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- PDB-5mgx: The structure of FKBP38 in complex with the MEEVD tetratricopepti... -

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Basic information

Entry
Database: PDB / ID: 5mgx
TitleThe structure of FKBP38 in complex with the MEEVD tetratricopeptide binding-motif of Hsp90
Components
  • Peptidyl-prolyl cis-trans isomerase FKBP8
  • yeast HSP90 C-terminus
KeywordsISOMERASE / Hsp90 / PPIase / teratricopeptide / immunophilin
Function / homology
Function and homology information


The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / neuron fate specification / regulation of mitophagy / HSF1 activation ...The NLRP3 inflammasome / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / neuron fate specification / regulation of mitophagy / HSF1 activation / dorsal/ventral neural tube patterning / response to oxygen levels / protein localization to mitochondrion / positive regulation of BMP signaling pathway / mitochondrial envelope / camera-type eye development / box C/D snoRNP assembly / regulation of telomere maintenance / response to osmotic stress / protein targeting to mitochondrion / 'de novo' protein folding / smoothened signaling pathway / negative regulation of protein phosphorylation / BMP signaling pathway / proteasome assembly / positive regulation of telomere maintenance via telomerase / endomembrane system / Neutrophil degranulation / protein folding chaperone / protein maturation / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / ATP-dependent protein folding chaperone / mitochondrial membrane / multicellular organism growth / disordered domain specific binding / unfolded protein binding / protein folding / cellular response to heat / regulation of gene expression / protein refolding / calmodulin binding / Ub-specific processing proteases / intracellular signal transduction / protein stabilization / apoptotic process / endoplasmic reticulum membrane / negative regulation of apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Tetratricopeptide repeat / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / FKBP-type peptidyl-prolyl cis-trans isomerase ...: / Tetratricopeptide repeat / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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 / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ATP-dependent molecular chaperone HSP82 / Peptidyl-prolyl cis-trans isomerase FKBP8
Similarity search - Component
Biological speciesHomo sapiens (human)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsRoe, S.M. / Blundell, K.L. / Prodromou, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: PLoS ONE / Year: 2017
Title: The structure of FKBP38 in complex with the MEEVD tetratricopeptide binding-motif of Hsp90.
Authors: Blundell, K.L. / Pal, M. / Roe, S.M. / Pearl, L.H. / Prodromou, C.
History
DepositionNov 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 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

Downloads & links

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Assembly

Deposited unit
A: yeast HSP90 C-terminus
B: yeast HSP90 C-terminus
C: yeast HSP90 C-terminus
D: yeast HSP90 C-terminus
E: Peptidyl-prolyl cis-trans isomerase FKBP8
F: Peptidyl-prolyl cis-trans isomerase FKBP8
G: Peptidyl-prolyl cis-trans isomerase FKBP8
H: Peptidyl-prolyl cis-trans isomerase FKBP8


Theoretical massNumber of molelcules
Total (without water)131,0878
Polymers131,0878
Non-polymers00
Water19,0601058
1
A: yeast HSP90 C-terminus
F: Peptidyl-prolyl cis-trans isomerase FKBP8


Theoretical massNumber of molelcules
Total (without water)32,7722
Polymers32,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: yeast HSP90 C-terminus
F: Peptidyl-prolyl cis-trans isomerase FKBP8


Theoretical massNumber of molelcules
Total (without water)32,7722
Polymers32,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-3 kcal/mol
Surface area13720 Å2
MethodPISA
3
B: yeast HSP90 C-terminus
G: Peptidyl-prolyl cis-trans isomerase FKBP8


Theoretical massNumber of molelcules
Total (without water)32,7722
Polymers32,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: yeast HSP90 C-terminus
G: Peptidyl-prolyl cis-trans isomerase FKBP8


Theoretical massNumber of molelcules
Total (without water)32,7722
Polymers32,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-2 kcal/mol
Surface area13860 Å2
MethodPISA
5
C: yeast HSP90 C-terminus
E: Peptidyl-prolyl cis-trans isomerase FKBP8


Theoretical massNumber of molelcules
Total (without water)32,7722
Polymers32,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
C: yeast HSP90 C-terminus
E: Peptidyl-prolyl cis-trans isomerase FKBP8


Theoretical massNumber of molelcules
Total (without water)32,7722
Polymers32,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-2 kcal/mol
Surface area13950 Å2
MethodPISA
7
D: yeast HSP90 C-terminus
H: Peptidyl-prolyl cis-trans isomerase FKBP8


Theoretical massNumber of molelcules
Total (without water)32,7722
Polymers32,7722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.290, 105.640, 100.190
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
yeast HSP90 C-terminus


Mass: 966.963 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02829*PLUS
#2: Protein
Peptidyl-prolyl cis-trans isomerase FKBP8 / PPIase FKBP8 / 38 kDa FK506-binding protein / hFKBP38 / FK506-binding protein 8 / FKBP-8 / FKBPR38 / Rotamase


Mass: 31804.686 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP8, FKBP38 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q14318, peptidylprolyl isomerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1058 / 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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 0.02 M sodium potassium phosphate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.18→100 Å / Num. obs: 76276 / % possible obs: 95.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.1 Å2 / CC1/2: 0.947 / Rmerge(I) obs: 0.111 / Net I/σ(I): 5
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.733 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AWG and 2FBN

2awg

2fbn


Resolution: 2.18→100 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.814 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.284 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.308 3524 4.62 %RANDOM
Rwork0.246 ---
obs0.249 76276 94.7 %-
Displacement parametersBiso mean: 33.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.0112 Å20 Å2-0.9115 Å2
2--13.536 Å20 Å2
3----11.5249 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.18→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8162 0 0 1058 9220
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098293HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1511260HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3904SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes212HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1193HARMONIC5
X-RAY DIFFRACTIONt_it8293HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion2.93
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1116SEMIHARMONIC5
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_contact9945SEMIHARMONIC4
LS refinement shellResolution: 2.18→2.24 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 275 4.99 %
Rwork0.33 5234 -
all0.331 5509 -
obs--92.87 %

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