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- PDB-1qz2: Crystal Structure of FKBP52 C-terminal Domain complex with the C-... -

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Basic information

Entry
Database: PDB / ID: 1qz2
TitleCrystal Structure of FKBP52 C-terminal Domain complex with the C-terminal peptide MEEVD of Hsp90
Components
  • 5-mer peptide from Heat shock protein HSP 90
  • FK506-binding protein 4
KeywordsISOMERASE/CHAPERONE / Isomerase / Rotamase / chaperone / Heat shock / ISOMERASE-CHAPERONE COMPLEX
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 / : / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / prostate gland development ...steroid hormone receptor complex assembly / negative regulation of microtubule polymerization or depolymerization / male sex differentiation / copper-dependent protein binding / : / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / prostate gland development / dynein axonemal particle / aryl hydrocarbon receptor complex / nuclear glucocorticoid receptor binding / histone methyltransferase binding / copper ion transport / protein kinase regulator activity / positive regulation of protein localization to cell surface / protein-containing complex localization / ATP-dependent protein binding / negative regulation of protein metabolic process / negative regulation of microtubule polymerization / positive regulation of tau-protein kinase activity / telomerase holoenzyme complex assembly / FK506 binding / Uptake and function of diphtheria toxin / TPR domain binding / androgen receptor signaling pathway / positive regulation of transforming growth factor beta receptor signaling pathway / dendritic growth cone / positive regulation of phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / telomere maintenance via telomerase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / response to unfolded protein / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / Purinergic signaling in leishmaniasis infection / supramolecular fiber organization / DNA polymerase binding / axonal growth cone / chaperone-mediated protein folding / embryo implantation / positive regulation of telomerase activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / heat shock protein binding / cellular response to interleukin-4 / nitric-oxide synthase regulator activity / ESR-mediated signaling / placenta development / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / positive regulation of cell differentiation / phosphoprotein binding / peptide binding / ATP-dependent protein folding chaperone / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Regulation of actin dynamics for phagocytic cup formation / kinase binding / Chaperone Mediated Autophagy / histone deacetylase binding / The role of GTSE1 in G2/M progression after G2 checkpoint / positive regulation of nitric oxide biosynthetic process / regulation of protein localization / disordered domain specific binding / melanosome / unfolded protein binding / protein-macromolecule adaptor activity / protein folding / negative regulation of neuron projection development / double-stranded RNA binding / cellular response to heat / MHC class II protein complex binding / secretory granule lumen / Estrogen-dependent gene expression / microtubule / ficolin-1-rich granule lumen / Potential therapeutics for SARS / protein dimerization activity / protein stabilization / regulation of cell cycle / cadherin binding / neuronal cell body / ubiquitin protein ligase binding / Neutrophil degranulation / virion attachment to host cell / GTP binding / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / perinuclear region of cytoplasm / cell surface / ATP hydrolysis activity / protein homodimerization activity / protein-containing complex
Similarity search - Function
Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat domain / Chitinase A; domain 3 / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain ...Tetratricopeptide repeat 2 / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / Tetratricopeptide repeat / Chitinase A; domain 3 - #40 / Tetratricopeptide repeat domain / Chitinase A; domain 3 / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold / Roll / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Heat shock protein HSP 90-beta / Peptidyl-prolyl cis-trans isomerase FKBP4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWu, B. / Li, P. / Lou, Z. / Liu, Y. / Ding, Y. / Shu, C. / 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
DepositionSep 15, 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: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
G: 5-mer peptide from Heat shock protein HSP 90
H: 5-mer peptide from Heat shock protein HSP 90


Theoretical massNumber of molelcules
Total (without water)116,4505
Polymers116,4505
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.613, 144.417, 170.815
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 protein / 52 kDa FK506 binding protein / FKBP59


Mass: 38402.145 Da / Num. of mol.: 3 / Fragment: FKBP52 C-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q02790, peptidylprolyl isomerase
#2: Protein/peptide 5-mer peptide from Heat shock protein HSP 90 / Hsp90


Mass: 621.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: this sequence is occurs naturally in human / References: UniProt: P08238
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 3.4 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium Citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorDetector: CCD / Date: Aug 26, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 66586 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.9→3 Å / % possible all: 98.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å
RfactorNum. reflection
Rfree0.287 1271
Rwork0.23 -
all0.235 28008
obs0.235 26054
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7004 0 0 221 7225
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.358

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