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- PDB-5cjp: The Structural Basis for Cdc42-Induced Dimerization of IQGAPs -

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Basic information

Entry
Database: PDB / ID: 5cjp
TitleThe Structural Basis for Cdc42-Induced Dimerization of IQGAPs
Components
  • Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a
  • Ras GTPase-activating-like protein IQGAP2
KeywordsPROTEIN BINDING / IQGAP2 GAP related domain X-ray GTPase interactions Complex Cdc42
Function / homology
Function and homology information


: / intracellular protein localization => GO:0008104 / modification of synaptic structure / : / mitotic actomyosin contractile ring assembly actin filament organization / Cdc42 protein signal transduction / establishment or maintenance of apical/basal cell polarity / regulation of protein binding / GBD domain binding / submandibular salivary gland formation ...: / intracellular protein localization => GO:0008104 / modification of synaptic structure / : / mitotic actomyosin contractile ring assembly actin filament organization / Cdc42 protein signal transduction / establishment or maintenance of apical/basal cell polarity / regulation of protein binding / GBD domain binding / submandibular salivary gland formation / Arp2/3 complex binding / Golgi transport complex / positive regulation of pinocytosis / Arp2/3 complex-mediated actin nucleation / actin filament branching / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / GTPase inhibitor activity / organelle transport along microtubule / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / GTP-dependent protein binding / Inactivation of CDC42 and RAC1 / cardiac conduction system development / modulation by host of viral process / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / regulation of modification of postsynaptic structure / regulation of stress fiber assembly / regulation of lamellipodium assembly / adherens junction organization / embryonic heart tube development / RHO GTPases activate KTN1 / DCC mediated attractive signaling / regulation of postsynapse organization / CD28 dependent Vav1 pathway / sprouting angiogenesis / positive regulation of filopodium assembly / Wnt signaling pathway, planar cell polarity pathway / nuclear migration / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOV GTPase cycle / small GTPase-mediated signal transduction / Myogenesis / thrombin-activated receptor signaling pathway / heart contraction / establishment of cell polarity / establishment or maintenance of cell polarity / Golgi organization / RHOJ GTPase cycle / positive regulation of cytokinesis / RHOQ GTPase cycle / RHO GTPases activate PAKs / phosphatidylinositol-3,4,5-trisphosphate binding / microvillus / RHOU GTPase cycle / CDC42 GTPase cycle / macrophage differentiation / RHOG GTPase cycle / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / spindle midzone / RHO GTPases activate IQGAPs / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / GPVI-mediated activation cascade / phagocytic vesicle / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / RAC1 GTPase cycle / positive regulation of substrate adhesion-dependent cell spreading / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / secretory granule membrane / secretory granule / small monomeric GTPase / actin filament organization / positive regulation of DNA replication / integrin-mediated signaling pathway / cell projection / filopodium / regulation of actin cytoskeleton organization
Similarity search - Function
RasGAP protein, C-terminal / RasGAP C-terminus / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Cdc42 / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases ...RasGAP protein, C-terminal / RasGAP C-terminus / GTPase Activation - p120GAP; domain 1 / GTPase Activation - p120gap; domain 1 / Cdc42 / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / IQ calmodulin-binding motif / Small GTPase Rho / Calponin homology domain / small GTPase Rho family profile. / Calponin homology (CH) domain / Rho GTPase activation protein / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / IQ motif profile. / WW/rsp5/WWP domain signature. / WW/rsp5/WWP domain profile. / WW 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 / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a / Cell division control protein 42 homolog / Ras GTPase-activating-like protein IQGAP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsWorthylake, D.K. / Boyapati, V.K. / LeCour Jr, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01BM084072 United States
CitationJournal: Structure / Year: 2016
Title: The Structural Basis for Cdc42-Induced Dimerization of IQGAPs.
Authors: LeCour, L. / Boyapati, V.K. / Liu, J. / Li, Z. / Sacks, D.B. / Worthylake, D.K.
History
DepositionJul 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a
B: Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a
C: Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a
D: Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a
E: Ras GTPase-activating-like protein IQGAP2
F: Ras GTPase-activating-like protein IQGAP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,34114
Polymers167,1516
Non-polymers2,1908
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22830 Å2
ΔGint-111 kcal/mol
Surface area61860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.633, 120.169, 157.079
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
Cell division cycle 42 (GTP binding protein, 25kDa), isoform CRA_a


Mass: 19758.748 Da / Num. of mol.: 4 / Mutation: Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC42, hCG_1981007 / Plasmid: pPRO EX HTb
Details (production host): plasmid encodes a TEV protease cleavable 6xHis tag which leaves a Gly-Ala cloning artifact preceding the initiator methionine
Cell line (production host): RIL / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: A0A024RAE4, UniProt: P60953*PLUS
#2: Protein Ras GTPase-activating-like protein IQGAP2


Mass: 44058.094 Da / Num. of mol.: 2 / Fragment: unp reesidues 875-1258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IQGAP2 / Plasmid: pET Trx
Details (production host): kanamycin, encodes E. coli thioredoxin and a TEV protease-cleavable 6xHis tag N-terminal to the IQGAP2 GAP-related domain
Cell line (production host): RIL / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q13576
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 28.5% (v/v) polyethylene glycol (PEG) MW 400, 100mM 2-(N-morpholino)ethanesulfonic acid (MES) pH 6.5 and 40mM MgCl2.
PH range: 6.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 12, 2014
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.57→20 Å / Num. obs: 61742 / % possible obs: 99.7 % / Redundancy: 7.3 % / Net I/av σ(I): 2.9 / Net I/σ(I): 10.5
Reflection shellResolution: 2.57→2.71 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
PDB_EXTRACTdata extraction
MOLREPphasing
Omodel building
SCALAdata scaling
RefinementResolution: 2.6→20 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2873 2993 5 %
Rwork0.2474 56575 -
obs-59568 99.8 %
Solvent computationBsol: 33.9884 Å2
Displacement parametersBiso max: 198.96 Å2 / Biso mean: 72.6528 Å2 / Biso min: 19.35 Å2
Baniso -1Baniso -2Baniso -3
1--9.939 Å20 Å20 Å2
2---2.859 Å20 Å2
3---12.797 Å2
Refinement stepCycle: final / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11514 0 251 0 11765
Biso mean--47.49 --
Num. residues----1452
Refine LS restraintsType: c_angle_d / Dev ideal: 1.314

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