[English] 日本語
Yorodumi
- PDB-1fkk: ATOMIC STRUCTURE OF FKBP12, AN IMMUNOPHILIN BINDING PROTEIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fkk
TitleATOMIC STRUCTURE OF FKBP12, AN IMMUNOPHILIN BINDING PROTEIN
ComponentsFK506 BINDING PROTEIN
KeywordsROTAMASE / FK506 BINDING PROTEIN / FKBP12 / CIS-TRANS PROLYL-ISOMERASE
Function / homology
Function and homology information


mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / regulation of activin receptor signaling pathway / Calcineurin activates NFAT / cytoplasmic side of membrane / activin binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / negative regulation of release of sequestered calcium ion into cytosol / regulation of amyloid precursor protein catabolic process ...mTORC1-mediated signalling / TGF-beta receptor signaling activates SMADs / regulation of activin receptor signaling pathway / Calcineurin activates NFAT / cytoplasmic side of membrane / activin binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / negative regulation of release of sequestered calcium ion into cytosol / regulation of amyloid precursor protein catabolic process / ryanodine receptor complex / response to caffeine / protein peptidyl-prolyl isomerization / negative regulation of ryanodine-sensitive calcium-release channel activity / ventricular cardiac muscle tissue morphogenesis / FK506 binding / SMAD binding / negative regulation of protein phosphorylation / regulation of ryanodine-sensitive calcium-release channel activity / regulation of immune response / positive regulation of protein binding / T cell proliferation / heart morphogenesis / calcium channel inhibitor activity / supramolecular fiber organization / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / muscle contraction / T cell activation / sarcoplasmic reticulum / positive regulation of protein ubiquitination / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / cytokine-mediated signaling pathway / regulation of protein localization / amyloid fibril formation / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / protein homodimerization activity / extracellular exosome / membrane / cytoplasm / cytosol
Similarity search - Function
Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsWilson, K.P. / Sintchak, M.D. / Thomson, J.A. / Navia, M.A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Comparative X-ray structures of the major binding protein for the immunosuppressant FK506 (tacrolimus) in unliganded form and in complex with FK506 and rapamycin.
Authors: Wilson, K.P. / Yamashita, M.M. / Sintchak, M.D. / Rotstein, S.H. / Murcko, M.A. / Boger, J. / Thomson, J.A. / Fitzgibbon, M.J. / Black, J.R. / Navia, M.A.
#1: Journal: 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.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Improved Calcineurin Inhibition by Yeast Fkbp12-Drug Complexes
Authors: Rotonda, J. / Burbaum, J.J. / Chan, H.K. / Marcy, A.I. / Becker, J.W.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Fk-506-Binding Protein: Three-Dimensional Structure of the Complex with the Antagonist L-685,818
Authors: Becker, J.W. / Rotonda, J. / Mckeever, B.M. / Chan, H.K. / Marcy, A.I. / Wiederrecht, G. / Hermes, J.D. / Springer, J.P.
#4: Journal: J.Mol.Biol. / Year: 1993
Title: Atomic Structures of Human Immunophilin Fkbp12 Complexes with Fk506 and Rapamycin
Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
#5: Journal: J.Am.Chem.Soc. / Year: 1991
Title: Atomic Structure of the Rapamycin Human Immunophilin Fkbp-12 Complex
Authors: Van Duyne, G.D. / Standaert, R.F. / Schreiber, S.L. / Clardy, J.
#6: Journal: Science / Year: 1991
Title: Atomic Structure of Fkbp-Fk506, an Immunophilin-Immunosuppressant Complex
Authors: Van Duyne, G.D. / Standaert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
History
DepositionAug 18, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FK506 BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8902
Polymers11,7941
Non-polymers961
Water1,20767
1
A: FK506 BINDING PROTEIN
hetero molecules

A: FK506 BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7814
Polymers23,5892
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1360 Å2
ΔGint-47 kcal/mol
Surface area10510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)34.100, 34.100, 202.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein FK506 BINDING PROTEIN / FKBP12


Mass: 11794.425 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MR 12,000 DALTONS / Source: (natural) Bos taurus (domestic cattle) / Organ: THYMUS / References: UniProt: P18203, peptidylprolyl isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1140 mg/mlprotein 1drop
21.4-1.6 Msodium sulfate1reservoir
3100 mMcacodylate1reservoir

-
Data collection

Diffraction sourceWavelength: 1.54
DetectorDetector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 3977 / % possible obs: 68 % / Num. measured all: 10574 / Rmerge(I) obs: 0.049

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
MANUFACTURERSUPPLIED (MSC)data reduction
X-PLORphasing
RefinementResolution: 2.2→7 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.158 -
obs0.158 3699
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 5 67 902
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg3.45
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_improper_angle_deg / Dev ideal: 1.9

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more