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- PDB-4d0n: AKAP13 (AKAP-Lbc) RhoGEF domain in complex with RhoA -

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Basic information

Entry
Database: PDB / ID: 4d0n
TitleAKAP13 (AKAP-Lbc) RhoGEF domain in complex with RhoA
Components
  • A-KINASE ANCHOR PROTEIN 13
  • TRANSFORMING PROTEIN RHOA
KeywordsCELL CYCLE / AKAP13 / LBC / AKAP-LBC / GEF / RHOGEF / DH DOMAIN / PH DOMAIN
Function / homology
Function and homology information


regulation of sarcomere organization / 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 ...regulation of sarcomere organization / 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 / 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 / MAP-kinase scaffold activity / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cardiac muscle cell differentiation / regulation of modification of postsynaptic structure / cell junction assembly / apical junction assembly / regulation of Rho protein signal transduction / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / regulation of systemic arterial blood pressure by endothelin / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / RHO GTPases Activate ROCKs / negative regulation of cell size / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / positive regulation of podosome assembly / regulation of small GTPase mediated signal transduction / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / 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 / RHOB GTPase cycle / protein kinase A binding / EPHA-mediated growth cone collapse / NRAGE signals death through JNK / apical junction complex / adrenergic receptor signaling pathway / stress fiber assembly / androgen receptor signaling pathway / myosin binding / positive regulation of Rho protein signal transduction / 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 / semaphorin-plexin signaling pathway / cleavage furrow / ficolin-1-rich granule membrane / positive regulation of protein serine/threonine kinase activity / negative regulation of cell-substrate adhesion / RHOA GTPase cycle / 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 / GPVI-mediated activation cascade / Rho protein signal transduction / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substantia nigra development / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / regulation of cell migration / secretory granule membrane / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cell periphery / regulation of actin cytoskeleton organization
Similarity search - Function
RII binding domain / RII binding domain / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / Small GTPase Rho domain profile. / Dbl homology (DH) domain superfamily ...RII binding domain / RII binding domain / : / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / 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. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / C1-like domain superfamily / 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 / 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
GUANOSINE-5'-DIPHOSPHATE / Transforming protein RhoA / A-kinase anchor protein 13
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAbdul Azeez, K.R. / Shrestha, L. / Krojer, T. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C. / Edwards, A.M. / Knapp, S. / Klussmann, E. / Elkins, J.M.
CitationJournal: Biochem.J. / Year: 2014
Title: The Crystal Structure of the Rhoa : Akap-Lbc Dh-Ph Domain Complex.
Authors: Abdul Azeez, K.R. / Knapp, S. / Fernandes, J.M.P. / Klussmann, E. / Elkins, J.M.
History
DepositionApr 29, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Nov 26, 2014Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSFORMING PROTEIN RHOA
B: A-KINASE ANCHOR PROTEIN 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3549
Polymers64,3692
Non-polymers9867
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-77.2 kcal/mol
Surface area25980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.320, 86.610, 116.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein TRANSFORMING PROTEIN RHOA / RHOA / RHO CDNA CLONE 12 / H12


Mass: 20925.975 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61586, small monomeric GTPase
#2: Protein A-KINASE ANCHOR PROTEIN 13 / AKAP13 / AKAP-13 / AKAP-LBC / BREAST CANCER NUCLEAR RECEPTOR-BINDING AUXILIARY PROTEIN / GUANINE ...AKAP13 / AKAP-13 / AKAP-LBC / BREAST CANCER NUCLEAR RECEPTOR-BINDING AUXILIARY PROTEIN / GUANINE NUCLEOTIDE EXCHANGE FACTOR LBC / HUMAN THYROID-ANCHORING PROTEIN 31 / LYMPHOID BLAST CRISIS ONCOGENE / LBC ONCOGENE / NON-ONCOGENIC RHO GTPASE-SPECIFIC GTP EXCHANGE FACTOR / PROTEIN KINASE A-ANCHORING PROTEIN 13 / PRKA13 / P47


Mass: 43442.586 Da / Num. of mol.: 1 / Fragment: RHOGEF DOMAIN, RESIDUES 1968-2338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12802

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Non-polymers , 4 types, 190 molecules

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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.24 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 5.5
Details: 0.2 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS PH 5.5, 25% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.1→82.32 Å / Num. obs: 49042 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.2
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.6 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→69.57 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 12.293 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23946 2476 5.1 %RANDOM
Rwork0.20943 ---
obs0.21098 46509 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.162 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å20 Å2
2--0.16 Å20 Å2
3---1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.1→69.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4365 0 57 183 4605
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194496
X-RAY DIFFRACTIONr_bond_other_d0.0010.024353
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9836063
X-RAY DIFFRACTIONr_angle_other_deg0.7393.00210020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3275552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8824.677201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47815857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8981528
X-RAY DIFFRACTIONr_chiral_restr0.0640.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024970
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02976
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0453.1462202
X-RAY DIFFRACTIONr_mcbond_other1.0443.1462201
X-RAY DIFFRACTIONr_mcangle_it1.7564.7112750
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.1613.3212294
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 172 -
Rwork0.368 3237 -
obs--94.93 %

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