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- PDB-1tco: TERNARY COMPLEX OF A CALCINEURIN A FRAGMENT, CALCINEURIN B, FKBP1... -

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Entry
Database: PDB / ID: 1tco
TitleTERNARY COMPLEX OF A CALCINEURIN A FRAGMENT, CALCINEURIN B, FKBP12 AND THE IMMUNOSUPPRESSANT DRUG FK506 (TACROLIMUS)
Components
  • (SERINE/THREONINE PHOSPHATASE ...) x 2
  • FK506-BINDING PROTEIN
KeywordsCOMPLEX (HYDROLASE/ISOMERASE) / COMPLEX (HYDROLASE-ISOMERASE) / IMMUNOSUPPRESSANT / COMPLEX (HYDROLASE-ISOMERASE) complex
Function / homology
Function and homology information


mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / CLEC7A (Dectin-1) induces NFAT activation / regulation of activin receptor signaling pathway / Calcineurin activates NFAT / FCERI mediated Ca+2 mobilization / Activation of BAD and translocation to mitochondria / calmodulin-dependent protein phosphatase activity / calcineurin complex / calcineurin-mediated signaling ...mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / CLEC7A (Dectin-1) induces NFAT activation / regulation of activin receptor signaling pathway / Calcineurin activates NFAT / FCERI mediated Ca+2 mobilization / Activation of BAD and translocation to mitochondria / calmodulin-dependent protein phosphatase activity / calcineurin complex / calcineurin-mediated signaling / macrolide binding / activin receptor binding / lung epithelial cell differentiation / cytoplasmic side of membrane / calcineurin-NFAT signaling cascade / signaling receptor inhibitor activity / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / myelination in peripheral nervous system / activin binding / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / negative regulation of release of sequestered calcium ion into cytosol / regulation of amyloid precursor protein catabolic process / Ca2+ pathway / response to caffeine / protein maturation by protein folding / ventricular cardiac muscle tissue morphogenesis / 'de novo' protein folding / branching involved in blood vessel morphogenesis / negative regulation of phosphoprotein phosphatase activity / postsynaptic modulation of chemical synaptic transmission / FK506 binding / protein-serine/threonine phosphatase / mTORC1-mediated signalling / SMAD binding / TGF-beta receptor signaling activates SMADs / phosphoprotein phosphatase activity / Calcineurin activates NFAT / regulation of immune response / negative regulation of ryanodine-sensitive calcium-release channel activity / epithelial to mesenchymal transition / calcium channel inhibitor activity / phosphatase binding / protein peptidyl-prolyl isomerization / T cell proliferation / supramolecular fiber organization / heart morphogenesis / dephosphorylation / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / T cell activation / protein dephosphorylation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / negative regulation of protein phosphorylation / peptidylprolyl isomerase / positive regulation of protein ubiquitination / sarcoplasmic reticulum / peptidyl-prolyl cis-trans isomerase activity / muscle contraction / calcium ion transmembrane transport / negative regulation of transforming growth factor beta receptor signaling pathway / Schaffer collateral - CA1 synapse / sarcolemma / cytokine-mediated signaling pathway / Z disc / response to calcium ion / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / regulation of protein localization / protein folding / positive regulation of protein binding / heart development / protein refolding / postsynapse / positive regulation of canonical NF-kappaB signal transduction / transmembrane transporter binding / amyloid fibril formation / Potential therapeutics for SARS / dendritic spine / calmodulin binding / calcium ion binding / protein homodimerization activity / extracellular exosome / membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 / Chitinase A; domain 3 - #40 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...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 / Chitinase A; domain 3 - #40 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / 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 / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / MYRISTIC ACID / PHOSPHATE ION / Peptidyl-prolyl cis-trans isomerase FKBP1A / Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform / Peptidyl-prolyl cis-trans isomerase FKBP1A / Calcineurin subunit B type 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsGriffith, J.P. / Kim, J.L. / Kim, E.E. / Sintchak, M.D. / Thomson, J.A. / Fitzgibbon, M.J. / Fleming, M.A. / Caron, P.R. / Hsiao, K. / Navia, M.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex.
Authors: Griffith, J.P. / Kim, J.L. / Kim, E.E. / Sintchak, M.D. / Thomson, J.A. / Fitzgibbon, M.J. / Fleming, M.A. / Caron, P.R. / Hsiao, K. / Navia, M.A.
History
DepositionAug 21, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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
A: SERINE/THREONINE PHOSPHATASE B2
B: SERINE/THREONINE PHOSPHATASE B2
C: FK506-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,36412
Polymers73,9553
Non-polymers1,4099
Water12,791710
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-156 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.050, 94.430, 116.760
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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SERINE/THREONINE PHOSPHATASE ... , 2 types, 2 molecules AB

#1: Protein SERINE/THREONINE PHOSPHATASE B2 / CALCINEURIN A / CAM-PRP CATALYTIC SUBUNIT / CALCINEURIN B / CAM-PRP REGULATORY SUBUNIT


Mass: 43012.969 Da / Num. of mol.: 1
Fragment: CHAIN A IS THE CATALYTIC SUBUNIT, RESIDUES 18 -392. CHAIN B IS THE REGULATORY SUBUNIT, RESIDUES 1 - 169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: CALF BRAIN / Production host: Escherichia coli (E. coli)
References: UniProt: P48452, protein-serine/threonine phosphatase
#2: Protein SERINE/THREONINE PHOSPHATASE B2 / CALCINEURIN A / CAM-PRP CATALYTIC SUBUNIT / CALCINEURIN B / CAM-PRP REGULATORY SUBUNIT


Mass: 19191.709 Da / Num. of mol.: 1
Fragment: CHAIN A IS THE CATALYTIC SUBUNIT, RESIDUES 18 -392. CHAIN B IS THE REGULATORY SUBUNIT, RESIDUES 1 - 169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: CALF BRAIN / Production host: Escherichia coli (E. coli)
References: UniProt: P63099, protein-serine/threonine phosphatase

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Protein , 1 types, 1 molecules C

#3: Protein FK506-BINDING PROTEIN / FKBP-12 / CIS-TRANS ISOMERASE


Mass: 11750.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli)
References: UniProt: P62942, UniProt: P18203*PLUS, peptidylprolyl isomerase

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Non-polymers , 7 types, 719 molecules

#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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#9: Chemical ChemComp-FK5 / 8-DEETHYL-8-[BUT-3-ENYL]-ASCOMYCIN / K506


Mass: 804.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H69NO12 / Comment: medication*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 3.35 Å3/Da / Density % sol: 63.34 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 %PEG80001reservoir
20.1 Mpotassium phosphate1reservoir
320 mMbeta-mercaptoethanol1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 41097 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 3 %
Reflection
*PLUS
Highest resolution: 2.3 Å / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.5→7 Å / σ(F): 1.5
RfactorNum. reflection
Rfree0.282 -
Rwork0.195 -
obs0.195 30613
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5040 0 68 710 5818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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