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- PDB-1p5q: Crystal Structure of FKBP52 C-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 1p5q
TitleCrystal Structure of FKBP52 C-terminal Domain
ComponentsFK506-binding protein 4
KeywordsISOMERASE
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 / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / 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 ...Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Tetratricopeptide repeat domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Roll / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsWu, B. / Li, P. / Lou, Z. / Shu, C. / Ding, Y. / Shen, B. / Rao, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: 3D structure of human FK506-binding protein 52: Implications for the assembly of the glucocorticoid receptor/Hsp90/immunophilin heterocomplex
Authors: Wu, B. / Li, P. / Liu, Y. / Lou, Z. / Ding, Y. / Shu, C. / Ye, S. / Bartlam, M. / Shen, B. / Rao, Z.
History
DepositionApr 28, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FK506-binding protein 4
B: FK506-binding protein 4
C: FK506-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,17212
Polymers115,3083
Non-polymers8659
Water9,494527
1
A: FK506-binding protein 4
B: FK506-binding protein 4
C: FK506-binding protein 4
hetero molecules

A: FK506-binding protein 4
B: FK506-binding protein 4
C: FK506-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,34424
Polymers230,6156
Non-polymers1,72918
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area22630 Å2
ΔGint-304 kcal/mol
Surface area81040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.274, 142.927, 170.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein FK506-binding protein 4 / FKBP52


Mass: 38435.840 Da / Num. of mol.: 3 / Fragment: FKBP52 C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: Q02790, peptidylprolyl isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 3.35 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium Sulfate, Tris, Ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9798, 0.9800, 0.9000
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 26, 2003
RadiationMonochromator: Melting Silicom + Fuzed Quartz / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.981
30.91
ReflectionResolution: 2.7→50 Å / Num. all: 291352 / Num. obs: 291337 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 99

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.8→50 Å / σ(F): -2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.284 3164 RANDOM
Rwork0.212 --
all0.216 291352 -
obs0.216 291337 -
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6876 0 45 527 7448
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg2.042
X-RAY DIFFRACTIONc_dihedral_angle_d22.189
X-RAY DIFFRACTIONc_improper_angle_d1.234

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