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- PDB-4d0o: AKAP13 (AKAP-Lbc) DH domain -

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Basic information

Entry
Database: PDB / ID: 4d0o
TitleAKAP13 (AKAP-Lbc) DH domain
ComponentsA-KINASE ANCHOR PROTEIN 13
KeywordsCELL CYCLE / AKAP-LBC / GEF / RHOGEF / PH DOMAIN
Function / homology
Function and homology information


regulation of sarcomere organization / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / MAP-kinase scaffold activity / cardiac muscle cell differentiation / regulation of Rho protein signal transduction / regulation of small GTPase mediated signal transduction / protein kinase A binding / RHOB GTPase cycle / positive regulation of Rho protein signal transduction / adrenergic receptor signaling pathway ...regulation of sarcomere organization / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / MAP-kinase scaffold activity / cardiac muscle cell differentiation / regulation of Rho protein signal transduction / regulation of small GTPase mediated signal transduction / protein kinase A binding / RHOB GTPase cycle / positive regulation of Rho protein signal transduction / adrenergic receptor signaling pathway / NRAGE signals death through JNK / RHOC GTPase cycle / RHOA GTPase cycle / guanyl-nucleotide exchange factor activity / bone development / small GTPase binding / G alpha (12/13) signalling events / actin cytoskeleton / heart development / cell cortex / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / G protein-coupled receptor signaling pathway / membrane / nucleus / metal ion binding / cytosol
Similarity search - Function
RII binding domain / RII binding domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain ...RII binding domain / RII binding domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / 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 / C1-like domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
A-kinase anchor protein 13
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: A-KINASE ANCHOR PROTEIN 13
B: A-KINASE ANCHOR PROTEIN 13


Theoretical massNumber of molelcules
Total (without water)57,5232
Polymers57,5232
Non-polymers00
Water00
1
A: A-KINASE ANCHOR PROTEIN 13


Theoretical massNumber of molelcules
Total (without water)28,7611
Polymers28,7611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: A-KINASE ANCHOR PROTEIN 13


Theoretical massNumber of molelcules
Total (without water)28,7611
Polymers28,7611
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.130, 94.840, 109.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.34059, -0.03735, -0.93947), (0.03377, -0.99905, 0.02748), (-0.9396, -0.02237, 0.34153)
Vector: -8.62884, -8.85407, -5.95361)

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Components

#1: Protein A-KINASE ANCHOR PROTEIN 13 / AKAP-13 / AKAP-LBC / BREAST CANCER NUCLEAR RECEPTOR-BINDING AUXILIARY PROTEIN / GUANINE NUCLEOTIDE ...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 / AKAP13


Mass: 28761.432 Da / Num. of mol.: 2 / Fragment: RHOGEF DOMAIN, RESIDUES 1972-2207
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: Q12802

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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: 49 % / 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: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.75→42.13 Å / Num. obs: 14660 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 7.2
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→71.55 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.84 / SU B: 41.167 / SU ML: 0.361 / Cross valid method: THROUGHOUT / ESU R Free: 0.445 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30849 711 4.9 %RANDOM
Rwork0.23641 ---
obs0.23969 13897 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.658 Å2
Baniso -1Baniso -2Baniso -3
1--3.5 Å20 Å20 Å2
2--1.28 Å20 Å2
3---2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.75→71.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 0 0 3692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193751
X-RAY DIFFRACTIONr_bond_other_d0.0020.023567
X-RAY DIFFRACTIONr_angle_refined_deg0.8871.9535059
X-RAY DIFFRACTIONr_angle_other_deg0.77438138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.145471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31624.699166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11715673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.641517
X-RAY DIFFRACTIONr_chiral_restr0.0480.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024258
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02879
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_it0.6582.371893
X-RAY DIFFRACTIONr_mcbond_other0.6582.3691892
X-RAY DIFFRACTIONr_mcangle_it1.1933.5522361
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5672.3831858
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: 2.75→2.822 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 53 -
Rwork0.324 984 -
obs--99.52 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.88650.0859-0.7733.0310.48592.2042-0.1450.07560.066-0.00350.2397-0.2322-0.35030.1363-0.09470.4108-0.0715-0.02870.1142-0.04840.2142-15.0046.82521.221
22.8588-0.6233-1.15222.05190.56632.6531-0.0301-0.16530.14130.1376-0.02620.1846-0.2157-0.10970.05630.27460.0016-0.03370.0272-0.03230.1476-23.41-15.71615.143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1960 - 2211
2X-RAY DIFFRACTION2B1960 - 2211

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