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- PDB-5njx: Human FKBP51 protein in complex with C-terminal peptide of Human ... -

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Basic information

Entry
Database: PDB / ID: 5njx
TitleHuman FKBP51 protein in complex with C-terminal peptide of Human HSP 90-alpha
Components
  • HSP90AA1 protein
  • Peptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / HSP90 / FKBP51 / TPR / C-terminal peptide of HSP90
Function / homology
Function and homology information


Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / telomerase holoenzyme complex assembly / regulation of protein ubiquitination / chaperone-mediated protein complex assembly / telomere maintenance via telomerase / MECP2 regulates neuronal receptors and channels / : / DNA polymerase binding ...Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / telomerase holoenzyme complex assembly / regulation of protein ubiquitination / chaperone-mediated protein complex assembly / telomere maintenance via telomerase / MECP2 regulates neuronal receptors and channels / : / DNA polymerase binding / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / peptidylprolyl isomerase / response to bacterium / peptidyl-prolyl cis-trans isomerase activity / ATP-dependent protein folding chaperone / histone deacetylase binding / disordered domain specific binding / unfolded protein binding / protein folding / secretory granule lumen / protein-macromolecule adaptor activity / ficolin-1-rich granule lumen / ATP hydrolysis activity / extracellular exosome / nucleoplasm / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / Tetratricopeptide repeat / Tetratricopeptide repeat / HSP90, C-terminal domain / Heat shock protein Hsp90 family / Hsp90 protein / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. ...: / Tetratricopeptide repeat / Tetratricopeptide repeat / HSP90, C-terminal domain / Heat shock protein Hsp90 family / Hsp90 protein / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP5 / HSP90AA1 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsKumar, R. / Moche, M. / Winblad, B. / Pavlov, P.
Funding support Sweden, 6items
OrganizationGrant numberCountry
Swedish Research Council2015-02774 Sweden
Stiftelsen For Gamla Tjanarinnor2016-00302 Sweden
Gun och Bertil Stohnes stiftelse4-2919/2016 Sweden
Gunvor och Josef Aners stiftelseFB16-0111 Sweden
Tore Nilsons stiftelse for medicinsk forskning2016-00304 Sweden
Foundation for Geriatric Diseases at Karolinska Institutet2016alde51194 Sweden
CitationJournal: Sci Rep / Year: 2017
Title: Combined x-ray crystallography and computational modeling approach to investigate the Hsp90 C-terminal peptide binding to FKBP51.
Authors: Kumar, R. / Moche, M. / Winblad, B. / Pavlov, P.F.
History
DepositionMar 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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
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 FKBP5
B: HSP90AA1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0165
Polymers53,7282
Non-polymers2883
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-32 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.160, 92.160, 132.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated ...PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase


Mass: 51701.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The full length human FKBP51 containing first 5 N-terminus amino acids from the expression vector.
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Protein/peptide HSP90AA1 protein


Mass: 2026.089 Da / Num. of mol.: 1 / Fragment: UNP residues 413-422 / Source method: obtained synthetically
Details: The peptide contains 10 amino acids from C- terminal of human HSP 90-alpha
Source: (synth.) Homo sapiens (human) / References: UniProt: Q96HX7
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 175 / 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: 3.01 Å3/Da / Density % sol: 59.17 %
Preparation: The completeness of our data is low to 2.49A resolution being 62% overall and 2.5% in the highest resolution shell since we kept only the strongest reflections in each direction. This is ...Preparation: The completeness of our data is low to 2.49A resolution being 62% overall and 2.5% in the highest resolution shell since we kept only the strongest reflections in each direction. This is the purpose of the diffraction anisotropy server (https://services.mbi.ucla.edu/anisoscale/) and also staraniso (http://staraniso.globalphasing.org/cgi-bin/staraniso.cgi). We used the diffraction anisotropy server to keep the good reflections only for structure refinement
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 18 %w/v PEG MME 5K, 0.2 M NH4SO4, 0.1 M MES pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.49→44 Å / Num. obs: 280852 / % possible obs: 62.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.36 % / Biso Wilson estimate: 57.38 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 19.3
Reflection shellResolution: 2.49→2.55 Å / Redundancy: 17 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 3.84 / Num. measured obs: 733 / Num. unique all: 43 / Num. unique obs: 43 / CC1/2: 0.959 / Rsym value: 0.756 / % possible all: 2.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSMay 1, 2016 BUILT=20160617data reduction
XSCALEMay 1, 2016 BUILT=20160617data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KT0

1kt0


Resolution: 2.49→44 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.838 / SU R Cruickshank DPI: 1.839 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.377 / SU Rfree Cruickshank DPI: 0.373
RfactorNum. reflection% reflectionSelection details
Rfree0.26 729 5.03 %RANDOM
Rwork0.195 ---
obs0.198 14504 62.3 %-
Displacement parametersBiso mean: 61.32 Å2
Baniso -1Baniso -2Baniso -3
1-5.5586 Å20 Å20 Å2
2--5.5586 Å20 Å2
3----11.1171 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.49→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 15 175 3525
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083423HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084583HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1653SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes100HARMONIC2
X-RAY DIFFRACTIONt_gen_planes487HARMONIC5
X-RAY DIFFRACTIONt_it3423HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion3.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion421SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3872SEMIHARMONIC4
LS refinement shellResolution: 2.49→2.69 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.4835 -6.55 %
Rwork0.2601 328 -
all0.2727 351 -
obs--7.44 %
Refinement TLS params.Method: refined / Origin x: -34.3543 Å / Origin y: 38.7724 Å / Origin z: -10.9071 Å
111213212223313233
T0.1098 Å2-0.0026 Å2-0.0466 Å2-0.0746 Å2-0.013 Å2---0.2396 Å2
L1.0861 °20.0318 °2-0.6038 °2-1.165 °2-0.242 °2--2.1007 °2
S0.0368 Å °0.0545 Å °0.1194 Å °0.2576 Å °-0.0831 Å °0.0058 Å °-0.4062 Å °-0.2477 Å °0.0463 Å °
Refinement TLS groupSelection details: { A|* }

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