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- PDB-1am4: COMPLEX BETWEEN CDC42HS.GMPPNP AND P50 RHOGAP (H. SAPIENS) -

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Basic information

Entry
Database: PDB / ID: 1am4
TitleCOMPLEX BETWEEN CDC42HS.GMPPNP AND P50 RHOGAP (H. SAPIENS)
Components
  • CDC42HS
  • P50-RHOGAP
KeywordsCOMPLEX (GTPASE-ACTIVATING/GTP-BINDING) / COMPLEX (GTPASE-ACTIVATING-GTP-BINDING) / GTPASE ACTIVATION / COMPLEX (GTPASE-ACTIVATING-GTP-BINDING) complex
Function / homologyRho GTPase cycle / CRAL-TRIO lipid binding domain / Inactivation of CDC42 and RAC1 / small GTPase Rho family profile. / DCC mediated attractive signaling / Regulation of actin dynamics for phagocytic cup formation / G alpha (12/13) signalling events / EPHB-mediated forward signaling / CD28 dependent Vav1 pathway / CDO in myogenesis ...Rho GTPase cycle / CRAL-TRIO lipid binding domain / Inactivation of CDC42 and RAC1 / small GTPase Rho family profile. / DCC mediated attractive signaling / Regulation of actin dynamics for phagocytic cup formation / G alpha (12/13) signalling events / EPHB-mediated forward signaling / CD28 dependent Vav1 pathway / CDO in myogenesis / Rho GTPase-activating protein domain / Small GTPase / RHO GTPases activate KTN1 / Small GTPase Rho / Small GTP-binding protein domain / Rho GTPase activation protein / P-loop containing nucleoside triphosphate hydrolase / CRAL-TRIO lipid binding domain superfamily / Cdc42 / Ras family / RhoGAP domain / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / VEGFA-VEGFR2 Pathway / Rho GTPase-activating proteins domain profile. / GPVI-mediated activation cascade / Factors involved in megakaryocyte development and platelet production / RHO GTPases activate PAKs / RHO GTPases Activate WASPs and WAVEs / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / RHO GTPases activate IQGAPs / EGFR downregulation / negative regulation of endocytic recycling / iron ion import across cell outer membrane / regulation of modification of postsynaptic structure / GBD domain binding / submandibular salivary gland formation / neuron fate determination / modification of synaptic structure / Golgi transport complex / dendritic cell migration / Cdc42 protein signal transduction / cardiac conduction system development / positive regulation of synapse structural plasticity / organelle transport along microtubule / storage vacuole / transferrin transport / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / positive regulation of pseudopodium assembly / regulation of attachment of spindle microtubules to kinetochore / GTP-dependent protein binding / regulation of filopodium assembly / leading edge membrane / establishment of epithelial cell apical/basal polarity / Rho GDP-dissociation inhibitor binding / filopodium assembly / actin filament branching / establishment or maintenance of cell polarity / positive regulation of intracellular protein transport / nuclear migration / establishment of Golgi localization / neuropilin signaling pathway / regulation of protein heterodimerization activity / regulation of lamellipodium assembly / thioesterase binding / negative regulation of protein complex assembly / dendritic spine morphogenesis / sprouting angiogenesis / cell junction assembly / positive regulation of filopodium assembly / positive regulation of lamellipodium assembly / Wnt signaling pathway, planar cell polarity pathway / regulation of stress fiber assembly / positive regulation of cytokinesis / macrophage differentiation / Golgi organization / heart contraction / mitogen-activated protein kinase kinase kinase binding / small GTPase mediated signal transduction / regulation of mitotic nuclear division / adherens junction organization / positive regulation of phosphatidylinositol 3-kinase activity / Rho protein signal transduction / SH3/SH2 adaptor activity / regulation of small GTPase mediated signal transduction / positive regulation of muscle cell differentiation / cellular protein localization / negative regulation of epidermal growth factor receptor signaling pathway / positive regulation of actin cytoskeleton reorganization / positive regulation of substrate adhesion-dependent cell spreading / Rab GTPase binding / spindle midzone / phagocytic vesicle / substantia nigra development / positive regulation of stress fiber assembly / actin filament organization / Schaffer collateral - CA1 synapse
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.7 Å resolution
AuthorsRittinger, K. / Walker, P. / Gamblin, S.J. / Smerdon, S.J.
CitationJournal: Nature / Year: 1997
Title: Crystal structure of a small G protein in complex with the GTPase-activating protein rhoGAP.
Authors: Rittinger, K. / Walker, P.A. / Eccleston, J.F. / Nurmahomed, K. / Owen, D. / Laue, E. / Gamblin, S.J. / Smerdon, S.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 22, 1997 / Release: Jul 15, 1998
RevisionDateData content typeGroupProviderType
1.0Jul 15, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P50-RHOGAP
D: CDC42HS
B: P50-RHOGAP
E: CDC42HS
C: P50-RHOGAP
F: CDC42HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,78412
Polyers127,1456
Non-polymers1,6406
Water5,441302
1
A: P50-RHOGAP
D: CDC42HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9284
Polyers42,3822
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: P50-RHOGAP
F: CDC42HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9284
Polyers42,3822
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)2800
ΔGint (kcal/M)-20
Surface area (Å2)17200
MethodPISA
3
B: P50-RHOGAP
E: CDC42HS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9284
Polyers42,3822
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)78.110, 78.120, 78.100
Angle α, β, γ (deg.)90.01, 90.00, 90.05
Int Tables number1
Space group name H-MP 1

