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- PDB-6g3r: Structure of tellurium-centred Anderson-Evans polyoxotungstate (T... -

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Basic information

Entry
Database: PDB / ID: 6g3r
TitleStructure of tellurium-centred Anderson-Evans polyoxotungstate (TEW) bound to the nucleotide binding domain of HSP70. Structure one of two TEW-HSP70 structures deposited.
ComponentsHeat shock 70 kDa protein 1A
KeywordsCHAPERONE / ATPase domain
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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / 6-tungstotellurate(VI) / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMac Sweeney, A. / Chambovey, A. / Wicki, M. / Mueller, M. / Artico, N. / Lange, R. / Bijelic, A. / Breibeck, J. / Rompel, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP27534 Austria
CitationJournal: PLoS ONE / Year: 2018
Title: The crystallization additive hexatungstotellurate promotes the crystallization of the HSP70 nucleotide binding domain into two different crystal forms.
Authors: Mac Sweeney, A. / Chambovey, A. / Wicki, M. / Muller, M. / Artico, N. / Lange, R. / Bijelic, A. / Breibeck, J. / Rompel, A.
History
DepositionMar 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,0897
Polymers41,8821
Non-polymers2,2076
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-54 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.441, 64.691, 143.426
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


Mass: 41882.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSP72, HSPA1, HSX70 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DMV8

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Non-polymers , 6 types, 323 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O24TeW6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→48.03 Å / Num. obs: 151677 / % possible obs: 92.4 % / Redundancy: 5 % / Net I/σ(I): 10.14
Reflection shellResolution: 1.4→1.49 Å / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.31 / CC1/2: 0.78 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→48.03 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.203 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.056 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17998 3970 5 %RANDOM
Rwork0.13876 ---
obs0.14083 75412 92.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--0.37 Å2-0 Å2
3----1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.4→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 66 317 3309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0193145
X-RAY DIFFRACTIONr_bond_other_d0.0010.022896
X-RAY DIFFRACTIONr_angle_refined_deg2.3761.9214355
X-RAY DIFFRACTIONr_angle_other_deg1.70636707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7295405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.03124.028144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33115531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4661525
X-RAY DIFFRACTIONr_chiral_restr0.1660.2481
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023525
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02645
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0691.9171560
X-RAY DIFFRACTIONr_mcbond_other3.0451.9111559
X-RAY DIFFRACTIONr_mcangle_it3.5192.8911961
X-RAY DIFFRACTIONr_mcangle_other3.5582.8931962
X-RAY DIFFRACTIONr_scbond_it5.9322.411585
X-RAY DIFFRACTIONr_scbond_other5.8252.3831540
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.4113.4032252
X-RAY DIFFRACTIONr_long_range_B_refined5.49124.273510
X-RAY DIFFRACTIONr_long_range_B_other5.40823.8893458
X-RAY DIFFRACTIONr_rigid_bond_restr5.97536041
X-RAY DIFFRACTIONr_sphericity_free23.7095216
X-RAY DIFFRACTIONr_sphericity_bonded12.88756072
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 294 -
Rwork0.273 5575 -
obs--93.68 %

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