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- PDB-1kz7: Crystal Structure of the DH/PH Fragment of Murine Dbs in Complex ... -

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Basic information

Entry
Database: PDB / ID: 1kz7
TitleCrystal Structure of the DH/PH Fragment of Murine Dbs in Complex with the Placental Isoform of Human Cdc42
Components
  • CDC42 HOMOLOG
  • GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS
KeywordsSIGNALING PROTEIN / guanine nucleotide exchange factor (GEF) / small G-protein
Function / homology
Function and homology information


RHOC GTPase cycle / CDC42 GTPase cycle / NRAGE signals death through JNK / 1-phosphatidylinositol binding / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / RAC1 GTPase cycle / dendritic cell migration / endothelin receptor signaling pathway involved in heart process ...RHOC GTPase cycle / CDC42 GTPase cycle / NRAGE signals death through JNK / 1-phosphatidylinositol binding / GBD domain binding / Golgi transport complex / positive regulation of pinocytosis / RAC1 GTPase cycle / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / RHOB GTPase cycle / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / G alpha (12/13) signalling events / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / RHOA GTPase cycle / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / RHOG GTPase cycle / Inactivation of CDC42 and RAC1 / positive regulation of pseudopodium assembly / cardiac conduction system development / host-mediated perturbation of viral process / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / establishment of Golgi localization / GTP-dependent protein binding / adherens junction organization / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / regulation of lamellipodium assembly / thioesterase binding / regulation of stress fiber assembly / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / Wnt signaling pathway, planar cell polarity pathway / positive regulation of filopodium assembly / RHOV GTPase cycle / phagocytosis, engulfment / nuclear migration / small GTPase-mediated signal transduction / regulation of mitotic nuclear division / Myogenesis / heart contraction / positive regulation of cytokinesis / spindle midzone / RHOJ GTPase cycle / establishment of cell polarity / RHOQ GTPase cycle / Golgi organization / establishment or maintenance of cell polarity / RHO GTPases activate PAKs / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / Rho protein signal transduction / positive regulation of stress fiber assembly / phagocytic vesicle / RAC1 GTPase cycle / EPHB-mediated forward signaling / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / actin filament organization / guanyl-nucleotide exchange factor activity / small monomeric GTPase / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / filopodium / FCGR3A-mediated phagocytosis / EGFR downregulation / RHO GTPases Activate Formins / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / endocytosis / cytoplasmic ribonucleoprotein granule / apical part of cell / G beta:gamma signalling through CDC42 / mitotic spindle / cell-cell junction / ubiquitin protein ligase activity / intracellular protein localization
Similarity search - Function
DBS, SH3 domain / DBS, PH domain / : / Guanine nucleotide exchange factor DBS-like, spectrin-like / : / Cdc42 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site ...DBS, SH3 domain / DBS, PH domain / : / Guanine nucleotide exchange factor DBS-like, spectrin-like / : / Cdc42 / 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 / : / SOS1/NGEF-like PH domain / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / 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. / 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 / 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
Cell division control protein 42 homolog / Guanine nucleotide exchange factor DBS
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsRossman, K.L. / Worthylake, D.K. / Snyder, J.T. / Siderovski, D.P. / Campbell, S.L. / Sondek, J.
CitationJournal: EMBO J. / Year: 2002
Title: A crystallographic view of interactions between Dbs and Cdc42: PH domain-assisted guanine nucleotide exchange.
Authors: Rossman, K.L. / Worthylake, D.K. / Snyder, J.T. / Siderovski, D.P. / Campbell, S.L. / Sondek, J.
History
DepositionFeb 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 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 / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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: CDC42 HOMOLOG
C: GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS
D: CDC42 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)125,3044
Polymers125,3044
Non-polymers00
Water5,819323
1
A: GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS
B: CDC42 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)62,6522
Polymers62,6522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-12 kcal/mol
Surface area25940 Å2
MethodPISA
2
C: GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS
D: CDC42 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)62,6522
Polymers62,6522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-13 kcal/mol
Surface area24190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.500, 87.980, 230.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS / DBL'S BIG SISTER / DBS


Mass: 41710.141 Da / Num. of mol.: 2 / Fragment: DH/PH fragment (residues 623-967) / Mutation: E940A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dbs / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q64096
#2: Protein CDC42 HOMOLOG / G25K GTP-BINDING PROTEIN


Mass: 20942.070 Da / Num. of mol.: 2 / Fragment: residues 1-188 / Mutation: C188S
Source method: isolated from a genetically manipulated source
Details: PLACENTAL ISOFORM / Source: (gene. exp.) Homo sapiens (human) / Gene: Cdc42 / Plasmid: pET-21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60953
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 8000, sodium formate, Tris HCL, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
210 mMTris1droppH8.0
325 mM1dropNaCl
42 mMdithiothreitol1drop
51 mMEDTA1drop
650 mMTris1reservoirpH7.0
712 %PEG80001reservoir
8650 mMsodium formate1reservoir
92 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 15, 2000
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 46595 / Num. obs: 46595 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31.1 Å2 / Limit h max: 26 / Limit h min: 0 / Limit k max: 31 / Limit k min: 0 / Limit l max: 91 / Limit l min: 0 / Observed criterion F max: 1908848.01 / Observed criterion F min: 5.5
Reflection shellResolution: 2.4→2.49 Å / % possible all: 58
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / Num. obs: 49528 / Num. measured all: 418244 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
% possible obs: 58 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.99 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2460 5 %random
Rwork0.197 ---
all-46595 --
obs-46595 91.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 36.4139 Å2 / ksol: 0.359574 e/Å3
Displacement parametersBiso max: 124.35 Å2 / Biso mean: 41.82 Å2 / Biso min: 12.95 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2---6.37 Å20 Å2
3---4.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Luzzati d res high-2.4
Refinement stepCycle: LAST / Resolution: 2.4→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8275 0 0 323 8598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg21.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.76
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.510.2352183.30.23637900.0166618400860.6
2.51-2.640.2312363.60.23247680.0156627500475.5
2.64-2.810.2363024.50.23658910.0146665619392.9
2.81-3.020.233515.30.2363220.0126682667399.9
3.02-3.320.2193164.70.21863550.01266736671100
3.32-3.80.23485.20.19863620.0116715671099.9
3.8-4.780.1643344.90.16364330.0096772676799.9
4.78-19.990.17935550.18166740.017037702999.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.23
LS refinement shell
*PLUS
Rfactor obs: 0.236

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