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- PDB-4io8: Crystal structure of human HSP70 complexed with 4-{(2R,3S,4R)-5-[... -

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Basic information

Entry
Database: PDB / ID: 4io8
TitleCrystal structure of human HSP70 complexed with 4-{(2R,3S,4R)-5-[(R)-6-Amino-8-(3,4-dichloro-benzylamino)-purin-9-yl]-3,4-dihydroxy-tetrahydro-furan-2-ylmethoxymethyl}-benzonitrile
ComponentsHeat shock 70kDa protein 1A variant
KeywordsCHAPERONE / Hsp70 / ATPase / molecular chaperone
Function / homology
Function and homology information


: / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / death receptor agonist activity / Viral RNP Complexes in the Host Cell Nucleus / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation ...: / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / death receptor agonist activity / Viral RNP Complexes in the Host Cell Nucleus / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation / misfolded protein binding / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / regulation of mitotic spindle assembly / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / : / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of protein ubiquitination / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / response to unfolded protein / cellular response to unfolded protein / Mitochondrial unfolded protein response (UPRmt) / Attenuation phase / chaperone-mediated protein complex assembly / transcription regulator inhibitor activity / ATP metabolic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / inclusion body / heat shock protein binding / negative regulation of protein ubiquitination / centriole / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / negative regulation of transforming growth factor beta receptor signaling pathway / ATP-dependent protein folding chaperone / G protein-coupled receptor binding / negative regulation of cell growth / PKR-mediated signaling / histone deacetylase binding / positive regulation of NF-kappaB transcription factor activity / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cellular response to heat / virus receptor activity / protein refolding / cellular response to oxidative stress / vesicle / blood microparticle / ficolin-1-rich granule lumen / protein stabilization / nuclear speck / cadherin binding / receptor ligand activity / ribonucleoprotein complex / signaling receptor binding / negative regulation of cell population proliferation / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / 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-3FD / Heat shock 70 kDa protein 1A / Heat shock 70kDa protein 1A variant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsMusil, D. / Scholz, S.
CitationJournal: Plos One / Year: 2013
Title: Functional analysis of hsp70 inhibitors.
Authors: Schlecht, R. / Scholz, S.R. / Dahmen, H. / Wegener, A. / Sirrenberg, C. / Musil, D. / Bomke, J. / Eggenweiler, H.M. / Mayer, M.P. / Bukau, B.
History
DepositionJan 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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 70kDa protein 1A variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6272
Polymers42,0711
Non-polymers5561
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.680, 53.973, 70.796
Angle α, β, γ (deg.)90.00, 101.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heat shock 70kDa protein 1A variant


Mass: 42070.637 Da / Num. of mol.: 1
Fragment: HSP70 N-TERMINAL ATP-ASE DOMAIN (UNP Residues 69-450)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59EJ3, UniProt: P0DMV8*PLUS
#2: Chemical ChemComp-3FD / 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile


Mass: 556.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23Cl2N7O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1 M Tris HCl, 22% PEG 10000, 0.1 M NaCl, 20% Glycerol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→42.62 Å / Num. all: 13840 / Num. obs: 12776 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 45.77 Å2 / Rmerge(I) obs: 0.011 / Net I/σ(I): 10.1

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Processing

Software
NameVersionClassification
MOLREPphasing
BUSTER2.11.4refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S3X

1s3x


Resolution: 2.58→42.62 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.8907 / SU R Cruickshank DPI: 1.285 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 639 5.01 %RANDOM
Rwork0.1694 ---
obs0.1721 12766 91.94 %-
all-13840 --
Displacement parametersBiso mean: 34.05 Å2 /
Baniso -2Baniso -3
1-0 Å2-
2--0 Å2
Refine analyzeLuzzati coordinate error obs: 0.292 Å
Refinement stepCycle: LAST / Resolution: 2.58→42.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 38 121 3085
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013029HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.094098HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1073SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes83HARMONIC2
X-RAY DIFFRACTIONt_gen_planes441HARMONIC5
X-RAY DIFFRACTIONt_it3029HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion18.57
X-RAY DIFFRACTIONt_chiral_improper_torsion405SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3319SEMIHARMONIC4
LS refinement shellResolution: 2.58→2.83 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2459 139 5 %
Rwork0.1779 2639 -
all0.1815 2778 -
obs--91.94 %
Refinement TLS params.Method: refined / Origin x: 9.2859 Å / Origin y: -0.2458 Å / Origin z: 16.0547 Å
111213212223313233
T-0.0581 Å20.0192 Å2-0.0422 Å2--0.0639 Å2-0.0107 Å2---0.095 Å2
L1.1915 °2-0.0713 °20.0264 °2-0.5863 °20.1621 °2--0.6897 °2
S-0.0325 Å °-0.0984 Å °0.0415 Å °0.1159 Å °0.0315 Å °-0.0967 Å °-0.0122 Å °0.022 Å °0.001 Å °
Refinement TLS groupSelection details: { A|* }

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