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- PDB-3tmh: Crystal structure of dual-specific A-kinase anchoring protein 2 i... -

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Basic information

Entry
Database: PDB / ID: 3tmh
TitleCrystal structure of dual-specific A-kinase anchoring protein 2 in complex with cAMP-dependent protein kinase A type II alpha and PDZK1
Components
  • A-kinase anchor protein 10, mitochondrial
  • Na(+)/H(+) exchange regulatory cofactor NHE-RF3
  • cAMP-dependent protein kinase type II-alpha regulatory subunit
KeywordsTRANSPORT PROTEIN/SIGNALING PROTEIN / alpha helical bundle / PDZ fold / Anchoring protein / PKA / PDZ proteins / membrane / TRANSPORT PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


positive regulation of cation transmembrane transport / carnitine transport / GPER1 signaling / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Factors involved in megakaryocyte development and platelet production / positive regulation of ion transmembrane transporter activity / Hedgehog 'off' state / PKA activation ...positive regulation of cation transmembrane transport / carnitine transport / GPER1 signaling / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Factors involved in megakaryocyte development and platelet production / positive regulation of ion transmembrane transporter activity / Hedgehog 'off' state / PKA activation / scavenger receptor binding / cAMP-dependent protein kinase regulator activity / nucleotide-activated protein kinase complex / xenobiotic detoxification by transmembrane export across the plasma membrane / positive regulation of protein localization to membrane / Vasopressin regulates renal water homeostasis via Aquaporins / cAMP-dependent protein kinase inhibitor activity / protein kinase A binding / microvillus membrane / cAMP-dependent protein kinase complex / plasma membrane raft / protein kinase A catalytic subunit binding / brush border / positive regulation of protein targeting to membrane / small molecule binding / beta-2 adrenergic receptor binding / protein-membrane adaptor activity / cAMP binding / T-tubule / regulation of monoatomic anion transport / protein localization to plasma membrane / PDZ domain binding / brush border membrane / regulation of protein phosphorylation / modulation of chemical synaptic transmission / protein localization / Factors involved in megakaryocyte development and platelet production / apical plasma membrane / protein domain specific binding / signaling receptor binding / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / synapse / protein-containing complex binding / perinuclear region of cytoplasm / signal transduction / protein-containing complex / mitochondrion / extracellular exosome / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
A-kinase anchor protein 10, PKA-binding (AKB) domain / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / PDZ domain / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. ...A-kinase anchor protein 10, PKA-binding (AKB) domain / cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / PDZ domain / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / PDZ domain / Pdz3 Domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / PDZ domain / RmlC-like jelly roll fold / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
A-kinase anchor protein 10, mitochondrial / cAMP-dependent protein kinase type II-alpha regulatory subunit / Na(+)/H(+) exchange regulatory cofactor NHE-RF3
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsSarma, G.N. / Phan, R.H. / Sankaran, B. / Taylor, S.S.
CitationJournal: To be Published
Title: Differential mode of D-AKAP2 to PKA isoforms: Insights from D-AKAP2 PKA RII PDZK1 ternary complex structure
Authors: Sarma, G.N. / Phan, R.H. / Sankaran, B. / Taylor, S.S.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
C: cAMP-dependent protein kinase type II-alpha regulatory subunit
D: A-kinase anchor protein 10, mitochondrial
E: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
F: cAMP-dependent protein kinase type II-alpha regulatory subunit
G: cAMP-dependent protein kinase type II-alpha regulatory subunit
H: A-kinase anchor protein 10, mitochondrial
I: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
L: A-kinase anchor protein 10, mitochondrial


Theoretical massNumber of molelcules
Total (without water)65,26210
Polymers65,26210
Non-polymers00
Water1448
1
A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
C: cAMP-dependent protein kinase type II-alpha regulatory subunit
D: A-kinase anchor protein 10, mitochondrial
E: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
F: cAMP-dependent protein kinase type II-alpha regulatory subunit
G: cAMP-dependent protein kinase type II-alpha regulatory subunit
H: A-kinase anchor protein 10, mitochondrial
I: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
L: A-kinase anchor protein 10, mitochondrial

A: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
C: cAMP-dependent protein kinase type II-alpha regulatory subunit
D: A-kinase anchor protein 10, mitochondrial
E: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
F: cAMP-dependent protein kinase type II-alpha regulatory subunit
G: cAMP-dependent protein kinase type II-alpha regulatory subunit
H: A-kinase anchor protein 10, mitochondrial
I: Na(+)/H(+) exchange regulatory cofactor NHE-RF3
L: A-kinase anchor protein 10, mitochondrial


Theoretical massNumber of molelcules
Total (without water)130,52420
Polymers130,52420
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area24670 Å2
ΔGint-195 kcal/mol
Surface area46620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.472, 121.472, 88.282
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32
42
13
23
33

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 375:456 )
211chain E and (resseq 375:456 )
311chain I and (resseq 375:456 )
112chain B and (resseq 8:43 )
212chain C and (resseq 3:41 )
312chain F and (resseq 5:43 )
412chain G and (resseq 7:39 )
113chain D and (resseq 635:662 )
213chain H and (resseq 640:662 )
313chain L and (resseq 636:662 )

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Na(+)/H(+) exchange regulatory cofactor NHE-RF3 / NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi ...NHERF-3 / CFTR-associated protein of 70 kDa / Na(+)/H(+) exchanger regulatory factor 3 / Na/Pi cotransporter C-terminal-associated protein 1 / NaPi-Cap1 / PDZ domain-containing protein 1 / Sodium-hydrogen exchanger regulatory factor 3


