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- PDB-4zp3: AKAP18:PKA-RIIalpha structure reveals crucial anchor points for r... -

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Basic information

Entry
Database: PDB / ID: 4zp3
TitleAKAP18:PKA-RIIalpha structure reveals crucial anchor points for recognition of regulatory subunits of PKA
Components
  • A-kinase anchor protein 7 isoforms alpha and beta
  • cAMP-dependent protein kinase type II-alpha regulatory subunitCAMP-dependent pathway
KeywordsSIGNALING PROTEIN / anchor points / amphiphathic helix / AKAP / DD-domain
Function / homology
Function and homology information


positive regulation of delayed rectifier potassium channel activity / ROBO receptors bind AKAP5 / regulation of membrane repolarization / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / positive regulation of potassium ion transmembrane transport / nucleotide-activated protein kinase complex / regulation of protein kinase A signaling / cAMP-dependent protein kinase inhibitor activity / protein kinase A binding ...positive regulation of delayed rectifier potassium channel activity / ROBO receptors bind AKAP5 / regulation of membrane repolarization / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / positive regulation of potassium ion transmembrane transport / nucleotide-activated protein kinase complex / regulation of protein kinase A signaling / cAMP-dependent protein kinase inhibitor activity / protein kinase A binding / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / action potential / ciliary base / cAMP-dependent protein kinase complex / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / plasma membrane raft / PKA activation in glucagon signalling / DARPP-32 events / lateral plasma membrane / Hedgehog 'off' state / monoatomic ion transport / cAMP binding / cellular response to cAMP / hippocampal mossy fiber to CA3 synapse / FCGR3A-mediated IL10 synthesis / modulation of chemical synaptic transmission / protein localization / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / intracellular signal transduction / apical plasma membrane / protein domain specific binding / nucleotide binding / focal adhesion / centrosome / ubiquitin protein ligase binding / protein kinase binding / protein-containing complex / extracellular exosome / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
A-kinase anchor protein 7, RI-RII subunit-binding domain / PKA-RI-RII subunit binding domain of A-kinase anchor protein / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / 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 ...A-kinase anchor protein 7, RI-RII subunit-binding domain / PKA-RI-RII subunit binding domain of A-kinase anchor protein / Protein kinase A anchor protein, nuclear localisation signal domain / AKAP7 2'5' RNA ligase-like domain / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / cAMP-dependent Protein Kinase, Chain A / 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 phosphodiesterase / 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 / RmlC-like jelly roll fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / A-kinase anchor protein 7 isoforms alpha and beta / cAMP-dependent protein kinase type II-alpha regulatory subunit / A-kinase anchor protein 7 isoform gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.63 Å
AuthorsGoetz, F. / Roske, Y. / Faelber, K. / Zuehlke, K. / Autenrieth, K. / Kreuchwig, A. / Krause, G. / Herberg, F.W. / Daumke, O. / Heinemann, U. / Klussmann, E.
CitationJournal: Biochem.J. / Year: 2016
Title: AKAP18:PKA-RII alpha structure reveals crucial anchor points for recognition of regulatory subunits of PKA.
Authors: Gotz, F. / Roske, Y. / Schulz, M.S. / Autenrieth, K. / Bertinetti, D. / Faelber, K. / Zuhlke, K. / Kreuchwig, A. / Kennedy, E.J. / Krause, G. / Daumke, O. / Herberg, F.W. / Heinemann, U. / Klussmann, E.
History
DepositionMay 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Structure summary
Revision 1.2Jul 6, 2016Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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 II-alpha regulatory subunit
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
C: cAMP-dependent protein kinase type II-alpha regulatory subunit
D: cAMP-dependent protein kinase type II-alpha regulatory subunit
E: cAMP-dependent protein kinase type II-alpha regulatory subunit
F: cAMP-dependent protein kinase type II-alpha regulatory subunit
G: cAMP-dependent protein kinase type II-alpha regulatory subunit
H: cAMP-dependent protein kinase type II-alpha regulatory subunit
I: cAMP-dependent protein kinase type II-alpha regulatory subunit
J: cAMP-dependent protein kinase type II-alpha regulatory subunit
K: cAMP-dependent protein kinase type II-alpha regulatory subunit
L: cAMP-dependent protein kinase type II-alpha regulatory subunit
M: A-kinase anchor protein 7 isoforms alpha and beta
N: A-kinase anchor protein 7 isoforms alpha and beta
O: A-kinase anchor protein 7 isoforms alpha and beta
P: A-kinase anchor protein 7 isoforms alpha and beta
Q: A-kinase anchor protein 7 isoforms alpha and beta
R: A-kinase anchor protein 7 isoforms alpha and beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,38622
Polymers86,93618
Non-polymers4504
Water1,13563
1
A: cAMP-dependent protein kinase type II-alpha regulatory subunit
B: cAMP-dependent protein kinase type II-alpha regulatory subunit
M: A-kinase anchor protein 7 isoforms alpha and beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7145
Polymers14,4893
Non-polymers2252
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: cAMP-dependent protein kinase type II-alpha regulatory subunit
D: cAMP-dependent protein kinase type II-alpha regulatory subunit
N: A-kinase anchor protein 7 isoforms alpha and beta


