide exchange factor DBS
D: Transforming protein RhoA
E: Guanine nucleotide exchange factor DBS
F: Transforming protein RhoA
G: Guanine nucleotide exchange factor DBS
H: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)251,3528
Polymers251,3528
Non-polymers00
Water0
1
A: Guanine nucleotide exchange factor DBS
B: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)62,8382
Polymers62,8382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-14 kcal/mol
Surface area23690 Å2
MethodPISA
2
C: Guanine nucleotide exchange factor DBS
D: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)62,8382
Polymers62,8382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-14 kcal/mol
Surface area23680 Å2
MethodPISA
3
E: Guanine nucleotide exchange factor DBS
F: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)62,8382
Polymers62,8382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-12 kcal/mol
Surface area23660 Å2
MethodPISA
4
G: Guanine nucleotide exchange factor DBS
H: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)62,8382
Polymers62,8382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-13 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.897, 158.897, 151.791
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Guanine nucleotide exchange factor DBS / DBL'S BIG SISTER / DBS


Mass: 41252.332 Da / Num. of mol.: 4
Fragment: DBL homology domain (residues 623-818) and pleckstrin homology domain (residues 819-967)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dbs / Plasmid: PET-28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q64096
#2: Protein
Transforming protein RhoA / / H12


Mass: 21585.775 Da / Num. of mol.: 4 / Fragment: residues 1-190 / Mutation: C190S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RhoA / Plasmid: pPro EX HT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61586

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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: 3.81 Å3/Da / Density % sol: 67.72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: PEG 3350, lithium citrate, Inositol 1,4,5-trisphosphate, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris1droppH8.0
225 mM1dropNaCl
32 mMdithiothreitol1drop
40.5 mMEDTA1drop
515 mg/mlprotein1drop
617 %(w/w)PEG33501reservoir
7200 mMlithium citrate1reservoir
81 mMinositol 1,4,5-triphosphate1reservoir

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.81→47.7 Å / Num. all: 85993 / Num. obs: 85993 / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 87.9 Å2 / Limit h max: 56 / Limit h min: 0 / Limit k max: 56 / Limit k min: 0 / Limit l max: 53 / Limit l min: 0 / Observed criterion F max: 2986395.32 / Observed criterion F min: 8.8
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. obs: 86038 / % possible obs: 99.1 % / Num. measured all: 269910 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 94.1 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dbs-Cdc42 (pdb code 1KZ7)

1kz7


Resolution: 2.81→47.7 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 4358 5.1 %Random
Rwork0.236 ---
all-91758 --
obs-85993 93.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 45.4826 Å2 / ksol: 0.33567 e/Å3
Displacement parametersBiso max: 200.54 Å2 / Biso mean: 80.6 Å2 / Biso min: 4.81 Å2
Baniso -1Baniso -2Baniso -3
1--7.23 Å20 Å20 Å2
2---7.23 Å20 Å2
3---14.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.53 Å
Luzzati d res high-2.81
Refinement stepCycle: LAST / Resolution: 2.81→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16236 0 0 0 16236
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg21.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.79
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.81-2.940.4375275.10.40398800.019114341040791
2.94-3.090.3495194.80.337102800.015114591079994.2
3.09-3.290.3465174.80.297102850.015114221080294.6
3.29-3.540.2955364.90.266103750.013114501091195.3
3.54-3.890.2685595.10.238104050.011114751096495.5
3.89-4.460.2485815.40.214102760.01114551085794.8
4.46-5.620.2285885.50.201101500.009114991073893.4
5.62-47.70.23553150.299840.01116291051590.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Rfactor obs: 0.236 / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0072
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.437 / Rfactor Rwork: 0.403 / Rfactor obs: 0.403

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