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- PDB-5nin: Crystal Structure of AKAP79 calmodulin binding domain peptide in ... -

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Basic information

Entry
Database: PDB / ID: 5nin
TitleCrystal Structure of AKAP79 calmodulin binding domain peptide in complex with Ca2+/Calmodulin
Components
  • A-kinase anchor protein 5
  • Calmodulin
KeywordsSIGNALING PROTEIN / Calmodulin / Calcium / AKAP79 / AKAP150 / AKAP5 / AKAP / EF hand / Ca2+
Function / homology
Function and homology information


positive regulation of endosome to plasma membrane protein transport / : / postsynaptic recycling endosome membrane / postsynaptic recycling endosome / positive regulation of calcium ion import across plasma membrane / ROBO receptors bind AKAP5 / protein serine/threonine phosphatase complex / : / : / : ...positive regulation of endosome to plasma membrane protein transport / : / postsynaptic recycling endosome membrane / postsynaptic recycling endosome / positive regulation of calcium ion import across plasma membrane / ROBO receptors bind AKAP5 / protein serine/threonine phosphatase complex / : / : / : / : / calcineurin-NFAT signaling cascade / : / positive regulation of protein autophosphorylation / negative regulation of peptidyl-threonine phosphorylation / positive regulation of calcineurin-NFAT signaling cascade / GABA receptor binding / negative regulation of adenylate cyclase activity / protein phosphatase 2B binding / Trafficking of AMPA receptors / establishment of protein localization to mitochondrial membrane / type 3 metabotropic glutamate receptor binding / beta-2 adrenergic receptor binding / CaM pathway / positive regulation of peptidyl-threonine phosphorylation / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / positive regulation of DNA binding / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / response to corticosterone / CaMK IV-mediated phosphorylation of CREB / PKA activation / negative regulation of high voltage-gated calcium channel activity / protein kinase A binding / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / protein kinase A regulatory subunit binding / nitric-oxide synthase binding / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / regulation of synaptic vesicle exocytosis / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / adenylate cyclase binding / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / excitatory synapse / positive regulation of protein serine/threonine kinase activity / DARPP-32 events / Smooth Muscle Contraction / glutamate receptor binding / detection of calcium ion / catalytic complex / regulation of synaptic vesicle endocytosis / regulation of cardiac muscle contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / activation of adenylate cyclase activity / cellular response to interferon-beta / Protein methylation / phosphatidylinositol 3-kinase binding / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / presynaptic cytosol / positive regulation of nitric-oxide synthase activity / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / enzyme regulator activity / eNOS activation / titin binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / sperm midpiece / regulation of calcium-mediated signaling / voltage-gated potassium channel complex / dendrite membrane / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / regulation of heart rate
Similarity search - Function
A kinase-anchoring protein AKAP5 and AKAP12, calmodulin (CaM)-binding motif / A-kinase anchor protein 5 / WSK motif / A kinase-anchoring proteins AKAP-5 and AKAP-12 calmodulin (CaM)-binding motif profile. / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site ...A kinase-anchoring protein AKAP5 and AKAP12, calmodulin (CaM)-binding motif / A-kinase anchor protein 5 / WSK motif / A kinase-anchoring proteins AKAP-5 and AKAP-12 calmodulin (CaM)-binding motif profile. / EF-hand / : / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Calmodulin-1 / A-kinase anchor protein 5 / Calmodulin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGold, M.G. / Patel, N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust104194/Z/14/Z United Kingdom
Royal Society104194/Z/14/Z United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/N015274/1 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Molecular basis of AKAP79 regulation by calmodulin.
Authors: Patel, N. / Stengel, F. / Aebersold, R. / Gold, M.G.
History
DepositionMar 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Calmodulin
A: Calmodulin
C: A-kinase anchor protein 5
D: A-kinase anchor protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,12813
Polymers37,4884
Non-polymers6419
Water8,989499
1
B: Calmodulin
D: A-kinase anchor protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3049
Polymers18,7442
Non-polymers5607
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-86 kcal/mol
Surface area8540 Å2
MethodPISA
2
A: Calmodulin
C: A-kinase anchor protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8244
Polymers18,7442
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-39 kcal/mol
Surface area8490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.460, 76.460, 128.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Calmodulin / CaM


Mass: 16852.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62158, UniProt: P0DP23*PLUS
#2: Protein/peptide A-kinase anchor protein 5 / AKAP-5 / A-kinase anchor protein 79 kDa / AKAP 79 / H21 / cAMP-dependent protein kinase regulatory ...AKAP-5 / A-kinase anchor protein 79 kDa / AKAP 79 / H21 / cAMP-dependent protein kinase regulatory subunit II high affinity-binding protein


