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- PDB-5sve: Structure of Calcineurin in complex with NFATc1 LxVP peptide -

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Basic information

Entry
Database: PDB / ID: 5sve
TitleStructure of Calcineurin in complex with NFATc1 LxVP peptide
Components
  • Calcineurin subunit B type 1
  • NFATc1 LxVP peptide
  • Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
KeywordsHYDROLASE / protein binding
Function / homology
Function and homology information


skeletal muscle adaptation / 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 / negative regulation of signaling / protein serine/threonine phosphatase complex / positive regulation of saliva secretion ...skeletal muscle adaptation / 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 / negative regulation of signaling / protein serine/threonine phosphatase complex / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress / positive regulation of calcium ion import across plasma membrane / negative regulation of vascular associated smooth muscle cell differentiation / calmodulin-dependent protein phosphatase activity / calcineurin complex / positive regulation of connective tissue replacement / negative regulation of dendrite morphogenesis / calcineurin-mediated signaling / slit diaphragm / mononuclear cell differentiation / 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 / positive regulation of calcineurin-NFAT signaling cascade / pulmonary valve morphogenesis / myelination in peripheral nervous system / cardiac muscle hypertrophy in response to stress / positive regulation of osteoclast differentiation / aortic valve morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / response to muscle activity / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / cyclosporin A binding / myosin phosphatase activity / CLEC7A (Dectin-1) induces NFAT activation / branching involved in blood vessel morphogenesis / positive regulation of DNA biosynthetic process / postsynaptic modulation of chemical synaptic transmission / extrinsic component of plasma membrane / protein serine/threonine phosphatase activity / FK506 binding / mitogen-activated protein kinase p38 binding / negative regulation of Wnt signaling pathway / protein-serine/threonine phosphatase / positive regulation of activated T cell proliferation / positive regulation of endocytosis / Calcineurin activates NFAT / positive regulation of cell adhesion / sarcoplasm / DARPP-32 events / Activation of BAD and translocation to mitochondria / epidermis development / epithelial to mesenchymal transition / phosphatase binding / negative regulation of insulin secretion / multicellular organismal response to stress / positive regulation of osteoblast differentiation / skeletal muscle fiber development / dephosphorylation / keratinocyte differentiation / cellular response to transforming growth factor beta stimulus / response to amphetamine / T cell activation / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / FCERI mediated Ca+2 mobilization / protein dephosphorylation / cellular response to glucose stimulus / wound healing / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / sarcolemma / transcription coactivator binding / Z disc / response to calcium ion / G1/S transition of mitotic cell cycle / protein import into nucleus / calcium ion transport / sequence-specific double-stranded DNA binding / Ca2+ pathway / cellular response to tumor necrosis factor / heart development / ATPase binding / postsynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / nucleic acid binding / dendritic spine / nuclear body / protein dimerization activity / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / positive regulation of cell migration
Similarity search - Function
Nuclear factor of activated T cells (NFAT) / Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily ...Nuclear factor of activated T cells (NFAT) / Calcineurin B protein / PP2B, metallophosphatase domain / PP2B / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / 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 / ig-like, plexins, transcription factors / IPT domain / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / p53-like transcription factor, DNA-binding / 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 / Immunoglobulin E-set / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Nuclear factor of activated T-cells, cytoplasmic 1 / Calcineurin subunit B type 1 / Protein phosphatase 3 catalytic subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.596 Å
AuthorsSheftic, S.R. / Page, R. / Peti, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS091336 United States
CitationJournal: Sci Rep / Year: 2016
Title: Investigating the human Calcineurin Interaction Network using the pi LxVP SLiM.
Authors: Sheftic, S.R. / Page, R. / Peti, W.
History
DepositionAug 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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
A: Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
B: Calcineurin subunit B type 1
C: NFATc1 LxVP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4529
Polymers64,1703
Non-polymers2826
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-157 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.679, 106.046, 111.913
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 , 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: 42659.852 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 Calcineurin subunit B type 1 / Protein phosphatase 2B regulatory subunit 1 / Protein phosphatase 3 regulatory subunit B alpha isoform 1


Mass: 19322.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP3R1, CNA2, CNB / Production host: Escherichia coli (E. coli) / References: UniProt: P63098

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide NFATc1 LxVP peptide


Mass: 2187.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O95644*PLUS

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Non-polymers , 4 types, 59 molecules

#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES pH 7.0 15% Peg 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.59→39.04 Å / Num. obs: 21785 / % possible obs: 99.6 % / Redundancy: 7.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Net I/σ(I): 4.7
Reflection shellResolution: 2.6→2.71 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.7 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F0Z

4f0z


Resolution: 2.596→39.035 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.36
RfactorNum. reflection% reflection
Rfree0.2394 1149 5.27 %
Rwork0.1948 --
obs0.1972 21785 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.596→39.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4280 0 6 53 4339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044410
X-RAY DIFFRACTIONf_angle_d0.5975925
X-RAY DIFFRACTIONf_dihedral_angle_d11.2331622
X-RAY DIFFRACTIONf_chiral_restr0.023643
X-RAY DIFFRACTIONf_plane_restr0.003774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.596-2.71410.36131340.28252489X-RAY DIFFRACTION98
2.7141-2.85720.32291430.2612551X-RAY DIFFRACTION100
2.8572-3.03620.30861300.24992558X-RAY DIFFRACTION100
3.0362-3.27050.3211480.24742545X-RAY DIFFRACTION100
3.2705-3.59940.24631470.2142569X-RAY DIFFRACTION100
3.5994-4.11970.21971540.18852575X-RAY DIFFRACTION100
4.1197-5.18850.18791610.14742593X-RAY DIFFRACTION100
5.1885-39.03970.2041320.15972756X-RAY DIFFRACTION100

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