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- PDB-1cxz: CRYSTAL STRUCTURE OF HUMAN RHOA COMPLEXED WITH THE EFFECTOR DOMAI... -

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Basic information

Entry
Database: PDB / ID: 1cxz
TitleCRYSTAL STRUCTURE OF HUMAN RHOA COMPLEXED WITH THE EFFECTOR DOMAIN OF THE PROTEIN KINASE PKN/PRK1
Components
  • PROTEIN (HIS-TAGGED TRANSFORMING PROTEIN RHOA(0-181))
  • PROTEIN (PKN)
KeywordsSIGNALING PROTEIN / PROTEIN-PROTEIN COMPLEX / ANTIPARALLEL COILED-COIL
Function / homology
Function and homology information


epithelial cell migration / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration ...epithelial cell migration / protein kinase C / diacylglycerol-dependent serine/threonine kinase activity / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / renal system process / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / regulation of cell motility / regulation of modification of postsynaptic structure / cell junction assembly / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / histone H3T11 kinase activity / establishment of epithelial cell apical/basal polarity / beta selection / B cell apoptotic process / regulation of systemic arterial blood pressure by endothelin / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / regulation of germinal center formation / RHO GTPases activate CIT / RHO GTPases Activate ROCKs / negative regulation of cell size / PCP/CE pathway / regulation of immunoglobulin production / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / regulation of androgen receptor signaling pathway / positive regulation of podosome assembly / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / hyperosmotic response / apolipoprotein A-I-mediated signaling pathway / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / motor neuron apoptotic process / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / nuclear androgen receptor binding / RHOB GTPase cycle / EPHA-mediated growth cone collapse / apical junction complex / negative regulation of B cell proliferation / stress fiber assembly / androgen receptor signaling pathway / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / regulation of neuron projection development / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / B cell homeostasis / semaphorin-plexin signaling pathway / cleavage furrow / ficolin-1-rich granule membrane / positive regulation of protein serine/threonine kinase activity / RHOA GTPase cycle / negative regulation of cell-substrate adhesion / mitotic spindle assembly / positive regulation of T cell migration / endothelial cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / Rho protein signal transduction / GPVI-mediated activation cascade / spleen development / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / RAC1 GTPase cycle / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substantia nigra development / substrate adhesion-dependent cell spreading / post-translational protein modification / protein kinase C binding
Similarity search - Function
Serine/threonine-protein kinase N1, second HR1 domain / HR1 repeat / Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / HR1 rho-binding domain / REM-1 domain profile. / Protein kinase, C-terminal ...Serine/threonine-protein kinase N1, second HR1 domain / HR1 repeat / Serine/threonine-protein kinase N, first HR1 domain / Serine/threonine-protein kinase N, C2 domain / Hr1 repeat / Rho effector or protein kinase C-related kinase homology region 1 homologues / HR1 repeat superfamily / HR1 rho-binding domain / REM-1 domain profile. / Protein kinase, C-terminal / Protein kinase C terminal domain / Small GTPase Rho / Small GTPase Rho domain profile. / C2 domain / C2 domain profile. / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Helix Hairpins / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Transforming protein RhoA / Serine/threonine-protein kinase N1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMaesaki, R. / Ihara, K. / Shimizu, T. / Kuroda, S. / Kaibuchi, K. / Hakoshima, T.
Citation
Journal: Mol.Cell / Year: 1999
Title: The structural basis of Rho effector recognition revealed by the crystal structure of human RhoA complexed with the effector domain of PKN/PRK1.
Authors: Maesaki, R. / Ihara, K. / Shimizu, T. / Kuroda, S. / Kaibuchi, K. / Hakoshima, T.
#1: Journal: J.Struct.Biol. / Year: 1999
Title: Biochemical and crystallographic characterization of a Rho effector domain of the protein serine/threonine kinase N in a complex with RhoA
Authors: Maesaki, R. / Shimizu, T. / Ihara, K. / Kuroda, S. / Kaibuchi, K. / Hakoshima, T.
History
DepositionAug 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 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: PROTEIN (HIS-TAGGED TRANSFORMING PROTEIN RHOA(0-181))
B: PROTEIN (PKN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9714
Polymers30,4082
Non-polymers5642
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.9, 66.9, 149.5
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PROTEIN (HIS-TAGGED TRANSFORMING PROTEIN RHOA(0-181))


Mass: 20596.615 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 181 / Mutation: G14V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PRSET B / Production host: Escherichia coli (E. coli) / References: UniProt: P61586
#2: Protein PROTEIN (PKN)


Mass: 9811.257 Da / Num. of mol.: 1 / Fragment: RESIDUES 13 - 98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGET-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q16512
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.75 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 6.5 / Details: PEG 300, pH 6.5, MICROBATCH, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: batch method / Details: Maesaki, R., (1999) J.Struct.Biol., 126, 166.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlprotein11
250 mMBis-Tris11
315 mMcalcium acetate11
415 %PEG30011

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→49.8 Å / Num. all: 696854 / Num. obs: 17568 / % possible obs: 96 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 24
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.312 / % possible all: 86
Reflection
*PLUS
% possible obs: 96 % / Num. measured all: 696854 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 86 % / Mean I/σ(I) obs: 2.8

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→49.8 Å / σ(F): 2 / Stereochemistry target values: PROTEIN.PARAM
RfactorNum. reflection% reflectionSelection details
Rfree0.268 839 -RANDOM
Rwork0.214 ---
obs0.214 17346 95.6 %-
all-17473 --
Refine analyze
FreeObs
Luzzati coordinate error0.353 Å0.281 Å
Luzzati sigma a0.544 Å0.364 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 33 115 2273
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.217
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 49.8 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_dihedral_angle_deg / Dev ideal: 22.45
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å / Rfactor Rfree: 0.359 / Rfactor obs: 0.315

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