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- PDB-1ki1: Guanine Nucleotide Exchange Region of Intersectin in Complex with... -

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Basic information

Entry
Database: PDB / ID: 1ki1
TitleGuanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42
Components
  • G25K GTP-binding protein, placental isoform
  • intersectin long form
KeywordsSIGNALING PROTEIN / Protein-Protein complex / DH domain / PH domain / Rho GTPase
Function / homology
Function and homology information


clathrin-dependent synaptic vesicle endocytosis / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis ...clathrin-dependent synaptic vesicle endocytosis / GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / storage vacuole / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / GTP-dependent protein binding / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development / dendritic spine morphogenesis / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / proline-rich region binding / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / endosomal transport / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / establishment or maintenance of cell polarity / intracellular vesicle / NRAGE signals death through JNK / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / exocytosis / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RAC2 GTPase cycle / RAC3 GTPase cycle / spindle midzone / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / phagocytic vesicle / positive regulation of substrate adhesion-dependent cell spreading / clathrin-coated pit / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / positive regulation of DNA replication / secretory granule / filopodium / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation / positive regulation of JNK cascade / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / protein localization
Similarity search - Function
Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / Cdc42 / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain ...Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / Cdc42 / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Variant SH3 domain / Variant SH3 domain / 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. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / SH3 domain / Small GTPase / Ras family / Rab subfamily of small GTPases / EF-hand, calcium binding motif / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / 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
Cell division control protein 42 homolog / Intersectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSnyder, J.T. / Pruitt, W.M. / 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
DepositionDec 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G25K GTP-binding protein, placental isoform
B: intersectin long form
C: G25K GTP-binding protein, placental isoform
D: intersectin long form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,9496
Polymers123,7574
Non-polymers1922
Water3,261181
1
A: G25K GTP-binding protein, placental isoform
B: intersectin long form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9753
Polymers61,8792
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-29 kcal/mol
Surface area26820 Å2
MethodPISA
2
C: G25K GTP-binding protein, placental isoform
D: intersectin long form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9753
Polymers61,8792
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-30 kcal/mol
Surface area26820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.37, 79.23, 116.41
Angle α, β, γ (deg.)90, 111.51, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein G25K GTP-binding protein, placental isoform / CDC42


Mass: 20942.070 Da / Num. of mol.: 2 / Fragment: residues 1-188 / Mutation: C188S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P60953
#2: Protein intersectin long form


Mass: 40936.523 Da / Num. of mol.: 2
Fragment: Dbl homology and Pleckstrin homology domains (residues 1229-1580)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15811
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
215 %(w/w)PEG40001reservoir
3100 mMTris1reservoirpH7.5
4150 mMammonium sulfate1reservoir
51 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9787, 0.9792
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 2000
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.97921
ReflectionResolution: 2.3→30 Å / Num. all: 64188 / Num. obs: 61357 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.091 / Rsym value: 0.083 / Net I/σ(I): 34
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 4.2 / Num. unique all: 5135 / Rsym value: 0.256 / % possible all: 80.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 55366 / % possible obs: 85.3 % / Num. measured all: 572588 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 79.6 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 7

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Processing

Software
NameClassification
SHELXSphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→15 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3085 -random
Rwork0.2314 ---
all-64188 --
obs-61146 95.3 %-
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8374 0 10 181 8565
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008702
X-RAY DIFFRACTIONc_angle_d1.41664
LS refinement shellResolution: 2.3→2.38 Å /
Num. reflection% reflection
obs5135 80.5 %
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.231 / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0087
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.416

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