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- PDB-5ar0: HSP72 with adenosine-derived inhibitor -

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Basic information

Entry
Database: PDB / ID: 5ar0
TitleHSP72 with adenosine-derived inhibitor
ComponentsHEAT SHOCK 70 KDA PROTEIN 1A
KeywordsCHAPERONE / HEAT SHOCK PROTEIN / HSP70 / HSP72 / ATPASE / ADENOSINE / INHIBITOR
Function / homology
Function and homology information


positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / death receptor agonist activity / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation ...positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / death receptor agonist activity / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation / misfolded protein binding / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein complex assembly / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / inclusion body / ATP metabolic process / protein folding chaperone / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / positive regulation of interleukin-8 production / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / virus receptor activity / cellular response to heat / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / protein refolding / blood microparticle / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / protein stabilization / nuclear speck / cadherin binding / ribonucleoprotein complex / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily ...Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GB8 / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCheeseman, M.D. / Westwood, I.M. / Barbeau, O. / Rowlands, M.G. / Jones, A.M. / Jeganathan, F. / Burke, R. / Dobson, S.E. / Workman, P. / Collins, I. ...Cheeseman, M.D. / Westwood, I.M. / Barbeau, O. / Rowlands, M.G. / Jones, A.M. / Jeganathan, F. / Burke, R. / Dobson, S.E. / Workman, P. / Collins, I. / van Montfort, R.L.M. / Jones, K.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Exploiting Protein Conformational Change to Optimize Adenosine-Derived Inhibitors of Hsp70.
Authors: Cheeseman, M.D. / Westwood, I.M. / Barbeau, O. / Rowlands, M.G. / Dobson, S. / Jones, A.M. / Jeganathan, F. / Burke, R. / Kadi, N. / Workman, P. / Collins, I. / Van Montfort, R.L.M. / Jones, K.
History
DepositionSep 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEAT SHOCK 70 KDA PROTEIN 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0878
Polymers43,1961
Non-polymers8917
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.880, 80.545, 92.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HEAT SHOCK 70 KDA PROTEIN 1A / HEAT SHOCK 70 KDA PROTEIN 1 / HSP70-1 / HSP70.1


Mass: 43195.902 Da / Num. of mol.: 1 / Fragment: NUCLEOTIDE BINDING DOMAIN, UNP RESIDUES 1-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: P0DMV8, EC: 3.6.3.51

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Non-polymers , 5 types, 210 molecules

#2: Chemical ChemComp-GB8 / (2R,3R,4S,5R)-2-(6-amino-8-((quinolin-7-ylmethyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol


Mass: 423.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N7O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES 382 ONWARDS ARE A CLONING ARTEFACT DERIVED FROM THE EXPRESSION VECTOR PGEX-6P-1

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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: 2.08 Å3/Da / Density % sol: 40.73 % / Description: NONE
Crystal growpH: 7.5
Details: 17-28% (W/V) PEG3350, 0.1 M HEPES PH 7.5, 2 MM MGCL2, 2 MM NAH2PO4 AND 5 MM INHIBITOR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.9→46.49 Å / Num. obs: 25878 / % possible obs: 89.3 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 21.09 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 1.7 / % possible all: 51.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S3X

1s3x


Resolution: 1.9→46.49 Å / Cor.coef. Fo:Fc: 0.9391 / Cor.coef. Fo:Fc free: 0.9255 / SU R Cruickshank DPI: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.173 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 1274 4.93 %RANDOM
Rwork0.1725 ---
obs0.1744 25833 88.89 %-
Displacement parametersBiso mean: 26.22 Å2
Baniso -1Baniso -2Baniso -3
1-4.973 Å20 Å20 Å2
2---4.15 Å20 Å2
3----0.823 Å2
Refine analyzeLuzzati coordinate error obs: 0.215 Å
Refinement stepCycle: LAST / Resolution: 1.9→46.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 58 203 3123
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012964HARMONIC2
X-RAY DIFFRACTIONt_angle_deg14018HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1011SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes75HARMONIC2
X-RAY DIFFRACTIONt_gen_planes463HARMONIC5
X-RAY DIFFRACTIONt_it2964HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.19
X-RAY DIFFRACTIONt_other_torsion15.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion404SEMIHARMONIC5
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_contact3681SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2365 99 5.89 %
Rwork0.1983 1582 -
all0.2006 1681 -
obs--52.07 %
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)
12.00820.4743-0.04272.78180.06120.4832-0.0148-0.14270.25910.2726-0.01390.2838-0.0813-0.09860.0287-0.01740.01260.0216-0.0265-0.037-0.01389.2428.27846.5662
22.2321-0.5910.2152.37040.37950.5846-0.00880.09450.1424-0.0641-0.0258-0.0526-0.07250.11550.0347-0.045-0.01670.0147-0.01140.0035-0.049226.21364.3399-2.2371
31.17460.27180.04260.9642-0.01070.41170.029-0.08270.03860.1077-0.00570.02130.055-0.0036-0.0233-0.0202-0.0080.0193-0.0182-0.0049-0.05769.1127-4.60544.4549
42.82480.20910.59990-0.89271.2626-0.14330.07210.26180.08560.11180.05060.06370.16670.0314-0.0043-0.092-0.01740.0681-0.007-0.026913.567314.3886-22.6279
55.82591.484-0.18771.7962-0.69123.1317-0.1418-0.22920.54420.13040.07160.021-0.37170.28610.0702-0.0109-0.0643-0.0489-0.1062-0.04840.018613.849619.6843-16.7529
61.07850.7337-0.43372.4503-0.82571.0482-0.11620.19660.077-0.18580.1260.13940.04580.0014-0.0097-0.05-0.0297-0.01670.02610.0088-0.09281.5738-1.3967-15.9726
72.32110.48220.55060.59590.17582.36110.01540.1080.2673-0.0960.03480.19040.0368-0.1611-0.0501-0.0656-0.00020.0113-0.01740.003-0.006-3.2551-2.3147-3.1911

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