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- PDB-3fap: ATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH H... -

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Basic information

Entry
Database: PDB / ID: 3fap
TitleATOMIC STRUCTURES OF THE RAPAMYCIN ANALOGS IN COMPLEX WITH BOTH HUMAN FKBP12 AND FRB DOMAIN OF FRAP
Components
  • FK506-BINDING PROTEIN
  • FKBP12-RAPAMYCIN ASSOCIATED PROTEIN
KeywordsCELL CYCLE / FKBP12 / FRAP / RAPAMYCIN / COMPLEX / GENE THERAPY
Function / homology
Function and homology information


RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability ...RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 signaling / TORC2 complex / regulation of membrane permeability / cellular response to leucine starvation / macrolide binding / negative regulation of lysosome organization / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / activin receptor binding / TORC1 complex / voluntary musculoskeletal movement / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / calcineurin-NFAT signaling cascade / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of keratinocyte migration / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / regulation of osteoclast differentiation / transforming growth factor beta receptor binding / cytoplasmic side of membrane / regulation of lysosome organization / MTOR signalling / TGFBR1 LBD Mutants in Cancer / cellular response to nutrient / cellular response to L-leucine / energy reserve metabolic process / Amino acids regulate mTORC1 / regulation of autophagosome assembly / type I transforming growth factor beta receptor binding / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / negative regulation of activin receptor signaling pathway / ruffle organization / serine/threonine protein kinase complex / cellular response to methionine / heart trabecula formation / I-SMAD binding / negative regulation of cell size / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to osmotic stress / negative regulation of protein localization to nucleus / anoikis / inositol hexakisphosphate binding / regulation of amyloid precursor protein catabolic process / signaling receptor inhibitor activity / terminal cisterna / ryanodine receptor complex / cardiac muscle cell development / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / 'de novo' protein folding / positive regulation of transcription by RNA polymerase III / negative regulation of macroautophagy / ventricular cardiac muscle tissue morphogenesis / Macroautophagy / positive regulation of myotube differentiation / FK506 binding / regulation of cell size / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of actin filament polymerization / germ cell development / TOR signaling / behavioral response to pain / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / positive regulation of translational initiation / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / CD28 dependent PI3K/Akt signaling / HSF1-dependent transactivation / regulation of macroautophagy / regulation of immune response / response to amino acid / 'de novo' pyrimidine nucleobase biosynthetic process / positive regulation of epithelial to mesenchymal transition / vascular endothelial cell response to laminar fluid shear stress / positive regulation of lipid biosynthetic process / heart morphogenesis / cellular response to nutrient levels / neuronal action potential / regulation of cellular response to heat / positive regulation of lamellipodium assembly / cardiac muscle contraction / phagocytic vesicle / T cell costimulation / positive regulation of stress fiber assembly / supramolecular fiber organization / cytoskeleton organization / endomembrane system / sarcoplasmic reticulum membrane / negative regulation of insulin receptor signaling pathway / negative regulation of autophagy
Similarity search - Function
FKBP12-rapamycin binding domain / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / Serine/threonine-protein kinase ATR-like, HEAT repeats ...FKBP12-rapamycin binding domain / Domain of unknown function DUF3385, target of rapamycin protein / Serine/threonine-protein kinase mTOR domain / Domain of unknown function / FKBP12-rapamycin binding domain / Serine/threonine-protein kinase TOR / FKBP12-rapamycin binding domain superfamily / FKBP12-rapamycin binding domain / Rapamycin binding domain / Serine/threonine-protein kinase ATR-like, HEAT repeats / : / FATC domain / Chitinase A; domain 3 - #40 / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / : / Chitinase A; domain 3 / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Roll / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
C15-(R)-METHYLTHIENYL RAPAMYCIN / Serine/threonine-protein kinase mTOR / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLiang, J. / Clardy, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Refined structure of the FKBP12-rapamycin-FRB ternary complex at 2.2 A resolution.
Authors: Liang, J. / Choi, J. / Clardy, J.
History
DepositionMay 6, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: FK506-BINDING PROTEIN
B: FKBP12-RAPAMYCIN ASSOCIATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1493
Polymers23,1682
Non-polymers9801
Water3,477193
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.400, 51.720, 101.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein FK506-BINDING PROTEIN / FKBP12


Mass: 11836.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HUMAN HIPPOCAMPAL CDNA LIBRARY SOURCE 8 (CLONTECH, PALO ALTO, CA)
Plasmid: PGEX-3X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) (NOVAGEN) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Protein FKBP12-RAPAMYCIN ASSOCIATED PROTEIN / FRAP


Mass: 11331.937 Da / Num. of mol.: 1 / Fragment: FRB / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42345
#3: Chemical ChemComp-ARD / C15-(R)-METHYLTHIENYL RAPAMYCIN / RAPAMYCIN IMMUNOSUPPRESSANT DRUG


Mass: 980.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H81NO12S / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growpH: 8
Details: 20% PEG8000, 10% MPD, 0.1 M TRIS-HCL PH 8.5, pH 8.00
Crystal grow
*PLUS
Method: other
Details: This particular structure is not described in this paper.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91
DetectorType: ADSC / Detector: CCD / Date: Feb 1, 1999 / Details: MIRROR
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. obs: 20139 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 4.7 / Net I/σ(I): 10.4
Reflection shellHighest resolution: 1.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.3 / Rsym value: 28.7 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FAP

2fap


Resolution: 1.85→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 1024989.71 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1980 9.9 %RANDOM
Rwork0.207 ---
obs-20084 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.54 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.93 Å20 Å20 Å2
2---1.79 Å20 Å2
3----7.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1628 0 69 193 1890
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.032
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.38
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.411.5
X-RAY DIFFRACTIONc_mcangle_it6.382
X-RAY DIFFRACTIONc_scbond_it7.162
X-RAY DIFFRACTIONc_scangle_it9.872.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 324 9.8 %
Rwork0.261 2969 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION21704.PAR1704.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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