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- PDB-4tw8: The Fk1-Fk2 domains of FKBP52 in complex with iFit-FL -

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Basic information

Entry
Database: PDB / ID: 4tw8
TitleThe Fk1-Fk2 domains of FKBP52 in complex with iFit-FL
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP4
KeywordsISOMERASE / Fk-506 binding domain / Hsp90 cochaperone / immunophiline / peptidyl-prolyl isomerase / ligand selectivity
Function / homology
Function and homology information


steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / prostate gland development / copper ion transport / nuclear glucocorticoid receptor binding / protein-containing complex localization / negative regulation of microtubule polymerization / FK506 binding ...steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / prostate gland development / copper ion transport / nuclear glucocorticoid receptor binding / protein-containing complex localization / negative regulation of microtubule polymerization / FK506 binding / androgen receptor signaling pathway / Attenuation phase / axonal growth cone / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / embryo implantation / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / tau protein binding / protein folding / negative regulation of neuron projection development / protein-macromolecule adaptor activity / microtubule / Estrogen-dependent gene expression / Potential therapeutics for SARS / neuronal cell body / GTP binding / perinuclear region of cytoplasm / protein-containing complex / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / cytoplasm / cytosol
Similarity search - Function
Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily ...Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-37M / Peptidyl-prolyl cis-trans isomerase FKBP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.003 Å
AuthorsGaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Almeida, O.F.X. / Ruehter, G. ...Gaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Almeida, O.F.X. / Ruehter, G. / Uhr, M. / Schmidt, M.V. / Touma, C. / Bracher, A. / Hausch, F.
Citation
Journal: Nat.Chem.Biol. / Year: 2015
Title: Selective inhibitors of the FK506-binding protein 51 by induced fit.
Authors: Gaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Sippel, C. / Zannas, A.S. / Draenert, R. / Binder, E.B. / ...Authors: Gaali, S. / Kirschner, A. / Cuboni, S. / Hartmann, J. / Kozany, C. / Balsevich, G. / Namendorf, C. / Fernandez-Vizarra, P. / Sippel, C. / Zannas, A.S. / Draenert, R. / Binder, E.B. / Almeida, O.F. / Ruhter, G. / Uhr, M. / Schmidt, M.V. / Touma, C. / Bracher, A. / Hausch, F.
#1: Journal: J. Mol. Biol. / Year: 2013
Title: Crystal structures of the free and ligand-bound FK1-FK2 domain segment of FKBP52 reveal a flexible inter-domain hinge.
Authors: Bracher, A. / Kozany, C. / Hahle, A. / Wild, P. / Zacharias, M. / Hausch, F.
History
DepositionJun 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Dec 20, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP4
B: Peptidyl-prolyl cis-trans isomerase FKBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1184
Polymers52,9402
Non-polymers2,1782
Water181
1
A: Peptidyl-prolyl cis-trans isomerase FKBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5592
Polymers26,4701
Non-polymers1,0891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase FKBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5592
Polymers26,4701
Non-polymers1,0891
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.654, 46.351, 310.064
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 21 - 255 / Label seq-ID: 1 - 235

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsbiological unit is the same as asym.

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP4 / PPIase FKBP4 / 51 kDa FK506-binding protein / FKBP51 / 52 kDa FK506-binding protein / FKBP-52 / 59 ...PPIase FKBP4 / 51 kDa FK506-binding protein / FKBP51 / 52 kDa FK506-binding protein / FKBP-52 / 59 kDa immunophilin / p59 / FK506-binding protein 4 / FKBP-4 / FKBP59 / HSP-binding immunophilin / HBI / Immunophilin FKBP52 / Rotamase


Mass: 26470.018 Da / Num. of mol.: 2 / Fragment: UNP residues 21-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP4, FKBP52 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): codon plus RIL / References: UniProt: Q02790, peptidylprolyl isomerase
#2: Chemical ChemComp-37M / 2-(5-{[({3-[(1R)-1-[({(2S)-1-[(2S)-2-[(1S)-cyclohex-2-en-1-yl]-2-(3,4,5-trimethoxyphenyl)acetyl]piperidin-2-yl}carbonyl)oxy]-3-(3,4-dimethoxyphenyl)propyl]phenoxy}acetyl)amino]methyl}-6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid


