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- PDB-6oqa: Crystal structure of CEP250 bound to FKBP12 in the presence of FK... -

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Basic information

Entry
Database: PDB / ID: 6oqa
TitleCrystal structure of CEP250 bound to FKBP12 in the presence of FK506-like novel natural product
Components
  • Centrosome-associated protein CEP250
  • Peptidyl-prolyl cis-trans isomerase FKBP1A
KeywordsCELL CYCLE / ISOMERASE / FKBP12 / CEP250 / natural product / ternary complex
Function / homology
Function and homology information


protein localization to organelle / centriole-centriole cohesion / regulation of centriole-centriole cohesion / macrolide binding / detection of light stimulus involved in visual perception / activin receptor binding / positive regulation of protein localization to centrosome / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding ...protein localization to organelle / centriole-centriole cohesion / regulation of centriole-centriole cohesion / macrolide binding / detection of light stimulus involved in visual perception / activin receptor binding / positive regulation of protein localization to centrosome / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / cytoplasmic side of membrane / transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / negative regulation of activin receptor signaling pathway / signaling receptor inhibitor activity / heart trabecula formation / non-motile cilium assembly / I-SMAD binding / protein localization to centrosome / regulation of amyloid precursor protein catabolic process / terminal cisterna / ryanodine receptor complex / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / FK506 binding / TGF-beta receptor signaling activates SMADs / microtubule organizing center / mTORC1-mediated signalling / cilium assembly / Calcineurin activates NFAT / photoreceptor outer segment / regulation of immune response / heart morphogenesis / supramolecular fiber organization / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / photoreceptor inner segment / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / sarcoplasmic reticulum membrane / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / T cell activation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium channel regulator activity / centriole / negative regulation of transforming growth factor beta receptor signaling pathway / protein maturation / Z disc / SARS-CoV-1 activates/modulates innate immune responses / intracellular protein localization / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / regulation of protein localization / protein folding / protein refolding / amyloid fibril formation / Potential therapeutics for SARS / transmembrane transporter binding / positive regulation of canonical NF-kappaB signal transduction / ciliary basal body / protein domain specific binding / centrosome / perinuclear region of cytoplasm / protein-containing complex / extracellular exosome / membrane / cytoplasm / cytosol
Similarity search - Function
Ciliary rootlet component, centrosome cohesion / 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-60Z / MALONIC ACID / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Peptidyl-prolyl cis-trans isomerase FKBP1A / Centrosome-associated protein CEP250
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLee, S.-J. / Shigdel, U.K. / Townson, S.A. / Verdine, G.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Genomic discovery of an evolutionarily programmed modality for small-molecule targeting of an intractable protein surface.
Authors: Shigdel, U.K. / Lee, S.J. / Sowa, M.E. / Bowman, B.R. / Robison, K. / Zhou, M. / Pua, K.H. / Stiles, D.T. / Blodgett, J.A.V. / Udwary, D.W. / Rajczewski, A.T. / Mann, A.S. / Mostafavi, S. / ...Authors: Shigdel, U.K. / Lee, S.J. / Sowa, M.E. / Bowman, B.R. / Robison, K. / Zhou, M. / Pua, K.H. / Stiles, D.T. / Blodgett, J.A.V. / Udwary, D.W. / Rajczewski, A.T. / Mann, A.S. / Mostafavi, S. / Hardy, T. / Arya, S. / Weng, Z. / Stewart, M. / Kenyon, K. / Morgenstern, J.P. / Pan, E. / Gray, D.C. / Pollock, R.M. / Fry, A.M. / Klausner, R.D. / Townson, S.A. / Verdine, G.L.
History
DepositionApr 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: Peptidyl-prolyl cis-trans isomerase FKBP1A
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
C: Centrosome-associated protein CEP250
D: Centrosome-associated protein CEP250
E: Peptidyl-prolyl cis-trans isomerase FKBP1A
F: Peptidyl-prolyl cis-trans isomerase FKBP1A
G: Centrosome-associated protein CEP250
H: Centrosome-associated protein CEP250
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,33050
Polymers93,5908
Non-polymers6,74042
Water4,071226
1
A: Peptidyl-prolyl cis-trans isomerase FKBP1A
B: Peptidyl-prolyl cis-trans isomerase FKBP1A
C: Centrosome-associated protein CEP250
D: Centrosome-associated protein CEP250
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,36335
Polymers46,7954
Non-polymers4,56831
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Peptidyl-prolyl cis-trans isomerase FKBP1A
F: Peptidyl-prolyl cis-trans isomerase FKBP1A
G: Centrosome-associated protein CEP250
H: Centrosome-associated protein CEP250
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,96815
Polymers46,7954
Non-polymers2,17311
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.832, 64.952, 136.055
Angle α, β, γ (deg.)90.000, 90.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ABEFCDGH

#1: 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: 11967.705 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Protein
Centrosome-associated protein CEP250 / 250 kDa centrosomal protein / Cep250 / Centrosomal Nek2-associated protein 1 / C-Nap1 / Centrosomal protein 2


Mass: 11429.831 Da / Num. of mol.: 4 / Fragment: UNP residues 2078-2175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP250, CEP2, CNAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BV73

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Non-polymers , 9 types, 268 molecules

#3: Chemical
ChemComp-60Z / (3R,4E,7E,10R,11S,12R,13S,16R,17R,24aS)-11,17-dihydroxy-10,12,16-trimethyl-3-[(2R)-1-phenylbutan-2-yl]-6,9,10,11,12,13,14,15,16,17,22,23,24,24a-tetradecahydro-3H-13,17-epoxypyrido[2,1-c][1,4]oxazacyclohenicosine-1,18,19(21H)-trione


Mass: 609.793 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C36H51NO7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O9
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H4O4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.0, 0.2 M sodium malonate, 21% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 14, 2013
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→136.05 Å / Num. obs: 53422 / % possible obs: 99.5 % / Redundancy: 3.7 % / Net I/σ(I): 12.9
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 4.1 / Num. unique obs: 5345 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→136.05 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.519 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.21
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 2723 5.1 %RANDOM
Rwork0.2077 ---
obs0.2102 50564 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 157.52 Å2 / Biso mean: 48.317 Å2 / Biso min: 22.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å2-0.01 Å2
2---1.11 Å20 Å2
3----1.05 Å2
Refinement stepCycle: final / Resolution: 2.2→136.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6124 0 457 226 6807
Biso mean--61.4 51.86 -
Num. residues----767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0196544
X-RAY DIFFRACTIONr_bond_other_d0.0060.024888
X-RAY DIFFRACTIONr_angle_refined_deg1.1652.038709
X-RAY DIFFRACTIONr_angle_other_deg1.374311777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.59923.677291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.114151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0061563
X-RAY DIFFRACTIONr_chiral_restr0.0660.2952
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021265
LS refinement shellResolution: 2.203→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 168 -
Rwork0.255 3309 -
all-3477 -
obs--90.03 %

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