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- PDB-6nuc: Structure of Calcineurin in complex with NHE1 peptide -

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Basic information

Entry
Database: PDB / ID: 6nuc
TitleStructure of Calcineurin in complex with NHE1 peptide
Components
  • Calcineurin subunit B type 1
  • Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform
  • Sodium/hydrogen exchanger 1
KeywordsHYDROLASE/Calcium Binding Protein / Ser/thr phosphatase / complex / HYDROLASE / HYDROLASE-Calcium Binding Protein complex
Function / homology
Function and homology information


cation-transporting ATPase complex / positive regulation of calcium:sodium antiporter activity / negative regulation of angiotensin-activated signaling pathway / Sodium/Proton exchangers / 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 ...cation-transporting ATPase complex / positive regulation of calcium:sodium antiporter activity / negative regulation of angiotensin-activated signaling pathway / Sodium/Proton exchangers / 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 / regulation of the force of heart contraction by cardiac conduction / positive regulation of saliva secretion / positive regulation of cardiac muscle hypertrophy in response to stress / Hyaluronan uptake and degradation / calmodulin-dependent protein phosphatase activity / regulation of cardiac muscle cell membrane potential / positive regulation of calcium ion import across plasma membrane / calcineurin complex / positive regulation of connective tissue replacement / calcineurin-mediated signaling / negative regulation of dendrite morphogenesis / protein serine/threonine phosphatase complex / cellular response to electrical stimulus / slit diaphragm / potassium:proton antiporter activity / peptidyl-serine dephosphorylation / sodium:proton antiporter activity / positive regulation of action potential / renal filtration / lung epithelial cell differentiation / calcineurin-NFAT signaling cascade / transition between fast and slow fiber / maintenance of cell polarity / regulation of synaptic vesicle cycle / regulation of pH / positive regulation of calcineurin-NFAT signaling cascade / sodium ion export across plasma membrane / myelination in peripheral nervous system / cardiac muscle cell differentiation / cellular response to acidic pH / sodium ion import across plasma membrane / skeletal muscle tissue regeneration / protein phosphatase 2B binding / intracellular sodium ion homeostasis / response to acidic pH / regulation of stress fiber assembly / positive regulation of osteoclast differentiation / cardiac muscle hypertrophy in response to stress / cardiac muscle cell contraction / regulation of cardiac muscle contraction by calcium ion signaling / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of mitochondrial membrane permeability / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / cellular response to cold / cellular response to antibiotic / regulation of focal adhesion assembly / extrinsic component of plasma membrane / CLEC7A (Dectin-1) induces NFAT activation / protein serine/threonine phosphatase activity / branching involved in blood vessel morphogenesis / postsynaptic modulation of chemical synaptic transmission / cyclosporin A binding / dephosphorylation / myosin phosphatase activity / protein-serine/threonine phosphatase / positive regulation of cardiac muscle hypertrophy / positive regulation of activated T cell proliferation / positive regulation of the force of heart contraction / cellular response to organic cyclic compound / positive regulation of endocytosis / protein complex oligomerization / Calcineurin activates NFAT / intercalated disc / DARPP-32 events / epithelial to mesenchymal transition / Activation of BAD and translocation to mitochondria / multicellular organismal response to stress / epidermis development / phosphatase binding / negative regulation of insulin secretion / positive regulation of osteoblast differentiation / skeletal muscle fiber development / monoatomic ion transport / phosphatidylinositol-4,5-bisphosphate binding / keratinocyte differentiation / T-tubule / potassium ion transmembrane transport / cellular response to epinephrine stimulus / response to muscle stretch / protein dephosphorylation / response to amphetamine / hippocampal mossy fiber to CA3 synapse / positive regulation of cell adhesion / FCERI mediated Ca+2 mobilization / proton transmembrane transport / T cell activation / excitatory postsynaptic potential / stem cell differentiation / regulation of intracellular pH
Similarity search - Function
Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Calcineurin B protein / Na+/H+ exchanger / PP2B, metallophosphatase domain / PP2B / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family ...Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Calcineurin B protein / Na+/H+ exchanger / PP2B, metallophosphatase domain / PP2B / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / 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
: / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Sodium/hydrogen exchanger 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: 1.9 Å
AuthorsWang, X. / 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)R01NS091336 United States
CitationJournal: Nat Commun / Year: 2019
Title: Molecular basis for the binding and selective dephosphorylation of Na+/H+exchanger 1 by calcineurin.
Authors: Hendus-Altenburger, R. / Wang, X. / Sjogaard-Frich, L.M. / Pedraz-Cuesta, E. / Sheftic, S.R. / Bendsoe, A.H. / Page, R. / Kragelund, B.B. / Pedersen, S.F. / Peti, W.
History
DepositionJan 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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: Sodium/hydrogen exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,38412
Polymers65,8783
Non-polymers5069
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-162 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.549, 127.073, 127.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-792-

