[English] 日本語
Yorodumi
- PDB-1f40: SOLUTION STRUCTURE OF FKBP12 COMPLEXED WITH GPI-1046, A NEUROTROP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f40
TitleSOLUTION STRUCTURE OF FKBP12 COMPLEXED WITH GPI-1046, A NEUROTROPHIC LIGAND
ComponentsFK506 BINDING PROTEIN (FKBP12)
KeywordsISOMERASE
Function / homology
Function and homology information


macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding ...macrolide binding / activin receptor binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / transforming growth factor beta receptor binding / cytoplasmic side of membrane / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / heart trabecula formation / I-SMAD binding / regulation of amyloid precursor protein catabolic process / signaling receptor inhibitor activity / terminal cisterna / ryanodine receptor complex / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / regulation of immune response / heart morphogenesis / supramolecular fiber organization / sarcoplasmic reticulum membrane / T cell activation / sarcoplasmic reticulum / protein maturation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / Z disc / SARS-CoV-1 activates/modulates innate immune responses / protein folding / regulation of protein localization / protein refolding / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / 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
Chem-GPI / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSich, C. / Improta, S. / Cowley, D.J. / Guenet, C. / Merly, J.P. / Teufel, M. / Saudek, V.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: Solution structure of a neurotrophic ligand bound to FKBP12 and its effects on protein dynamics.
Authors: Sich, C. / Improta, S. / Cowley, D.J. / Guenet, C. / Merly, J.P. / Teufel, M. / Saudek, V.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Neurotrophic Immunophilin Ligands Stimulate Structural and Functional Recovery in Neurodegenerative Animal Models
Authors: Steiner, J.P. / Hamilton, G.S. / Ross, D.T. / Valentine, H.L. / Guo, H. / Connolly, M.A. / Liang, S. / Ramsey, C. / Li, J.H. / Huang, W. / Howorth, P. / Soni, R. / Fuller, M. / Sauer, H. / ...Authors: Steiner, J.P. / Hamilton, G.S. / Ross, D.T. / Valentine, H.L. / Guo, H. / Connolly, M.A. / Liang, S. / Ramsey, C. / Li, J.H. / Huang, W. / Howorth, P. / Soni, R. / Fuller, M. / Sauer, H. / Nowotnik, A.C. / Suzdak, P.D.
#2: Journal: Science / Year: 1991
Title: Atomic Structure of FKBP-FK506, an Immunophilin-immunosuppressant Complex
Authors: van Duyne, G.D. / Staendert, R.F. / Karplus, P.A. / Schreiber, S.L. / Clardy, J.
#3: Journal: J.Am.Chem.Soc. / Year: 1993
Title: Design, Synthesis, and Kinetic Evaluation of high-affinity FKBP Ligands and the X-ray Structure of their Complexes with FKBP12
Authors: Holt, D.A. / Luengo, J.I. / Yamashita, D.S. / Oh, H.-J. / Konalian, A.L. / Yen, H.-K. / Rozamus, L.W. / Brandt, M. / Bossard, M.J. / Levy, M.A. / Eggleston, D.S. / Lian, J. / Schultz, L.W. / ...Authors: Holt, D.A. / Luengo, J.I. / Yamashita, D.S. / Oh, H.-J. / Konalian, A.L. / Yen, H.-K. / Rozamus, L.W. / Brandt, M. / Bossard, M.J. / Levy, M.A. / Eggleston, D.S. / Lian, J. / Schultz, L.W. / Stout, T.J. / Clardy, J.
#4: Journal: Biochemistry / Year: 1994
Title: 15N NMR Relaxation Studies of the FK506 Binding Protein: Dynamic Effects of Ligand Binding and Implications for Calcinerin Inhibition
Authors: Cheng, J.W. / Lepre, C.A. / Moore, J.M.
History
DepositionJun 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FK506 BINDING PROTEIN (FKBP12)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1972
Polymers11,8371
Non-polymers3601
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: Protein FK506 BINDING PROTEIN (FKBP12)


Mass: 11836.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROTEIN COORDINATES WERE TAKEN FROM THE CRYSTAL STRUCTURE BY HOLT ET AL. (1993, PDB ACCESSION CODE 1FKG).
Source: (gene. exp.) Homo sapiens (human) / Organ: BRAIN / Plasmid: PARS-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942
#2: Chemical ChemComp-GPI / (2S)-[3-PYRIDYL-1-PROPYL]-1-[3,3-DIMETHYL-1,2-DIOXOPENTYL]-2-PYRROLIDINECARBOXYLATE / GPI-1046


Mass: 360.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N2O4

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1133D 13C-separated NOESY
1232D 15N,13C-filtered NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM FKBP12 U-15N; 100 mM phosphate buffer; 0.01% NaN390% H2O/10% D2O
20.5 mM FKBP12 U-15N; 1mM GPI-1046; 100 mM phosphate buffer; 0.01% NaN390% H2O/10% D2O
32mM FKBP12 U-15N,13C; 2mM GPI-1046; 100 mM phosphate buffer; 0.01% NaN390% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 6.5 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.1collection
XwinNMR1.1processing
AURELIA2.1Neidig, P.data analysis
Felix97.2data analysis
X-PLOR3.851Brunger A.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures were calculated using a total of 50 ligand-ligand and 18 protein-ligand distance restraints. NOEs involving degenerate protons were incorporated as ambiguous restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

+
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