Mass: 9277.620 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 375-459
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDZK1, CAP70, NHERF3, PDZD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T2W1
#2: Protein/peptide
cAMP-dependent protein kinase type II-alpha regulatory subunit


Mass: 5542.311 Da / Num. of mol.: 4
Fragment: Dimerization/docking domain (D/D), UNP RESIDUES 3-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Prkar2a / Production host: Escherichia coli (E. coli) / References: UniProt: P12368
#3: Protein/peptide A-kinase anchor protein 10, mitochondrial / AKAP-10 / Dual specificity A kinase-anchoring protein 2 / D-AKAP-2 / Protein kinase A-anchoring ...AKAP-10 / Dual specificity A kinase-anchoring protein 2 / D-AKAP-2 / Protein kinase A-anchoring protein 10 / PRKA10


Mass: 5086.658 Da / Num. of mol.: 3
Fragment: A-kinase binding domain (AKB), UNP RESIDUES 623-662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKAP10 / Production host: Escherichia coli (E. coli) / References: UniProt: O43572
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS IS A NATURAL VARIANT

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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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7
Details: 100 mM HEPES, pH 7, 20% PEG MME, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2010
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 3.7→100 Å / Num. all: 8304 / Num. obs: 8304 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.7 % / Biso Wilson estimate: 117 Å2 / Rmerge(I) obs: 0.71 / Net I/σ(I): 16.9
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.8 / Num. unique all: 805 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→50.038 Å / SU ML: 0.54 / σ(F): 0 / Phase error: 33.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3284 572 7.46 %Random
Rwork0.2683 ---
obs0.2727 7666 99.86 %-
all-8238 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 115.468 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7506 Å2-0 Å2-0 Å2
2--0.7506 Å20 Å2
3----1.5013 Å2
Refinement stepCycle: LAST / Resolution: 3.8→50.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 0 8 3553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193739
X-RAY DIFFRACTIONf_angle_d1.8354889
X-RAY DIFFRACTIONf_dihedral_angle_d15.351319
X-RAY DIFFRACTIONf_chiral_restr0.096576
X-RAY DIFFRACTIONf_plane_restr0.01644
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A561X-RAY DIFFRACTIONPOSITIONAL
12E561X-RAY DIFFRACTIONPOSITIONAL0.07
13I516X-RAY DIFFRACTIONPOSITIONAL0.095
21B282X-RAY DIFFRACTIONPOSITIONAL
22C282X-RAY DIFFRACTIONPOSITIONAL0.116
23F292X-RAY DIFFRACTIONPOSITIONAL0.045
24G262X-RAY DIFFRACTIONPOSITIONAL0.1
31D179X-RAY DIFFRACTIONPOSITIONAL
32H179X-RAY DIFFRACTIONPOSITIONAL0.078
33L211X-RAY DIFFRACTIONPOSITIONAL0.074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.18260.37351550.27131724X-RAY DIFFRACTION100
4.1826-4.78740.28781390.21211747X-RAY DIFFRACTION100
4.7874-6.030.32141240.25241794X-RAY DIFFRACTION100
6.03-50.04220.33591540.29991829X-RAY DIFFRACTION100
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)
11.2571-0.3561-0.55450.289-0.27011.10880.17530.6299-0.81010.0918-0.10380.55821.0918-0.56271.3696-0.0628-0.7826-0.4631-0.7371-0.65940.1464-21.300758.3582-32.6037
20.116-0.0465-0.45210.04120.25772.0982-0.21820.158-1.0553-0.3408-0.80880.69180.71321.0567-5.23941.60660.4064-0.94711.02820.20662.5739-15.185635.91457.8166
30.0861-0.0497-0.04480.06060.17030.4087-0.2165-0.42060.14890.16130.1182-0.2298-0.03690.2124-1.27480.55631.3063-0.39071.1207-0.28790.4045-11.751339.1535-0.8863
42.09770.41870.07840.81120.00590.28860.3841-0.6606-0.3101-0.030.3534-0.36220.00380.05441.80840.9078-0.3577-0.28820.6588-0.05280.9991-16.124252.2999-4.7777
51.0153-0.3990.06791.07950.56822.5785-0.6971-0.7475-0.17830.8230.1163-0.07650.3088-0.5951-1.52320.91990.2115-0.06770.58920.13050.2606-15.938771.6799-6.3898
62.19981.22930.41661.3259-0.02510.1765-0.16620.28570.31820.5012-1.3261.29670.2327-0.7618-1.66791.45510.1435-0.0061.2258-0.29490.856-51.176297.22733.6547
70.45190.33620.670.99951.09971.46540.3088-0.23720.30690.2579-0.2120.11610.4276-0.32990.64180.3477-0.2126-0.11930.4845-0.76491.1763-40.303495.80083.4155
80.4071-0.1467-0.59130.3908-0.18721.4733-0.287-0.2418-0.41740.0077-0.11980.19830.09020.3061-0.38650.71890.0798-0.19410.330.01580.6482-34.770488.5647-8.36
93.0420.56420.97621.68460.14880.7822-0.1384-0.98060.06220.55930.1427-0.5853-0.1584-0.02080.18170.07530.1652-0.30230.6224-0.37080.7002-57.040871.8223-2.359
101.8664-0.69471.1681.4614-0.51510.7855-0.0456-1.1702-0.88950.37460.12130.18470.2396-0.216-0.03871.15890.0937-0.31420.75040.14350.5749-34.098163.773911.3385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain L

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