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- PDB-3pna: Crystal Structure of cAMP bound (91-244)RIa Subunit of cAMP-depen... -

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Basic information

Entry
Database: PDB / ID: 3pna
TitleCrystal Structure of cAMP bound (91-244)RIa Subunit of cAMP-dependent Protein Kinase
ComponentscAMP-dependent protein kinase type I-alpha regulatory subunit
KeywordsTRANSFERASE / beta-barrel / cAMP-binding / catalytic subunit
Function / homology
Function and homology information


sperm head-tail coupling apparatus / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / negative regulation of cAMP/PKA signal transduction ...sperm head-tail coupling apparatus / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / PKA activation / nucleotide-activated protein kinase complex / Hedgehog 'off' state / negative regulation of cAMP/PKA signal transduction / cAMP-dependent protein kinase inhibitor activity / sarcomere organization / cardiac muscle cell proliferation / cAMP-dependent protein kinase complex / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / protein kinase A catalytic subunit binding / negative regulation of activated T cell proliferation / mesoderm formation / plasma membrane raft / immunological synapse / axoneme / cAMP binding / multivesicular body / cellular response to glucagon stimulus / neuromuscular junction / positive regulation of insulin secretion / adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein domain specific binding / negative regulation of gene expression / centrosome / ubiquitin protein ligase binding / glutamatergic synapse / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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 / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding 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 / : / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-dependent protein kinase type I-alpha regulatory subunit
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.503 Å
AuthorsKim, C. / Taylor, S.
CitationJournal: Mol Cell Proteomics / Year: 2011
Title: Cyclic AMP Analog Blocks Kinase Activation by Stabilizing Inactive Conformation: Conformational Selection Highlights a New Concept in Allosteric Inhibitor Design.
Authors: Badireddy, S. / Yunfeng, G. / Ritchie, M. / Akamine, P. / Wu, J. / Kim, C.W. / Taylor, S.S. / Qingsong, L. / Swaminathan, K. / Anand, G.S.
History
DepositionNov 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: cAMP-dependent protein kinase type I-alpha regulatory subunit
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4305
Polymers34,6792
Non-polymers7513
Water7,512417
1
A: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6692
Polymers17,3401
Non-polymers3291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7613
Polymers17,3401
Non-polymers4212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: cAMP-dependent protein kinase type I-alpha regulatory subunit
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules

A: cAMP-dependent protein kinase type I-alpha regulatory subunit
B: cAMP-dependent protein kinase type I-alpha regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,85910
Polymers69,3584
Non-polymers1,5016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-y,-x,-z+1/31
Buried area7280 Å2
ΔGint-45 kcal/mol
Surface area23750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.642, 62.642, 158.197
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-278-

