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- PDB-6zyi: Crystal structure of HSP70 ATPase domain in complex with ADP and ... -

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Basic information

Entry
Database: PDB / ID: 6zyi
TitleCrystal structure of HSP70 ATPase domain in complex with ADP and calcium
ComponentsHeat shock 70kDa protein 1A variant
KeywordsCHAPERONE / HSP70 / NBD / ATPase domain / ADP
Function / homology
Function and homology information


: / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / death receptor agonist activity / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity ...: / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / death receptor agonist activity / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / 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 / : / regulation of protein ubiquitination / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Mitochondrial unfolded protein response (UPRmt) / Attenuation phase / chaperone-mediated protein complex assembly / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / transcription regulator inhibitor activity / heat shock protein binding / inclusion body / protein folding chaperone / negative regulation of protein ubiquitination / centriole / 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 / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / : / negative regulation of cell growth / G protein-coupled receptor binding / PKR-mediated signaling / histone deacetylase binding / disordered domain specific binding / transcription corepressor activity / 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 / blood microparticle / vesicle / 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 / ubiquitin protein ligase binding / Neutrophil degranulation / centrosome / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 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: 1.52 Å
AuthorsYan, Y. / Preissler, S. / Ron, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWellcome 200848/Z/16/Z United Kingdom
CitationJournal: Elife / Year: 2020
Title: Calcium depletion challenges endoplasmic reticulum proteostasis by destabilising BiP-substrate complexes.
Authors: Preissler, S. / Rato, C. / Yan, Y. / Perera, L.A. / Czako, A. / Ron, D.
History
DepositionAug 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,1894
Polymers41,6821
Non-polymers5073
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-30 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.168, 63.711, 144.499
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 41682.133 Da / Num. of mol.: 1
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.4 / Details: 10% PEG8000, 0.1M Tris Ph8.4, 0.2M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.52→29.53 Å / Num. obs: 66932 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 14
Reflection shellResolution: 1.52→1.54 Å / Rmerge(I) obs: 0.703 / Num. unique obs: 3125 / CC1/2: 0.814

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3iuc

3iuc


Resolution: 1.52→29.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.418 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 3300 5 %RANDOM
Rwork0.1957 ---
obs0.1965 63212 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.08 Å2 / Biso mean: 18.596 Å2 / Biso min: 10.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.48 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: final / Resolution: 1.52→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 29 430 3359
Biso mean--13.19 30.72 -
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133042
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172849
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.6454131
X-RAY DIFFRACTIONr_angle_other_deg1.1241.5836603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7865389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.63822.298161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51315525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4681522
X-RAY DIFFRACTIONr_chiral_restr0.0390.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023453
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02640
LS refinement shellResolution: 1.52→1.559 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 261 -
Rwork0.253 4574 -
all-4835 -
obs--99.96 %

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