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

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Basic information

Entry
Database: PDB / ID: 5aqz
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 / G protein-coupled receptor binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / 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
SANGIVAMYCIN / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)43,7536
Polymers43,1961
Non-polymers5585
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.938, 89.504, 96.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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
#2: Chemical ChemComp-SGV / SANGIVAMYCIN / 4-amino-7-beta-D-ribofuranosyl-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide / Sangivamycin


Mass: 309.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N5O5 / Comment: inhibitor*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
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: 2.41 Å3/Da / Density % sol: 48.89 % / 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: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.65→48.46 Å / Num. obs: 50487 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 25.86 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.1
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 0.5 / % possible all: 97.1

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Processing

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

1s3x


Resolution: 1.65→48.46 Å / Cor.coef. Fo:Fc: 0.9538 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.097
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 2460 4.9 %RANDOM
Rwork0.1862 ---
obs0.1878 50223 98.55 %-
Displacement parametersBiso mean: 33.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.5303 Å20 Å20 Å2
2---6.4509 Å20 Å2
3---4.9206 Å2
Refine analyzeLuzzati coordinate error obs: 0.256 Å
Refinement stepCycle: LAST / Resolution: 1.65→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 38 432 3452
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013109HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014207HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1094SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes472HARMONIC5
X-RAY DIFFRACTIONt_it3109HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion15.52
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion419SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3835SEMIHARMONIC4
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1972 179 4.99 %
Rwork0.2129 3408 -
all0.2121 3587 -
obs--96.66 %
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)
11.65760.3841-0.14010.4518-0.04431.0379-0.03010.0224-0.16160.04390.0303-0.01720.10410.0562-0.0002-0.10740.0138-0.0155-0.0166-0.0245-0.01735.3403-11.59813.6699
22.4825-0.22950.28085.3338-0.41151.25680.09150.4360.1683-0.3737-0.13560.125-0.0235-0.09810.0441-0.10590.0324-0.03640.083-0.02150.0053-10.5049-4.8441-1.7807
31.29690.4399-0.25350.17690.3690.6935-0.00430.0066-0.09340.0542-0.01440.18850.045-0.03250.0186-0.08120.0019-0.0143-0.004-0.0180.00924.0845-8.052810.2163
42.89131.2439-0.57951.0694-0.071.13270.0765-0.08350.13760.0105-0.0780.1478-0.07190.03070.0015-0.05240.0049-0.0169-0.0058-0.02510.01357.62961.837710.398
50.5561-0.5761-0.42952.34652.21596.4028-0.03210.00080.2384-0.13230.0505-0.1986-0.5150.1141-0.0184-0.0568-0.0415-0.0055-0.030.0068-0.030118.62438.3903-1.1842
61.81851.74060.4391.2739-0.2730.01310.0315-0.1331-0.0379-0.0007-0.0934-0.04870.2268-0.06160.06190.025-0.0564-0.00570.08290.0243-0.07516.7317-14.1498-25.8041
72.85472.00090.44963.00951.04541.3134-0.0172-0.1008-0.24930.21260.0288-0.18370.399-0.0567-0.01170.0024-0.0453-0.02020.01730.0243-0.10697.496-20.8148-21.1445
80.66720.14920.06811.172.75544.81830.05860.12580.0339-0.11750.1557-0.1665-0.31930.2615-0.2143-0.0763-0.025-0.01510.01560.0142-0.082817.7231.3331-15.9003
91.62370.441-0.58940.409-0.75957.15970.06790.0367-0.004-0.0204-0.0093-0.04650.03850.5442-0.0586-0.14690.0128-0.01170.0476-0.0176-0.054323.18510.64341.0174

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