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Components

#1: Protein/peptide P50-RHOGAP


Mass: 22741.998 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Cellular location: CYTOPLASM / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: Q07960
#2: Protein/peptide CDC42HS


Mass: 19639.521 Da / Num. of mol.: 3 / Details: HETERODIMER / Mutation: M501P / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Cellular location: CYTOPLASM / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P60953
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Formula: Mg / Magnesium
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 3 / Formula: C10H17N6O13P3
Comment: GppNHp (GMPPNP, energy-carrying molecule analogue) *YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Formula: H2O / Water

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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: 3.75 / Density percent sol: 55 %
Crystal growpH: 5.9 / Details: pH 5.9
Crystal grow
*PLUS
Temp: 4 ℃ / Method: vapor diffusion
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
120 %PEG40001reservoir
2100 mMsodium cacodylate1reservoir
310 mM1reservoirMgCl2
43 mMdithiothreitol1reservoir
53 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX7.2 / Synchrotron site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: Mar 1, 1997
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 25 Å2 / D resolution high: 2.7 Å / D resolution low: 25 Å / Number obs: 49357 / Rmerge I obs: 0.064 / NetI over sigmaI: 26 / Redundancy: 5 % / Percent possible obs: 97.6
Reflection shellRmerge I obs: 0.247 / Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / MeanI over sigI obs: 5 / Redundancy: 3.5 % / Percent possible all: 96.5
Reflection
*PLUS
Number measured all: 246060
Reflection shell
*PLUS
Percent possible obs: 96.5

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Processing

Software
NameClassification
AMoREphasing
CCP4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1RGP, 1MH1
R Free selection details: RANDOM / Cross valid method: THROUGHOUT
Displacement parametersB iso mean: 18 Å2
Least-squares processR factor R free: 0.28 / R factor R work: 0.23 / Highest resolution: 2.7 Å / Lowest resolution: 12 Å / Percent reflection R free: 5 / Percent reflection obs: 96
Refine hist #LASTHighest resolution: 2.7 Å / Lowest resolution: 12 Å
Number of atoms included #LASTProtein: 8907 / Nucleic acid: 0 / Ligand: 0 / Solvent: 297 / Total: 9204
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
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
Software
*PLUS
Name: CCP4 / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.231
Refine LS restraints
*PLUS
Type: p_angle_deg / Dev ideal: 2.7

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