Theoretical massNumber of molelcules
Total (without water)14,4893
Polymers14,4893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: cAMP-dependent protein kinase type II-alpha regulatory subunit
F: cAMP-dependent protein kinase type II-alpha regulatory subunit
O: A-kinase anchor protein 7 isoforms alpha and beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6024
Polymers14,4893
Non-polymers1121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: cAMP-dependent protein kinase type II-alpha regulatory subunit
H: cAMP-dependent protein kinase type II-alpha regulatory subunit
P: A-kinase anchor protein 7 isoforms alpha and beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6024
Polymers14,4893
Non-polymers1121
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
I: cAMP-dependent protein kinase type II-alpha regulatory subunit
J: cAMP-dependent protein kinase type II-alpha regulatory subunit
Q: A-kinase anchor protein 7 isoforms alpha and beta


Theoretical massNumber of molelcules
Total (without water)14,4893
Polymers14,4893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
K: cAMP-dependent protein kinase type II-alpha regulatory subunit
L: cAMP-dependent protein kinase type II-alpha regulatory subunit
R: A-kinase anchor protein 7 isoforms alpha and beta


Theoretical massNumber of molelcules
Total (without water)14,4893
Polymers14,4893
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.922, 120.988, 57.123
Angle α, β, γ (deg.)90.00, 93.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D
31F
41H
51J
61L
12A
22C
32E
42G
52I
62K

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114B5 - 43
2114D5 - 43
3114F5 - 43
4114H5 - 43
5114J5 - 43
6114L5 - 43
1124A5 - 43
2124C5 - 43
3124E5 - 43
4124G5 - 43
5124I5 - 43
6124K5 - 43

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.474423, -0.4421, 0.76123), (-0.395007, -0.879709, -0.264728), (0.786697, -0.175098, -0.591987)-20.85781, -5.36927, 36.78175
3given(0.795355, -0.411552, -0.445012), (-0.262521, -0.895622, 0.359087), (-0.546345, -0.168777, -0.820379)27.75875, 2.91862, 44.63747
4given(0.033976, 0.026741, -0.999065), (0.048523, 0.998419, 0.028373), (0.998244, -0.049442, 0.032625)25.81005, -29.81089, 31.83716
5given(-0.493303, -0.272346, 0.826123), (0.3496, 0.807569, 0.474986), (-0.796512, 0.523125, -0.303164)-3.8568, -23.80486, 63.05707
6given(0.784672, -0.295407, 0.545), (0.518995, 0.793847, -0.316941), (-0.33902, 0.531547, 0.776224)-11.39641, -4.0029, -28.21012

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Components

#1: Protein/peptide
cAMP-dependent protein kinase type II-alpha regulatory subunit / CAMP-dependent pathway


Mass: 5015.697 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRKAR2A, PKR2, PRKAR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P13861
#2: Protein/peptide
A-kinase anchor protein 7 isoforms alpha and beta / AKAP-7 isoforms alpha and beta / A-kinase anchor protein 18 kDa / AKAP 18 / Protein kinase A- ...AKAP-7 isoforms alpha and beta / A-kinase anchor protein 18 kDa / AKAP 18 / Protein kinase A-anchoring protein 7 isoforms alpha/beta / PRKA7 isoforms alpha/beta


Mass: 4457.950 Da / Num. of mol.: 6 / Fragment: UNP residues 43-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKAP7, AKAP15, AKAP18 / Production host: Escherichia coli (E. coli) / References: UniProt: O43687, UniProt: Q9P0M2*PLUS
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Cadmium chloride, Sodium acetate / PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.914
11L, K, -H20.086
ReflectionResolution: 2.63→41.5 Å / Num. obs: 22903 / % possible obs: 99.4 % / Redundancy: 3.25 % / Net I/σ(I): 10.61

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.63→41.5 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.872 / SU B: 10.616 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.861 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 1142 5 %RANDOM
Rwork0.22233 ---
obs0.22452 21760 85.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.886 Å2
Baniso -1Baniso -2Baniso -3
1-10.22 Å20 Å21.4 Å2
2---13.82 Å2-0 Å2
3---3.61 Å2
Refinement stepCycle: 1 / Resolution: 2.63→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5351 0 4 63 5418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195430
X-RAY DIFFRACTIONr_bond_other_d0.0010.025382
X-RAY DIFFRACTIONr_angle_refined_deg0.9712.0027372
X-RAY DIFFRACTIONr_angle_other_deg0.735312322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7335634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26823.833287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60415949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1731560
X-RAY DIFFRACTIONr_chiral_restr0.0460.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216020
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021210
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_it1.5043.6192590
X-RAY DIFFRACTIONr_mcbond_other1.5043.6192589
X-RAY DIFFRACTIONr_mcangle_it2.695.3943206
X-RAY DIFFRACTIONr_mcangle_other2.695.3953207
X-RAY DIFFRACTIONr_scbond_it1.0873.7392840
X-RAY DIFFRACTIONr_scbond_other1.0843.7382838
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9715.5554166
X-RAY DIFFRACTIONr_long_range_B_refined4.93827.7576271
X-RAY DIFFRACTIONr_long_range_B_other4.92127.7596268
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11B636medium positional0.570.5
11D636medium positional0.480.5
11F636medium positional0.450.5
11H636medium positional0.560.5
11J636medium positional0.820.5
11L636medium positional0.80.5
22B618medium positional1.310.5
22D618medium positional0.750.5
22F618medium positional0.720.5
22H618medium positional1.040.5
22J618medium positional0.670.5
22L618medium positional0.620.5
11A636medium thermal3.462
11C636medium thermal7.492
11E636medium thermal3.162
11G636medium thermal4.062
11I636medium thermal4.622
11K636medium thermal5.632
22A618medium thermal5.472
22C618medium thermal6.812
22E618medium thermal4.222
22G618medium thermal5.322
22I618medium thermal7.452
22K618medium thermal6.042
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0 0 -
obs--0 %

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