HOH

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Components

#1: Protein cAMP-dependent protein kinase type I-alpha regulatory subunit


Mass: 17339.561 Da / Num. of mol.: 2
Fragment: N-terminal cAMP binding domain (UNP residues 92-245)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: skeletal muscle / Gene: PRKAR1A / Plasmid: pUC vector / Production host: Escherichia coli (E. coli) / References: UniProt: P00514, EC: 2.7.1.37
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.58 Å3/Da / Density % sol: 52.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate trihydrate, 2.0 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 24, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→22.3 Å / Num. obs: 56705 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.8
Reflection shellResolution: 1.5→1.52 Å / Redundancy: 6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine: 1.6_289)refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.503→22.259 Å / SU ML: 0.16 / σ(F): 0.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1822 2772 5.08 %RANDOM
Rwork0.1568 ---
obs0.1582 54558 95.73 %-
all-56705 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.491 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1081 Å2-0 Å2-0 Å2
2--1.1081 Å20 Å2
3----2.2163 Å2
Refinement stepCycle: LAST / Resolution: 1.503→22.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 50 417 2453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062149
X-RAY DIFFRACTIONf_angle_d1.1372912
X-RAY DIFFRACTIONf_dihedral_angle_d19.303776
X-RAY DIFFRACTIONf_chiral_restr0.072330
X-RAY DIFFRACTIONf_plane_restr0.004362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5027-1.55640.18052530.1734814X-RAY DIFFRACTION90
1.5564-1.61870.1812670.15814973X-RAY DIFFRACTION93
1.6187-1.69240.17652450.15515102X-RAY DIFFRACTION94
1.6924-1.78160.18312710.15265101X-RAY DIFFRACTION95
1.7816-1.89310.16532810.15515067X-RAY DIFFRACTION94
1.8931-2.03920.16872660.15255318X-RAY DIFFRACTION98
2.0392-2.24430.15783170.14725346X-RAY DIFFRACTION99
2.2443-2.56860.18932650.15675346X-RAY DIFFRACTION99
2.5686-3.23460.20153130.15415408X-RAY DIFFRACTION99
3.2346-22.26140.17032940.14945311X-RAY DIFFRACTION95
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)
11.3874-0.0381-0.73771.13760.65541.61130.19150.54420.0516-0.078-0.61590.10370.002-0.55210.24250.13130.0677-0.04180.24510.00170.127210.1314-0.667819.4913
20.75940.162-0.17390.6061-0.26690.54230.035-0.18280.04090.1727-0.01780.1080.01850.2663-0.01270.1546-0.0213-0.01920.1886-0.0020.108323.0242-2.235626.9754
31.45610.1148-0.24130.4360.46161.15120.278-0.20430.63870.0771-0.21810.054-0.6640.0459-0.06540.2766-0.0890.00930.0987-0.01640.209124.452110.739621.2544
41.0320.3261-0.48080.5192-0.04050.735-0.09050.00230.13620.17270.1287-0.1791-0.22750.1446-0.00050.2051-0.01-0.00670.13480.01420.152417.22134.149520.8099
50.50620.54260.1131.379-0.45630.5574-0.0192-0.0104-0.1841-0.07730.0082-0.29250.01670.02650.02590.14940.00220.02750.11840.02780.178926.3077-11.299210.391
60.8763-0.8364-0.07211.2958-0.61470.89720.10540.2731-0.0603-0.4103-0.0691-0.09230.2412-0.1403-0.03740.1934-0.0163-0.00650.150.00590.119821.7978-3.06063.2178
70.90060.3369-0.58262.1647-0.92962.1212-0.2065-0.5304-0.22030.41540.0342-0.4211-0.11570.50060.1760.171-0.022-0.04480.18510.0550.209331.5371-4.642516.8371
80.6959-0.31140.15861.0610.08011.08670.23060.0324-0.0055-0.1544-0.0134-0.651-0.32240.1083-0.17030.19980.02120.13540.15760.05450.308536.2695-4.21271.764
90.5894-0.0621-0.34440.6066-0.09030.7902-0.0463-0.2455-0.01330.08050.0028-0.3167-0.1897-0.1611-0.05080.1095-0.0311-0.03110.13690.0270.175730.7057-0.145912.8738
100.59340.476-0.1071.96870.28010.72660.01150.19950.1416-0.4093-0.0419-0.2108-0.30730.10820.20480.13790.0041-0.01260.12060.04020.13121.46816.20172.5879
110.2470.2928-0.2551.75810.36280.57210.17450.19820.0563-0.5447-0.2603-0.36440.11080.06180.06660.16840.00920.04810.12130.03570.157928.3773-4.1362.0682
