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- PDB-4wv7: HEAT SHOCK PROTEIN 70 SUBSTRATE BINDING DOMAIN WITH COVALENTLY LI... -

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Basic information

Entry
Database: PDB / ID: 4wv7
TitleHEAT SHOCK PROTEIN 70 SUBSTRATE BINDING DOMAIN WITH COVALENTLY LINKED NOVOLACTONE
ComponentsHeat shock 70 kDa protein 1A/1B
Keywordschaperone/chaperone inhibitor / Allosteric Inhibitor / chaperone-chaperone inhibitor complex
Function / homology
Function and homology information


: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / death receptor agonist activity / 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 / : / C3HC4-type RING finger domain binding ...: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / death receptor agonist activity / 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 / : / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / protein folding chaperone / vesicle-mediated transport / inclusion body / 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 / positive regulation of interleukin-8 production / G protein-coupled receptor binding / 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 / positive regulation of NF-kappaB transcription factor activity / cellular response to heat / cellular response to oxidative stress / protein refolding / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / blood microparticle / protein stabilization / nuclear speck / ribonucleoprotein complex / cadherin binding / negative regulation of cell population proliferation / focal adhesion / signaling receptor binding / 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 / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 ...Substrate Binding Domain Of DNAk; Chain A, domain 1 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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, nucleotide binding domain / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-3UM / Heat shock 70 kDa protein 1B / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsKirby, C.A. / Baird, J. / Stams, T.
CitationJournal: Chem.Biol. / Year: 2015
Title: The novolactone natural product disrupts the allosteric regulation of hsp70.
Authors: Hassan, A.Q. / Kirby, C.A. / Zhou, W. / Schuhmann, T. / Kityk, R. / Kipp, D.R. / Baird, J. / Chen, J. / Chen, Y. / Chung, F. / Hoepfner, D. / Movva, N.R. / Pagliarini, R. / Petersen, F. / ...Authors: Hassan, A.Q. / Kirby, C.A. / Zhou, W. / Schuhmann, T. / Kityk, R. / Kipp, D.R. / Baird, J. / Chen, J. / Chen, Y. / Chung, F. / Hoepfner, D. / Movva, N.R. / Pagliarini, R. / Petersen, F. / Quinn, C. / Quinn, D. / Riedl, R. / Schmitt, E.K. / Schitter, A. / Stams, T. / Studer, C. / Fortin, P.D. / Mayer, M.P. / Sadlish, H.
History
DepositionNov 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock 70 kDa protein 1A/1B
B: Heat shock 70 kDa protein 1A/1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6364
Polymers32,9672
Non-polymers6692
Water1,38777
1
A: Heat shock 70 kDa protein 1A/1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8182
Polymers16,4841
Non-polymers3341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock 70 kDa protein 1A/1B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8182
Polymers16,4841
Non-polymers3341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.536, 87.779, 52.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Heat shock 70 kDa protein 1A/1B / Heat shock 70 kDa protein 1/2 / HSP70.1/HSP70.2


Mass: 16483.518 Da / Num. of mol.: 2 / Fragment: unp residues 395-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSPA1, HSX70, HSPA1B / Production host: Escherichia coli (E. coli) / References: UniProt: P08107, UniProt: P0DMV8*PLUS
#2: Chemical ChemComp-3UM / (5beta,6alpha,8alpha,14alpha)-13-ethenyl-5,6-dihydroxy-14-methylpodocarp-12-en-15-oic acid


Mass: 334.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 10 mg/ml covalently modified protein in 25 mM Tris-HCl, 50 mM NaCl, 1 mM TCEP was mixed 1:1 with reservior solution containing 0.1 M HEPES, pH 7.0, 70% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→87.78 Å / Num. obs: 12438 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 40.31 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.3
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YUW

1yuw


Resolution: 2.42→53.53 Å / Cor.coef. Fo:Fc: 0.8506 / Cor.coef. Fo:Fc free: 0.7962 / SU R Cruickshank DPI: 0.401 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.434 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.281
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 599 4.83 %RANDOM
Rwork0.2004 ---
obs0.2039 12404 99.89 %-
Displacement parametersBiso mean: 38.91 Å2
Baniso -1Baniso -2Baniso -3
1-13.4353 Å20 Å20 Å2
2---31.3582 Å20 Å2
3---17.9229 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: LAST / Resolution: 2.42→53.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 48 77 2271
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012220HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.263019HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d787SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes302HARMONIC5
X-RAY DIFFRACTIONt_it2220HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion19.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion323SEMIHARMONIC5
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_contact2542SEMIHARMONIC4
LS refinement shellResolution: 2.42→2.65 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2685 125 4.32 %
Rwork0.2121 2771 -
all0.2147 2896 -
obs--99.89 %

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