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- PDB-6m4w: Crystal structure of MBP fused split FKBP-FRB T2098L mutant in co... -

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Basic information

Entry
Database: PDB / ID: 6m4w
TitleCrystal structure of MBP fused split FKBP-FRB T2098L mutant in complex with rapamycin
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
  • Serine/threonine-protein kinase mTOR
  • chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / Rapamycin / complex / kinase
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 / TORC1 complex / activin receptor binding / 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 L-leucine / energy reserve metabolic process / type I transforming growth factor beta receptor binding / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / cellular response to nutrient / Amino acids regulate mTORC1 / TORC1 signaling / negative regulation of activin receptor signaling pathway / serine/threonine protein kinase complex / ruffle organization / cellular response to methionine / heart trabecula formation / negative regulation of cell size / I-SMAD binding / positive regulation of ubiquitin-dependent protein catabolic process / cellular response to osmotic stress / negative regulation of protein localization to nucleus / anoikis / regulation of amyloid precursor protein catabolic process / inositol hexakisphosphate binding / signaling receptor inhibitor activity / cardiac muscle cell development / terminal cisterna / ryanodine receptor complex / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / positive regulation of transcription by RNA polymerase III / 'de novo' protein folding / negative regulation of macroautophagy / ventricular cardiac muscle tissue morphogenesis / Macroautophagy / positive regulation of myotube differentiation / FK506 binding / detection of maltose stimulus / regulation of cell size / Constitutive Signaling by AKT1 E17K in Cancer / maltose transport complex / positive regulation of actin filament polymerization / germ cell development / carbohydrate transport / behavioral response to pain / TOR signaling / TGF-beta receptor signaling activates SMADs / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / mTORC1-mediated signalling / positive regulation of translational initiation / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / CD28 dependent PI3K/Akt signaling / carbohydrate transmembrane transporter activity / maltose binding / HSF1-dependent transactivation / regulation of macroautophagy / maltose transport / maltodextrin transmembrane transport / 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 / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cardiac muscle contraction / T cell costimulation
Similarity search - Function
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 / : ...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. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / 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 / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Bacterial extracellular solute-binding protein / Peptidyl-prolyl cis-trans isomerase domain superfamily / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Roll / Protein kinase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Maltose/maltodextrin-binding periplasmic protein / Serine/threonine-protein kinase mTOR / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsKikuchi, M. / Wu, D. / Inoue, T. / Umehara, T.
CitationJournal: Nat.Methods / Year: 2020
Title: Rational design and implementation of a chemically inducible heterotrimerization system.
Authors: Wu, H.D. / Kikuchi, M. / Dagliyan, O. / Aragaki, A.K. / Nakamura, H. / Dokholyan, N.V. / Umehara, T. / Inoue, T.
History
DepositionMar 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
B: chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
C: chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
D: Peptidyl-prolyl cis-trans isomerase FKBP1A
E: Peptidyl-prolyl cis-trans isomerase FKBP1A
F: Peptidyl-prolyl cis-trans isomerase FKBP1A
G: Serine/threonine-protein kinase mTOR
H: Serine/threonine-protein kinase mTOR
I: Serine/threonine-protein kinase mTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,88816
Polymers192,0269
Non-polymers3,8627
Water3,441191
1
A: chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
D: Peptidyl-prolyl cis-trans isomerase FKBP1A
G: Serine/threonine-protein kinase mTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3576
Polymers64,0093
Non-polymers1,3493
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
E: Peptidyl-prolyl cis-trans isomerase FKBP1A
H: Serine/threonine-protein kinase mTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2655
Polymers64,0093
Non-polymers1,2562
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
F: Peptidyl-prolyl cis-trans isomerase FKBP1A
I: Serine/threonine-protein kinase mTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2655
Polymers64,0093
Non-polymers1,2562
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.546, 127.546, 278.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 3 types, 9 molecules ABCDEFGHI

#1: Protein chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / PPIase FKBP1A / 12 kDa FK506- ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / PPIase FKBP1A / 12 kDa FK506-binding protein / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 44074.879 Da / Num. of mol.: 3 / Mutation: D-288A, K-287A, E-198A, N-197A, K-131A
Source method: isolated from a genetically manipulated source
Details: This entity is chimeric. Organism is Homo sapiens and Eschrichia coli.
Source: (gene. exp.) Escherichia coli K-12 (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K-12 / Gene: malE, b4034, JW3994, FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEX9, UniProt: P62942, peptidylprolyl isomerase
#2: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / ...PPIase FKBP1A / 12 kDa FK506-binding protein / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 8486.715 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP1A, FKBP1, FKBP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P62942, peptidylprolyl isomerase
#3: Protein Serine/threonine-protein kinase mTOR / Mammalian target of rapamycin / mTOR / Mechanistic target of rapamycin


Mass: 11447.091 Da / Num. of mol.: 3 / Mutation: T2098L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MTOR / Production host: Escherichia coli (E. coli)
References: UniProt: P42345, non-specific serine/threonine protein kinase

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Sugars , 1 types, 3 molecules

#4: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 195 molecules

#5: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG


Mass: 914.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H79NO13 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-HCl buffer (pH 7.0), 200 mM calcium acetate and 20% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→48.6 Å / Num. obs: 42250 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 0.992 / Net I/σ(I): 9.5
Reflection shellResolution: 3.11→3.23 Å / Num. unique obs: 4337 / CC1/2: 0.522

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Processing

Software
NameVersionClassification
XDSdata reduction
MOLREPphasing
REFMAC5.8.0258refinement
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAP

1fap


Resolution: 3.11→48.65 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.88 / SU B: 27.493 / SU ML: 0.45 / Cross valid method: THROUGHOUT / ESU R Free: 0.517
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27844 2142 5.1 %RANDOM
Rwork0.23629 ---
obs0.23842 40024 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70.304 Å2
Baniso -1Baniso -2Baniso -3
1-1.38 Å2-0 Å2-0 Å2
2--1.38 Å2-0 Å2
3----2.75 Å2
Refinement stepCycle: 1 / Resolution: 3.11→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13335 0 270 191 13796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01213943
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6641.6518911
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.51551695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.85323.295689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.278152284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6541551
X-RAY DIFFRACTIONr_chiral_restr0.0540.21808
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9487.1376816
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73110.7018499
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7127.0467127
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.56396.03720747
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.11→3.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 157 -
Rwork0.354 2892 -
obs--100 %

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