120.9945-0.40750.68271.4967-0.45310.5972-0.2822-0.21430.00510.48210.1119-0.1941-0.1098-0.04870.1170.16580.0028-0.03410.12850.03820.138826.7847-6.24516.5762
130.5074-0.12430.26580.9744-0.42371.2232-0.1978-0.09960.00890.1960.41330.1568-0.4699-0.6423-0.17320.21140.070.0010.18770.05580.124415.4356.241810.6654
140.2082-0.5099-0.29562.5815-0.50433.2123-0.7336-0.22260.11760.44780.0637-1.5224-1.42920.03450.55110.557-0.0887-0.17610.24310.01250.409922.890414.01589.5642
152.376-0.4616-2.33871.72470.88953.45520.14130.2427-0.0302-0.3925-0.1169-0.2641-0.3372-0.1174-0.04720.1892-0.0610.03740.1621-0.00710.16117.9979-10.98096.869
160.2890.0081-0.28960.9122-0.44250.99590.00220.06460.08750.1671-0.0080.0775-0.2065-0.36450.04110.1431-0.02040.00670.1802-0.01160.12886.9391-10.683621.0129
170.3904-0.3333-0.76760.68650.65421.593-0.15190.1245-0.1410.21810.0381-0.11730.660.01050.06980.2226-0.05260.02530.1583-0.02670.12968.0474-23.481917.5925
180.56860.0357-0.31121.50380.09832.66470.16440.0275-0.16990.2624-0.3049-0.34310.8209-0.05440.08710.26410.0161-0.02940.19350.02440.197316.8658-27.037914.0686
191.14770.2584-0.17050.8580.27210.6911-0.0398-0.03-0.18960.1617-0.0496-0.02970.1843-0.09690.07390.1231-0.0362-0.00150.11420.00540.124817.3765-17.990613.3762
200.2988-0.10510.56841.0808-0.70491.6587-0.1633-0.31140.0202-0.04180.03090.2465-0.2251-0.41650.12540.11430.0051-0.00990.1903-0.04690.1845-1.6449-13.07936.702
211.0285-0.3848-0.43410.23690.10060.3632-0.07760.18520.1561-0.1726-0.03070.1176-0.2580.00880.12580.1549-0.0305-0.02930.2357-0.01580.17030.6364-17.2298-5.4435
220.90180.02240.80910.798-0.13610.88560.0602-0.10080.1270.00360.02260.1777-0.0332-0.335-0.04820.0945-0.02430.00050.1832-0.00550.13892.4572-19.867.0773
231.45690.9826-0.45940.9847-0.53060.74250.07530.1536-0.0775-0.17070.20240.19630.0583-0.2488-0.1410.1094-0.0434-0.05450.2256-0.05810.2281-6.2122-27.1501-2.6356
240.57980.11020.24650.42620.19810.18620.0581-0.2194-0.08930.0977-0.06490.11210.0942-0.18170.00670.12-0.06010.00020.2205-0.00160.15242.0111-24.78257.706
251.8873-0.6464-0.23360.71710.04031.15710.04510.0896-0.52050.1260.236-0.05010.48970.0478-0.24940.1523-0.0063-0.01960.1593-0.03910.170511.0099-24.4286-2.924
261.4943-0.52971.01551.3384-0.27190.78560.06780.023-0.1085-0.0647-0.06160.1816-0.0248-0.24060.02290.0887-0.038-0.0150.1595-0.02460.14420.0058-21.3076-0.5921
271.63950.39090.48470.90930.0920.1372-0.02860.25780.1515-0.21120.067-0.0804-0.0625-0.0401-0.00260.1228-0.04360.00270.14-0.00770.108111.4431-17.02534.3967
281.16372.32580.4745.8525-0.2032.2077-0.31960.7831-0.9648-0.97930.2373-0.72430.9446-0.16550.04940.1914-0.04250.06870.1695-0.07420.188720.261-21.44812.735
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 112:117)
2X-RAY DIFFRACTION2(chain A and resid 118:130)
3X-RAY DIFFRACTION3(chain A and resid 131:142)
4X-RAY DIFFRACTION4(chain A and resid 143:152)
5X-RAY DIFFRACTION5(chain A and resid 153:163)
6X-RAY DIFFRACTION6(chain A and resid 164:173)
7X-RAY DIFFRACTION7(chain A and resid 174:179)
8X-RAY DIFFRACTION8(chain A and resid 180:192)
9X-RAY DIFFRACTION9(chain A and resid 193:199)
10X-RAY DIFFRACTION10(chain A and resid 200:206)
11X-RAY DIFFRACTION11(chain A and resid 207:216)
12X-RAY DIFFRACTION12(chain A and resid 217:224)
13X-RAY DIFFRACTION13(chain A and resid 225:233)
14X-RAY DIFFRACTION14(chain A and resid 234:240)
15X-RAY DIFFRACTION15(chain B and resid 110:118)
16X-RAY DIFFRACTION16(chain B and resid 119:125)
17X-RAY DIFFRACTION17(chain B and resid 126:134)
18X-RAY DIFFRACTION18(chain B and resid 135:141)
19X-RAY DIFFRACTION19(chain B and resid 142:151)
20X-RAY DIFFRACTION20(chain B and resid 152:159)
21X-RAY DIFFRACTION21(chain B and resid 160:169)
22X-RAY DIFFRACTION22(chain B and resid 170:179)
23X-RAY DIFFRACTION23(chain B and resid 180:192)
24X-RAY DIFFRACTION24(chain B and resid 193:199)
25X-RAY DIFFRACTION25(chain B and resid 200:204)
26X-RAY DIFFRACTION26(chain B and resid 205:220)
27X-RAY DIFFRACTION27(chain B and resid 221:229)
28X-RAY DIFFRACTION28(chain B and resid 230:234)

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