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- PDB-1hh4: Rac1-RhoGDI complex involved in NADPH oxidase activation -

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Basic information

Entry
Database: PDB / ID: 1hh4
TitleRac1-RhoGDI complex involved in NADPH oxidase activation
Components
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
  • RHO GDP-DISSOCIATION INHIBITOR 1
KeywordsSIGNALING PROTEIN/INHIBITOR / SINGAL PROTEIN INHIBITOR COMPLEX / SMALL G PROTEIN / GTPASE ACTIVATION / GTP-BINDING / PRENYLATION / LIPOPROTEIN / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


Rho GDP-dissociation inhibitor activity / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration ...Rho GDP-dissociation inhibitor activity / embryonic olfactory bulb interneuron precursor migration / anatomical structure arrangement / regulation of ERK5 cascade / angiotensin-activated signaling pathway involved in heart process / positive regulation of ovarian follicle development / cerebral cortex GABAergic interneuron development / regulation of respiratory burst / auditory receptor cell morphogenesis / cerebral cortex radially oriented cell migration / erythrocyte enucleation / regulation of neutrophil migration / negative regulation of interleukin-23 production / localization within membrane / Activated NTRK2 signals through CDK5 / interneuron migration / kinocilium / regulation of hydrogen peroxide metabolic process / regulation of cell adhesion involved in heart morphogenesis / negative regulation of receptor-mediated endocytosis / engulfment of apoptotic cell / ruffle assembly / NTRK2 activates RAC1 / NADPH oxidase complex / Inactivation of CDC42 and RAC1 / cochlea morphogenesis / regulation of neuron maturation / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / respiratory burst / WNT5:FZD7-mediated leishmania damping / cortical cytoskeleton organization / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / positive regulation of skeletal muscle acetylcholine-gated channel clustering / hepatocyte growth factor receptor signaling pathway / GTP-dependent protein binding / regulation of Rho protein signal transduction / midbrain dopaminergic neuron differentiation / epithelial cell morphogenesis / cell projection assembly / positive regulation of bicellular tight junction assembly / ruffle organization / regulation of lamellipodium assembly / thioesterase binding / regulation of neuron migration / regulation of stress fiber assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / cell-cell junction organization / motor neuron axon guidance / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / RHO GTPases activate KTN1 / regulation of synaptic vesicle cycle / Activation of RAC1 / MET activates RAP1 and RAC1 / positive regulation of neutrophil chemotaxis / regulation of nitric oxide biosynthetic process / DCC mediated attractive signaling / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / Azathioprine ADME / Ephrin signaling / CD28 dependent Vav1 pathway / positive regulation of ruffle assembly / positive regulation of cell-substrate adhesion / superoxide anion generation / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / regulation of receptor signaling pathway via JAK-STAT / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Activation of RAC1 downstream of NMDARs / dendrite morphogenesis / Rho GDP-dissociation inhibitor binding / regulation of cell size / positive regulation of Rho protein signal transduction / RHOC GTPase cycle / synaptic transmission, GABAergic / positive regulation of dendritic spine development / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / pericentriolar material / Rac protein signal transduction / RHO GTPases activate PAKs / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / regulation of postsynapse assembly / RHOH GTPase cycle / immunological synapse / ficolin-1-rich granule membrane / RHOG GTPase cycle / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / regulation of neuronal synaptic plasticity / RHOA GTPase cycle / positive regulation of focal adhesion assembly / RHO GTPases Activate NADPH Oxidases
Similarity search - Function
Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase Rho / Small GTPase Rho domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase ...Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase Rho / Small GTPase Rho domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Distorted Sandwich / Rab subfamily of small GTPases / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GERAN-8-YL GERAN / Ras-related C3 botulinum toxin substrate 1 / Rho GDP-dissociation inhibitor 1 / Ras-related C3 botulinum toxin substrate 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGrizot, S. / Faure, J. / Fieschi, F. / Vignais, P.V. / Dagher, M.-C. / Pebay-Peyroula, E.
CitationJournal: Biochemistry / Year: 2001
Title: Crystal Structure of the Rac1-Rhogdi Complex Involved in Nadph Oxidase Activation
Authors: Grizot, S. / Faure, J. / Fieschi, F. / Vignais, P.V. / Dagher, M.-C. / Pebay-Peyroula, E.
History
DepositionDec 20, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
D: RHO GDP-DISSOCIATION INHIBITOR 1
E: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,72810
Polymers89,2444
Non-polymers1,4846
Water54030
1
A: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
D: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3645
Polymers44,6222
Non-polymers7423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
E: RHO GDP-DISSOCIATION INHIBITOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3645
Polymers44,6222
Non-polymers7423
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)154.700, 88.700, 62.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE ASYMMETRIC UNIT CONTAINS TWO HETERODIMERS RAC-RHOGDI,RELATED BY NCS. THE CHAIN IDENTIFIERS ARE A AND D FOR DIMER1,AND B AND E FOR DIMER 2.

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Components

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Protein , 2 types, 4 molecules ABDE

#1: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 / P21-RAC1 / RAS-LIKE PROTEIN TC25


Mass: 21383.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P15154, UniProt: P63000*PLUS
#2: Protein RHO GDP-DISSOCIATION INHIBITOR 1 / RHO GDI 1 / RHO-GDI ALPHA


Mass: 23238.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P52565

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Non-polymers , 4 types, 36 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H34
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsRACS ARE GTP-BINDING PROTEINS ASSOCIATED WITH PLASMA MEMBRANE WHICH COULD REGULATE SECRETORY ...RACS ARE GTP-BINDING PROTEINS ASSOCIATED WITH PLASMA MEMBRANE WHICH COULD REGULATE SECRETORY PROCESSES. RHO GDI 1 REGULATES THE GDP/GTP EXCHANGE REACTION OF THE RHO PROTEINS BY INHIBITING THE DISSOCIATION OF GDP FROM THEM.

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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: 2.41 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: HANGING DROP AT 20C WITH RESERVOIR: 30% PEG 4000, 100 MM NA CITRATE PH=5.6, 5 MM MGCL2, 200 MM AMMONIUM ACETATE, pH 5.60
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18-10 mg/mlprotein1drop
230 %PEG40001reservoir
3100 mMsodium citrate1reservoir
45 mM1reservoirMgCl2
5200 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.95
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 21165 / % possible obs: 84.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 58.7 Å2 / Rsym value: 0.062 / Net I/σ(I): 13
Reflection shellResolution: 2.7→2.76 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.434 / % possible all: 80.6
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 2.36 % / Num. measured all: 50106 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Highest resolution: 2.7 Å / % possible obs: 80.6 % / Redundancy: 2.28 % / Rmerge(I) obs: 0.434

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DOA

1doa


Resolution: 2.7→19.8 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0
Details: TWO GROUPS WERE DEFINED FOR NCS RESTRAINTS, GROUP 1 BETWEEN CHAIN ID A AND B (ALL RESIDUES EXCEPT 28 - 40 AND 178 - 189), GROUP2 BETWEEN CHAIN ID D AND E (RESIDUES 330 - 353 AND 390 - 500)
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1062 5 %RANDOM
Rwork0.256 ---
obs0.256 20669 85.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.5 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 58.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.18 Å20 Å20 Å2
2---4.29 Å20 Å2
3---0.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 98 30 5908
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.171.5
X-RAY DIFFRACTIONc_mcangle_it17.322
X-RAY DIFFRACTIONc_scbond_it14.592
X-RAY DIFFRACTIONc_scangle_it20.812.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.449 165 5 %
Rwork0.378 3068 -
obs--81.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER-REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4LIG.PARLIG.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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