HOH

31A-810-

HOH

41A-815-

HOH

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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: 42855.047 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: 17755.174 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 Sodium/hydrogen exchanger 1 / APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute ...APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute carrier family 9 member 1


Mass: 5268.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A1, APNH1, NHE1 / Production host: Escherichia coli (E. coli) / References: UniProt: P19634

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Non-polymers , 7 types, 445 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 40% (v/v) PEG 600, 100 mM CHES/ Sodium hydroxide pH 9.5, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→37.97 Å / Num. obs: 50521 / % possible obs: 98.8 % / Redundancy: 7.5 % / CC1/2: 0.977 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.033 / Rrim(I) all: 0.092 / Net I/σ(I): 13.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.923 / Num. unique obs: 3153 / CC1/2: 0.959 / Rpim(I) all: 0.364 / Rrim(I) all: 0.996 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimless0.6.3data scaling
XDSdata reduction
PHENIX1.14phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5sve

5sve


Resolution: 1.9→37.97 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.24
RfactorNum. reflection% reflection
Rfree0.194 2548 5.05 %
Rwork0.163 --
obs0.164 50470 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 19 436 4755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084459
X-RAY DIFFRACTIONf_angle_d0.7446043
X-RAY DIFFRACTIONf_dihedral_angle_d13.5992684
X-RAY DIFFRACTIONf_chiral_restr0.051659
X-RAY DIFFRACTIONf_plane_restr0.005792
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8991-1.93560.2931300.24732582X-RAY DIFFRACTION96
1.9356-1.97510.27521420.22412658X-RAY DIFFRACTION99
1.9751-2.01810.33141360.21422636X-RAY DIFFRACTION99
2.0181-2.0650.26021300.18882637X-RAY DIFFRACTION99
2.065-2.11670.23581340.18412672X-RAY DIFFRACTION99
2.1167-2.17390.21751370.17752609X-RAY DIFFRACTION98
2.1739-2.23780.19791370.16652633X-RAY DIFFRACTION97
2.2378-2.31010.26261390.18472653X-RAY DIFFRACTION99
2.3101-2.39260.16791160.15822685X-RAY DIFFRACTION100
2.3926-2.48840.18621560.16292666X-RAY DIFFRACTION99
2.4884-2.60160.19361560.16442641X-RAY DIFFRACTION99
2.6016-2.73880.22641500.16852609X-RAY DIFFRACTION97
2.7388-2.91030.20861320.16342698X-RAY DIFFRACTION100
2.9103-3.13490.17431430.17092692X-RAY DIFFRACTION99
3.1349-3.45020.22391480.16232661X-RAY DIFFRACTION98
3.4502-3.9490.17881580.14282660X-RAY DIFFRACTION98
3.949-4.97350.13791420.12382758X-RAY DIFFRACTION100
4.9735-37.97540.1691620.16952772X-RAY DIFFRACTION98

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