Mass: 1891.273 Da / Num. of mol.: 2 / Fragment: UNP residues 77-92 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P24588
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 2.4 M ammonium sulphate, 50 mM citrate pH 5.4, 0.3 M NDSB-195

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9685 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9685 Å / Relative weight: 1
ReflectionResolution: 1.7→65.77 Å / Num. obs: 42359 / % possible obs: 99.1 % / Redundancy: 7.4 % / CC1/2: 0.99 / Rpim(I) all: 0.063 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2193 / CC1/2: 0.552 / Rpim(I) all: 0.354 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IWQ (85-148)

1iwq


Resolution: 1.7→54.065 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.93
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 3860 4.94 %random selection
Rwork0.1644 ---
obs0.1659 42303 97.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→54.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2394 0 29 499 2922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092465
X-RAY DIFFRACTIONf_angle_d0.9043319
X-RAY DIFFRACTIONf_dihedral_angle_d10.6681501
X-RAY DIFFRACTIONf_chiral_restr0.052370
X-RAY DIFFRACTIONf_plane_restr0.005438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72070.25851110.23872659X-RAY DIFFRACTION98
1.7207-1.74250.2631590.22552660X-RAY DIFFRACTION98
1.7425-1.76550.26861240.23072670X-RAY DIFFRACTION99
1.7655-1.78960.22991320.21852715X-RAY DIFFRACTION98
1.7896-1.81520.28271130.2182734X-RAY DIFFRACTION98
1.8152-1.84230.21051510.20262639X-RAY DIFFRACTION98
1.8423-1.87110.24251160.19492691X-RAY DIFFRACTION98
1.8711-1.90180.23381340.20542690X-RAY DIFFRACTION98
1.9018-1.93460.25871300.18832680X-RAY DIFFRACTION98
1.9346-1.96970.19951230.17952703X-RAY DIFFRACTION98
1.9697-2.00760.1971510.1632647X-RAY DIFFRACTION98
2.0076-2.04860.17871480.15872615X-RAY DIFFRACTION97
2.0486-2.09320.18661540.15792675X-RAY DIFFRACTION98
2.0932-2.14190.19381620.14642661X-RAY DIFFRACTION98
2.1419-2.19540.15331280.14252638X-RAY DIFFRACTION97
2.1954-2.25480.16171500.13992636X-RAY DIFFRACTION97
2.2548-2.32110.18981030.13342666X-RAY DIFFRACTION97
2.3211-2.3960.15971470.13712648X-RAY DIFFRACTION97
2.396-2.48170.20781800.13962586X-RAY DIFFRACTION96
2.4817-2.5810.14681170.13732678X-RAY DIFFRACTION97
2.581-2.69850.17531360.13662640X-RAY DIFFRACTION97
2.6985-2.84080.18261540.14322659X-RAY DIFFRACTION97
2.8408-3.01870.21131480.15722598X-RAY DIFFRACTION96
3.0187-3.25180.1881360.1532642X-RAY DIFFRACTION97
3.2518-3.5790.18591250.14642682X-RAY DIFFRACTION97
3.579-4.09670.1581370.13862642X-RAY DIFFRACTION97
4.0967-5.16080.17661450.1612615X-RAY DIFFRACTION96
5.1608-54.09270.23261460.23432578X-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)
10.0162-0.0135-0.00040.0607-0.01030.00690.0038-0.074-0.0168-0.0394-0.00960.05440.0099-0.0019-0.00090.05290.01890.01150.06590.0010.05116.8674-26.9563-27.8416
20.0182-0.0026-0.00290.0014-0.00090.0042-0.0350.01310.0057-0.00940.0035-0.001-0.01230.0014-0.00010.11440.0153-0.0010.072-0.02130.07371.1044-21.5112-41.0999
30.0143-0.0148-0.0060.05220.01220.01990.04450.00510.0160.0194-0.0064-0.0188-0.078-0.00950.00170.0306-0.00530.01380.0263-0.00420.05642.5112-14.5323-27.5451
40.00310.0081-0.00550.006-0.00460.0113-0.0107-0.0264-0.0011-0.1050.0601-0.0192-0.00890.0090.01630.2004-0.1083-0.016-0.0233-0.02940.126410.0588-7.4539-28.2829
50.0184-0.007-0.0020.0050.00430.0049-0.0068-0.09120.05180.00110.01590.0136-0.1050.023200.0805-0.00140.00860.0635-0.01430.071812.2748-18.587-28.3505
