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- PDB-6uuq: Structure of Calcineurin bound to RCAN1 -

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Basic information

Entry
Database: PDB / ID: 6uuq
TitleStructure of Calcineurin bound to RCAN1
Components
  • Calcipressin-1
  • Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
KeywordsHYDROLASE/Signaling Protein / Ser/thr phosphatase / HYDROLASE / HYDROLASE-Signaling Protein complex
Function / homology
Function and homology information


negative regulation of angiotensin-activated signaling pathway / calcium-dependent protein serine/threonine phosphatase regulator activity / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / positive regulation of saliva secretion / locomotion involved in locomotory behavior / negative regulation of dendrite morphogenesis / calcineurin complex ...negative regulation of angiotensin-activated signaling pathway / calcium-dependent protein serine/threonine phosphatase regulator activity / regulation of cell proliferation involved in kidney morphogenesis / positive regulation of glomerulus development / negative regulation of calcium ion import across plasma membrane / negative regulation of signaling / positive regulation of saliva secretion / locomotion involved in locomotory behavior / negative regulation of dendrite morphogenesis / calcineurin complex / positive regulation of connective tissue replacement / positive regulation of calcium ion import across plasma membrane / slit diaphragm / positive regulation of cardiac muscle hypertrophy in response to stress / protein serine/threonine phosphatase complex / peptidyl-serine dephosphorylation / renal filtration / calcineurin-NFAT signaling cascade / short-term memory / positive regulation of calcineurin-NFAT signaling cascade / skeletal muscle tissue regeneration / transition between fast and slow fiber / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / negative regulation of calcineurin-NFAT signaling cascade / extrinsic component of plasma membrane / dendrite morphogenesis / dephosphorylation / CLEC7A (Dectin-1) induces NFAT activation / protein serine/threonine phosphatase activity / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / positive regulation of activated T cell proliferation / calcineurin-mediated signaling / positive regulation of endocytosis / Calcineurin activates NFAT / DARPP-32 events / epidermis development / postsynaptic modulation of chemical synaptic transmission / positive regulation of osteoblast differentiation / multicellular organismal response to stress / negative regulation of insulin secretion / skeletal muscle fiber development / keratinocyte differentiation / protein dephosphorylation / FCERI mediated Ca+2 mobilization / response to amphetamine / positive regulation of cell adhesion / T cell activation / response to ischemia / excitatory postsynaptic potential / wound healing / modulation of chemical synaptic transmission / calcium-mediated signaling / cellular response to glucose stimulus / sarcolemma / Schaffer collateral - CA1 synapse / Z disc / G1/S transition of mitotic cell cycle / response to calcium ion / protein import into nucleus / calcium ion transport / ATPase binding / Ca2+ pathway / dendritic spine / response to oxidative stress / nucleic acid binding / calmodulin binding / protein dimerization activity / positive regulation of cell migration / negative regulation of gene expression / calcium ion binding / positive regulation of gene expression / protein-containing complex binding / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Calcipressin / Calcipressin-1, RNA recognition motif / Calcipressin / 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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...Calcipressin / Calcipressin-1, RNA recognition motif / Calcipressin / 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 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / Calcipressin-1 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsSheftic, S. / Page, R. / Peti, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS091336 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098482 United States
CitationJournal: Sci Adv / Year: 2020
Title: The structure of the RCAN1:CN complex explains the inhibition of and substrate recruitment by calcineurin.
Authors: Li, Y. / Sheftic, S.R. / Grigoriu, S. / Schwieters, C.D. / Page, R. / Peti, W.
History
DepositionOct 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
B: Calcipressin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1236
Polymers40,8122
Non-polymers3114
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-83 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.841, 71.159, 92.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 36467.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3CA, CALNA, CNA / Production host: Escherichia coli (E. coli)
References: UniProt: Q08209, protein-serine/threonine phosphatase
#2: Protein/peptide Calcipressin-1 / Adapt78 / Down syndrome critical region protein 1 / Myocyte-enriched calcineurin-interacting ...Adapt78 / Down syndrome critical region protein 1 / Myocyte-enriched calcineurin-interacting protein 1 / MCIP1 / Regulator of calcineurin 1


Mass: 4343.842 Da / Num. of mol.: 1 / Mutation: V158I, H159T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RCAN1, ADAPT78, CSP1, DSC1, DSCR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P53805

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Non-polymers , 4 types, 317 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Sodium cacodylate, 12% Peg 8000, 0.1 M Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. obs: 33218 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 20.09 Å2 / Rrim(I) all: 0.091 / Net I/σ(I): 24.5
Reflection shellResolution: 1.849→1.88 Å / Num. unique obs: 1644 / CC1/2: 0.75 / Rrim(I) all: 0.735

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f0z

4f0z


Resolution: 1.849→36.014 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.5
RfactorNum. reflection% reflection
Rfree0.2049 1703 5.14 %
Rwork0.1635 --
obs0.1655 33163 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86 Å2 / Biso mean: 24.993 Å2 / Biso min: 7.94 Å2
Refinement stepCycle: final / Resolution: 1.849→36.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 12 313 2878
Biso mean--23.67 36.94 -
Num. residues----320
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.849-1.9030.26361390.226255099
1.903-1.96440.28661130.20752601100
1.9644-2.03460.24381270.19762617100
2.0346-2.11610.22691450.1832567100
2.1161-2.21240.22731630.16842577100
2.2124-2.3290.19671400.1652604100
2.329-2.47490.23651400.16172620100
2.4749-2.66590.18841410.16342601100
2.6659-2.93410.20271380.16252631100
2.9341-3.35840.18451560.15412625100
3.3584-4.23020.20121290.13982691100
4.2302-36.0140.17951720.15942776100

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