Mass: 1089.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C63H64N2O15
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 28 % PEG-6000, 2 % DMSO and TrisHCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.003→155.032 Å / Num. all: 13725 / Num. obs: 13725 / % possible obs: 97.8 % / Redundancy: 6 % / Rpim(I) all: 0.062 / Rrim(I) all: 0.157 / Rsym value: 0.143 / Net I/av σ(I): 5 / Net I/σ(I): 10.2 / Num. measured all: 81673
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
3-3.174.70.7591850317910.3570.759291
3.17-3.365.20.5181.5942518250.2390.5183.196.6
3.36-3.595.30.2992.6929617650.1390.2995.497.8
3.59-3.886.10.2233.4997416460.0960.2237.799.3
3.88-4.256.80.1415.41048415470.0580.1411299.8
4.25-4.756.90.1027.2955013940.0410.10216.799.9
4.75-5.486.40.1017.2804112600.0430.10115.3100
5.48-6.7170.1047.2766010910.0420.10414.6100
6.71-9.56.50.06510.257128810.0270.06520.199.9
9.5-46.3515.80.04512.530285250.020.04526.999.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.19 Å45.84 Å
Translation3.19 Å45.84 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.14data extraction
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q1C

1q1c


Resolution: 3.003→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.87 / WRfactor Rfree: 0.2337 / WRfactor Rwork: 0.1832 / FOM work R set: 0.8207 / SU B: 45.383 / SU ML: 0.355 / SU R Cruickshank DPI: 0.3655 / SU Rfree: 0.4307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 674 4.9 %RANDOM
Rwork0.2099 12971 --
obs0.2122 13645 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.58 Å2 / Biso mean: 55.192 Å2 / Biso min: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.68 Å20 Å2
3----0.24 Å2
Refinement stepCycle: final / Resolution: 3.003→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 142 1 3841
Biso mean--81.05 22.8 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.023936
X-RAY DIFFRACTIONr_angle_refined_deg1.1572.025312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.72324.719178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98915669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3221519
X-RAY DIFFRACTIONr_chiral_restr0.0750.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213021
Refine LS restraints NCS

Ens-ID: 1 / Number: 245 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.003→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 41 -
Rwork0.352 829 -
all-870 -
obs--85.21 %
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)
16.28060.08850.08124.30360.66094.4957-0.067-0.02590.1959-0.02150.2284-0.2350.30390.3121-0.16140.2774-0.01060.01170.18730.00940.11717.6995-9.906851.943
25.6775-2.0751-0.22075.10370.92174.46010.0589-0.198-0.15050.00840.09720.07080.03690.2003-0.15610.021-0.01970.03890.0412-0.01280.2183-11.6057-1.612176.892
311.28721.24543.41110.14350.37881.03310.1752-0.02910.12680.0904-0.11360.02810.11950.0044-0.06160.81370.10410.08590.4591-0.11310.46516.7859-20.647755.4968
44.411.84080.01885.7299-0.37635.9391-0.0692-0.09810.0043-0.09440.04130.10220.3826-0.42970.02790.3285-0.02570.03830.1737-0.0230.18720.3637-15.338628.1726
54.8706-1.88910.04895.31020.17134.4921-0.08060.16680.1093-0.14750.04780.134-0.09260.01690.03280.3511-0.0841-0.01130.03110.03880.18036.32970.36920.5104
60.0845-0.7211-1.45886.870813.788827.7232-0.11170.01590.0380.09170.3185-0.03460.37870.7558-0.20680.9122-0.0207-0.31790.74550.06270.41989.4566-22.089426.1065
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A21 - 139
2X-RAY DIFFRACTION2A140 - 255
3X-RAY DIFFRACTION3C1
4X-RAY DIFFRACTION4B21 - 139
5X-RAY DIFFRACTION5B140 - 255
6X-RAY DIFFRACTION6D1

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