60.00790.0032-0.00860.0141-0.01140.0407-0.0293-0.02140.01180.03580.0143-0.0117-0.1320.038-0.00460.0390.0042-0.00220.0498-0.00440.04140.1828-17.0062-11.6369
70.002-0.00010.00170.0045-0.01030.0109-0.00930.00430.0079-0.0119-0.0073-0.01510.0393-0.0411-00.0423-0.01530.00860.0504-0.00750.0353-8.2255-26.4649-21.2529
80.03610.03420.01670.04090.00630.0291-0.01990.0017-0.0339-0.0202-0.08060.06560.059-0.0318-0.0389-0.0129-0.1758-0.1277-0.0893-0.197-0.1327-9.6879-32.9721-12.7818
90.1659-0.0209-0.03430.1339-0.01270.01650.0557-0.0234-0.0183-0.03030.03670.03020.0758-0.02610.02760.0336-0.0052-0.00410.08190.00290.0149-2.5762-25.2121-5.2899
100.03480.0039-0.00910.03110.010.0317-0.0521-0.0344-0.0772-0.0211-0.03870.0083-0.0062-0.0153-0.05280.00620.08110.083-0.0339-0.08-0.037911.9528-31.5816-38.1399
110.02420.01570.03470.05090.05550.0671-0.0398-0.0414-0.01470.02650.1079-0.0692-0.03750.04580.03980.02180.02440.00830.0341-0.00970.055123.0075-35.816-34.8701
120.04930.03170.00280.0214-0.00760.01570.17780.0310.0156-0.02220.02020.011-0.02480.04750.01810.0411-0.0120.0060.0592-0.0080.098631.1052-28.3397-34.9807
130.00910.01360.00730.013-0.00120.0032-0.02280.08520.0398-0.10190.0202-0.0548-0.01730.0407-00.0607-0.00910.01880.0561-0.00940.057320.1764-25.2711-37.5392
140.00120.0012-0.00040.00510.0070.00760.0241-0.01280.0116-0.06430.0225-0.0259-0.01030.120800.0593-0.01430.00080.0535-0.01680.043722.7435-33.6442-52.8623
150.0014-0.0008-0.00010.0044-0.00090.00070.0730.0099-0.0014-0.01180.0172-0.04590.02720.0379-00.0820.0202-0.010.05080.00530.064223.1084-47.4618-53.2197
160.00040.00060.00410.00060.00160.00930.0787-0.0986-0.03190.0344-0.0590.03720.0948-0.0337-00.0726-0.0198-0.00640.07810.01070.08812.6815-46.1606-44.2871
170.00480.0023-0.00540.0041-0.00480.00450.0165-0.0856-0.0496-0.0142-0.00820.03340.0337-0.0822-0.00230.0801-0.0258-0.01040.08560.01990.06227.186-48.5065-53.0537
180.1449-0.031-0.05840.02150.04950.15220.165-0.0298-0.0726-0.05390.1263-0.00650.1621-0.06070.19680.0760.001-0.0524-0.0131-0.0761-0.095715.5895-41.6861-60.2842
190.03050.004-0.00790.02930.00210.0453-0.04950.05620.01360.0046-0.09910.0483-0.0385-0.0338-0.01380.06040.00010.01110.0613-0.01360.059411.1349-34.2167-50.0995
200.1111-0.00310.0130.0058-0.01810.0864-0.06310.0305-0.02850.0072-0.0698-0.0890.0286-0.0186-0.00910.0518-0.01740.02970.0064-0.00270.0814.2638-28.4329-15.8878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 19 )
2X-RAY DIFFRACTION2chain 'B' and (resid 20 through 25 )
3X-RAY DIFFRACTION3chain 'B' and (resid 26 through 44 )
4X-RAY DIFFRACTION4chain 'B' and (resid 45 through 61 )
5X-RAY DIFFRACTION5chain 'B' and (resid 62 through 78 )
6X-RAY DIFFRACTION6chain 'B' and (resid 79 through 101 )
7X-RAY DIFFRACTION7chain 'B' and (resid 102 through 117 )
8X-RAY DIFFRACTION8chain 'B' and (resid 118 through 128 )
9X-RAY DIFFRACTION9chain 'B' and (resid 129 through 147 )
10X-RAY DIFFRACTION10chain 'A' and (resid 2 through 19 )
11X-RAY DIFFRACTION11chain 'A' and (resid 20 through 44 )
12X-RAY DIFFRACTION12chain 'A' and (resid 45 through 61 )
13X-RAY DIFFRACTION13chain 'A' and (resid 62 through 78 )
14X-RAY DIFFRACTION14chain 'A' and (resid 79 through 92 )
15X-RAY DIFFRACTION15chain 'A' and (resid 93 through 101 )
16X-RAY DIFFRACTION16chain 'A' and (resid 102 through 117 )
17X-RAY DIFFRACTION17chain 'A' and (resid 118 through 128 )
18X-RAY DIFFRACTION18chain 'A' and (resid 129 through 147 )
19X-RAY DIFFRACTION19chain 'C' and (resid 78 through 88 )
20X-RAY DIFFRACTION20chain 'D' and (resid 78 through 88 )

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