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- PDB-6m4v: Crystal structure of MBP fused split FKBP in complex with rapamycin -

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Basic information

Entry
Database: PDB / ID: 6m4v
TitleCrystal structure of MBP fused split FKBP in complex with rapamycin
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
  • chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / Rapamycin / complex / kinase
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 / detection of maltose stimulus / maltose transport complex / carbohydrate transport / TGF-beta receptor signaling activates SMADs / mTORC1-mediated signalling / regulation of ryanodine-sensitive calcium-release channel activity / Calcineurin activates NFAT / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / regulation of immune response / heart morphogenesis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / supramolecular fiber organization / sarcoplasmic reticulum membrane / ATP-binding cassette (ABC) transporter complex / T cell activation / protein maturation / sarcoplasmic reticulum / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cell chemotaxis / 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 / outer membrane-bounded periplasmic space / protein refolding / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / periplasmic space / positive regulation of canonical NF-kappaB signal transduction / DNA damage response / membrane / cytosol / cytoplasm
Similarity search - Function
Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / 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. / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein ...Chitinase A; domain 3 - #40 / : / Chitinase A; domain 3 / 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. / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Peptidyl-prolyl cis-trans isomerase domain superfamily / Bacterial extracellular solute-binding protein / Roll / Alpha Beta
Similarity search - Domain/homology
RAPAMYCIN IMMUNOSUPPRESSANT DRUG / Maltose/maltodextrin-binding periplasmic protein / 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: 2.92 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

Downloads & links

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Assembly

Deposited unit
A: chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
B: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,0447
Polymers105,1234
Non-polymers1,9203
Water2,774154
1
A: chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4763
Polymers52,5622
Non-polymers9141
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-33 kcal/mol
Surface area20290 Å2
MethodPISA
2
C: chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1A
D: Peptidyl-prolyl cis-trans isomerase FKBP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5684
Polymers52,5622
Non-polymers1,0062
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-33 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.026, 48.144, 108.730
Angle α, β, γ (deg.)90.00, 106.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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.: 2 / Mutation: K-131A, N-197A, E-198A, K-287A, D-288A
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.: 2
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: Chemical ChemComp-RAP / RAPAMYCIN IMMUNOSUPPRESSANT DRUG


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


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


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Na-HEPES buffer (pH 7.5), 20% (w/v) PEG 8000

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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: Nov 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.92→48.14 Å / Num. obs: 23633 / % possible obs: 100 % / Redundancy: 3.8 % / CC1/2: 0.995 / Net I/σ(I): 7.4
Reflection shellResolution: 2.92→3.1 Å / Num. unique obs: 3775 / CC1/2: 0.79

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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: 2.92→48.14 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.886 / SU B: 52.166 / SU ML: 0.483 / Cross valid method: THROUGHOUT / ESU R Free: 0.513
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29762 1295 5.5 %RANDOM
Rwork0.20806 ---
obs0.21298 22328 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.568 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0 Å21.46 Å2
2---3.27 Å2-0 Å2
3---1.53 Å2
Refinement stepCycle: 1 / Resolution: 2.92→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7181 0 136 154 7471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137511
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176924
X-RAY DIFFRACTIONr_angle_refined_deg1.391.6710218
X-RAY DIFFRACTIONr_angle_other_deg1.1591.60916110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0735940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45224.421337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.937151174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0371521
X-RAY DIFFRACTIONr_chiral_restr0.050.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028425
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021474
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_it1.8542.3713769
X-RAY DIFFRACTIONr_mcbond_other1.8543768
X-RAY DIFFRACTIONr_mcangle_it2.744703
X-RAY DIFFRACTIONr_mcangle_other2.7394704
X-RAY DIFFRACTIONr_scbond_it2.0683742
X-RAY DIFFRACTIONr_scbond_other2.0683743
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9045515
X-RAY DIFFRACTIONr_long_range_B_refined4.2648278
X-RAY DIFFRACTIONr_long_range_B_other4.2638278
X-RAY DIFFRACTIONr_rigid_bond_restr1.99437260
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.92→2.996 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 82 -
Rwork0.308 1671 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9849-0.3712-1.17641.26130.67242.0878-0.02180.0398-0.1091-0.0589-0.0405-0.11470.14580.20530.06230.29590.0425-0.11370.72340.06280.097-53.6318-1.815622.8168
24.43310.87851.04145.3921.02825.47170.1339-0.104-0.32660.2594-0.0966-0.14880.0334-0.0743-0.03730.20140.0074-0.03780.25010.03960.0334-65.63976.231949.6303
31.08470.2584-0.61271.1223-0.49581.490.0284-0.0484-0.01960.0666-0.01690.02570.08510.0393-0.01150.3236-0.0428-0.11080.6283-0.040.0465-30.6672-3.004181.4031
45.5823-0.64221.82466.6463-0.16485.06870.20980.0936-0.0915-0.283-0.20680.20790.06050.0517-0.0030.2066-0.0474-0.00750.3521-0.06790.0188-18.86474.658954.6361
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-367 - 32
2X-RAY DIFFRACTION2B34 - 108
3X-RAY DIFFRACTION3C-367 - 32
4X-RAY DIFFRACTION4D34 - 108

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