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- PDB-3ll8: Crystal Structure of Calcineurin in Complex with AKAP79 Peptide -

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Basic information

Entry
Database: PDB / ID: 3ll8
TitleCrystal Structure of Calcineurin in Complex with AKAP79 Peptide
Components
  • AKAP79 peptide
  • Calcineurin subunit B type 1
  • Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
KeywordsHydrolase/calcium binding protein / protein-peptide docking / protein targeting / calcineurin / AKAP79 / beta-augmentation / Calmodulin-binding / Membrane / Hydrolase / Iron / Metal-binding / Nucleus / Phosphoprotein / Protein phosphatase / Lipoprotein / Myristate / Hydrolase-calcium binding protein complex
Function / homology
Function and homology information


positive regulation of endosome to plasma membrane protein transport / postsynaptic recycling endosome membrane / negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / protein serine/threonine phosphatase complex / negative regulation of signaling ...positive regulation of endosome to plasma membrane protein transport / postsynaptic recycling endosome membrane / negative regulation of angiotensin-activated signaling pathway / regulation of cell proliferation involved in kidney morphogenesis / calcium-dependent protein serine/threonine phosphatase regulator activity / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / calcium-dependent protein serine/threonine phosphatase activity / protein serine/threonine phosphatase complex / negative regulation of signaling / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress / postsynaptic recycling endosome / positive regulation of calcium ion import across plasma membrane / calmodulin-dependent protein phosphatase activity / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / slit diaphragm / ROBO receptors bind AKAP5 / peptidyl-serine dephosphorylation / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / renal filtration / skeletal muscle tissue regeneration / regulation of synaptic vesicle cycle / transition between fast and slow fiber / GABA receptor binding / positive regulation of calcineurin-NFAT signaling cascade / regulation of protein kinase A signaling / myelination in peripheral nervous system / negative regulation of adenylate cyclase activity / protein phosphatase 2B binding / Trafficking of AMPA receptors / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / regulation of postsynaptic neurotransmitter receptor internalization / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / protein kinase A binding / cyclosporin A binding / myosin phosphatase activity / CLEC7A (Dectin-1) induces NFAT activation / branching involved in blood vessel morphogenesis / postsynaptic modulation of chemical synaptic transmission / extrinsic component of plasma membrane / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / positive regulation of activated T cell proliferation / protein kinase A regulatory subunit binding / positive regulation of endocytosis / Calcineurin activates NFAT / adenylate cyclase binding / excitatory synapse / positive regulation of cell adhesion / DARPP-32 events / Activation of BAD and translocation to mitochondria / epidermis development / epithelial to mesenchymal transition / phosphatase binding / glutamate receptor binding / negative regulation of insulin secretion / multicellular organismal response to stress / positive regulation of osteoblast differentiation / skeletal muscle fiber development / beta-2 adrenergic receptor binding / dephosphorylation / keratinocyte differentiation / dendrite membrane / response to amphetamine / T cell activation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / FCERI mediated Ca+2 mobilization / protein dephosphorylation / positive regulation of long-term synaptic potentiation / cellular response to glucose stimulus / positive regulation of protein localization to plasma membrane / wound healing / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / cytoplasmic side of plasma membrane / sarcolemma / Z disc / SH3 domain binding / response to calcium ion / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G1/S transition of mitotic cell cycle / protein import into nucleus / calcium ion transport / Ca2+ pathway / heart development / ATPase binding / scaffold protein binding / postsynapse / chemical synaptic transmission / dendritic spine / molecular adaptor activity
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. / Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase ...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. / Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 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 / 4-Layer Sandwich / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / A-kinase anchor protein 5 / Calcineurin subunit B type 1 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLi, H. / Hogan, P.G.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Balanced interactions of calcineurin with AKAP79 regulate Ca(2+)-calcineurin-NFAT signaling.
Authors: Li, H. / Pink, M.D. / Murphy, J.G. / Stein, A. / Dell'acqua, M.L. / Hogan, P.G.
#1: Journal: Nature / Year: 1995
Title: Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex
Authors: Kissinger, C.R. / Parge, H.E. / Knighton, D.R. / Lewis, C.T. / Pelletier, L.A. / Tempczyk, A. / Kalish, V.J. / Tucker, K.D. / Showalter, R.E. / Moomaw, E.W. / Gastinel, L.N. / Habuka, N. / ...Authors: Kissinger, C.R. / Parge, H.E. / Knighton, D.R. / Lewis, C.T. / Pelletier, L.A. / Tempczyk, A. / Kalish, V.J. / Tucker, K.D. / Showalter, R.E. / Moomaw, E.W. / Gastinel, L.N. / Habuka, N. / Chen, X. / Maldonado, F. / Barker, J.E. / Bacquet, R. / Villafranca, J.E.
#2: Journal: J.Mol.Biol. / Year: 2007
Title: Structure of calcineurin in complex with PVIVIT peptide: portrait of a low-affinity signalling interaction
Authors: Li, H. / Zhang, L. / Rao, A. / Harrison, S.C. / Hogan, P.G.
History
DepositionJan 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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
E: AKAP79 peptide
A: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
B: Calcineurin subunit B type 1
C: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
D: Calcineurin subunit B type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,73419
Polymers118,9815
Non-polymers75314
Water10,503583
1
E: AKAP79 peptide
A: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
B: Calcineurin subunit B type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,47410
Polymers60,0983
Non-polymers3777
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-160 kcal/mol
Surface area22660 Å2
MethodPISA
2
C: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
D: Calcineurin subunit B type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2609
Polymers58,8832
Non-polymers3777
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-155 kcal/mol
Surface area22230 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-328 kcal/mol
Surface area41370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.275, 89.699, 158.914
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 1 molecules E

#1: Protein/peptide AKAP79 peptide


Mass: 1214.362 Da / Num. of mol.: 1 / Fragment: UNP residues 336-346 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P24588

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Protein , 2 types, 4 molecules ACBD

#2: Protein Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform / Calmodulin-dependent calcineurin A subunit alpha isoform / CAM-PRP catalytic subunit


Mass: 41259.223 Da / Num. of mol.: 2 / Fragment: UNP residues 14-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q08209, protein-serine/threonine phosphatase
#3: Protein Calcineurin subunit B type 1 / Protein phosphatase 2B regulatory subunit 1 / Protein phosphatase 3 regulatory subunit B alpha isoform 1


Mass: 17623.979 Da / Num. of mol.: 2 / Fragment: UNP residues 16-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3R1, CNA2, CNB / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63098

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Non-polymers , 5 types, 597 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 52.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 20,000 MgSO4 CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2008 / Details: 74MB unbinned
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 80437 / % possible obs: 95.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.072.90.503191.5
2.07-2.1530.395193.8
2.15-2.2530.289194.9
2.25-2.3730.229196.3
2.37-2.523.10.179197.4
2.52-2.713.10.138197.9
2.71-2.993.20.1198.1
2.99-3.423.20.072197.8
3.42-4.313.20.056196.6
4.31-503.20.039192.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å48.97 Å
Translation2.5 Å48.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.812 / SU ML: 0.107 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 3978 5 %RANDOM
Rwork0.178 ---
obs0.178 79480 95.5 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 39.29 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8363 0 22 583 8968
LS refinement shellResolution: 2→2.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 262 -
Rwork0.221 4977 -
obs--86.45 %

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