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- PDB-9co5: Crystal Structure of Macrocycle mediated complex of FKBP12 and MAPRE1 -

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Basic information

Entry
Database: PDB / ID: 9co5
TitleCrystal Structure of Macrocycle mediated complex of FKBP12 and MAPRE1
Components
  • Microtubule-associated protein RP/EB family member 1
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsISOMERASE / molecular glue / microtubule
Function / homology
Function and homology information


protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / macrolide binding / activin receptor binding / microtubule plus-end / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane ...protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / macrolide binding / activin receptor binding / microtubule plus-end / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / mitotic spindle microtubule / transforming growth factor beta receptor binding / cell projection membrane / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / attachment of mitotic spindle microtubules to kinetochore / negative regulation of activin receptor signaling pathway / microtubule plus-end binding / microtubule bundle formation / heart trabecula formation / non-motile cilium assembly / I-SMAD binding / signaling receptor inhibitor activity / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / protein localization to centrosome / 'de novo' protein folding / negative regulation of microtubule polymerization / ventricular cardiac muscle tissue morphogenesis / FK506 binding / mitotic spindle pole / microtubule organizing center / microtubule polymerization / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / mTORC1-mediated signalling / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / regulation of microtubule polymerization or depolymerization / spindle midzone / regulation of immune response / heart morphogenesis / cytoplasmic microtubule / spindle assembly / supramolecular fiber organization / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / sarcoplasmic reticulum membrane / calcium channel regulator activity / positive regulation of microtubule polymerization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein maturation / Resolution of Sister Chromatid Cohesion / T cell activation / peptidyl-prolyl cis-trans isomerase activity / sarcoplasmic reticulum / AURKA Activation by TPX2 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / negative regulation of transforming growth factor beta receptor signaling pathway / RHO GTPases Activate Formins / Z disc / SARS-CoV-1 activates/modulates innate immune responses / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / intracellular protein localization / cell migration / protein folding / regulation of protein localization / protein refolding / microtubule / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / ciliary basal body / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / RNA binding / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology (CH) domain / : / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. ...EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Calponin homology (CH) domain / : / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
: / Peptidyl-prolyl cis-trans isomerase FKBP1A / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsKing, D.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Identification and characterization of ternary complexes consisting of FKBP12, MAPRE1 and macrocyclic molecular glues.
Authors: Salcius, M. / Tutter, A. / Fouche, M. / Koc, H. / King, D. / Dhembi, A. / Golosov, A. / Jahnke, W. / Henry, C. / Argoti, D. / Jia, W. / Pedro, L. / Connor, L. / Piechon, P. / Fabbiani, F. / ...Authors: Salcius, M. / Tutter, A. / Fouche, M. / Koc, H. / King, D. / Dhembi, A. / Golosov, A. / Jahnke, W. / Henry, C. / Argoti, D. / Jia, W. / Pedro, L. / Connor, L. / Piechon, P. / Fabbiani, F. / Denay, R. / Sager, E. / Kuehnoel, J. / Lozach, M.A. / Lima, F. / Vitrey, A. / Chen, S.Y. / Michaud, G. / Roth, H.J.
History
DepositionJul 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
B: Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7923
Polymers19,0312
Non-polymers7621
Water362
1
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
B: Microtubule-associated protein RP/EB family member 1
hetero molecules

A: Peptidyl-prolyl cis-trans isomerase FKBP1A
B: Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5856
Polymers38,0614
Non-polymers1,5242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
Buried area8780 Å2
ΔGint-51 kcal/mol
Surface area17160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.800, 134.800, 53.440
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP1A / PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding ...PPIase FKBP1A / 12 kDa FK506-binding protein / 12 kDa FKBP / FKBP-12 / Calstabin-1 / FK506-binding protein 1A / FKBP-1A / Immunophilin FKBP12 / Rotamase


Mass: 12054.782 Da / Num. of mol.: 1
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
#2: Protein Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 6975.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15691
#3: Chemical ChemComp-A1AZI / (5S,14R,16aS,21R,28S,30aR)-14-[2-(3,4-dimethoxyphenyl)ethyl]-24,24,28-trimethyl-2-methylidene-1,3,4,17,18,19,20,24,25,28,29,30a-dodecahydro-2H,14H-9,13-(metheno)dipyrido[1,2-d:1',2'-o][1,10,18,4,7,15]trioxatriazacyclotetracosine-6,16,22,23,27,30(7H,16aH)-hexone


Mass: 761.857 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H51N3O11 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.5 M LiSO4, 0.1 M CH3COONa pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→116.74 Å / Num. obs: 7682 / % possible obs: 100 % / Redundancy: 18.7 % / Biso Wilson estimate: 59.03 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.221 / Net I/σ(I): 11.7
Reflection shellResolution: 2.773→2.782 Å / Num. unique obs: 72 / CC1/2: 0.766

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
autoPROCdata processing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→67.4 Å / SU ML: 0.3643 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2254 405 5.29 %
Rwork0.2059 7255 -
obs0.207 7660 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.32 Å2
Refinement stepCycle: LAST / Resolution: 2.77→67.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1334 0 55 2 1391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091416
X-RAY DIFFRACTIONf_angle_d1.1161913
X-RAY DIFFRACTIONf_chiral_restr0.0556204
X-RAY DIFFRACTIONf_plane_restr0.0051250
X-RAY DIFFRACTIONf_dihedral_angle_d20.8097844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-3.170.2911320.25252344X-RAY DIFFRACTION99.92
3.17-40.28051240.21352391X-RAY DIFFRACTION100
4-67.40.18371490.18862520X-RAY DIFFRACTION99.93

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