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- PDB-6zyj: Crystal structure of Hsc70 ATPase domain in complex with ADP and ... -

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Basic information

Entry
Database: PDB / ID: 6zyj
TitleCrystal structure of Hsc70 ATPase domain in complex with ADP and calcium
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE / Hsc70 / NBD / ATPase domain / ADP
Function / homology
Function and homology information


lumenal side of lysosomal membrane / regulation of protein import / protein transmembrane import into intracellular organelle / positive regulation of lysosomal membrane permeability / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity ...lumenal side of lysosomal membrane / regulation of protein import / protein transmembrane import into intracellular organelle / positive regulation of lysosomal membrane permeability / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / lysosomal matrix / A1 adenosine receptor binding / late endosomal microautophagy / protein carrier chaperone / response to nickel cation / Respiratory syncytial virus genome transcription / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Lipophagy / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / response to odorant / C3HC4-type RING finger domain binding / synaptic vesicle uncoating / positive regulation by host of viral genome replication / clathrin coat disassembly / CHL1 interactions / ATP-dependent protein disaggregase activity / negative regulation of NLRP3 inflammasome complex assembly / regulation of protein complex stability / photoreceptor ribbon synapse / maintenance of postsynaptic specialization structure / membrane organization / glycinergic synapse / Prp19 complex / presynaptic cytosol / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic specialization membrane / intermediate filament / regulation of postsynapse organization / Lysosome Vesicle Biogenesis / negative regulation of cardiac muscle cell apoptotic process / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / postsynaptic cytosol / Golgi Associated Vesicle Biogenesis / non-chaperonin molecular chaperone ATPase / phosphatidylserine binding / positive regulation of proteolysis / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / regulation of protein-containing complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / estrous cycle / Protein methylation / ATP metabolic process / positive regulation of phagocytosis / forebrain development / skeletal muscle tissue development / heat shock protein binding / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to cadmium ion / photoreceptor inner segment / autophagosome / lysosomal lumen / cellular response to starvation / mRNA Splicing - Major Pathway / cerebellum development / dendritic shaft / kidney development / response to activity / response to progesterone / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / spliceosomal complex / peptide binding / ADP binding / Late endosomal microautophagy / regulation of protein stability / PKR-mediated signaling / terminal bouton / mRNA splicing, via spliceosome / cellular response to hydrogen peroxide / Chaperone Mediated Autophagy / positive regulation of T cell mediated cytotoxicity / protein import into nucleus / G1/S transition of mitotic cell cycle / unfolded protein binding / melanosome / late endosome / protein folding / synaptic vesicle / MHC class II protein complex binding / response to estradiol / Clathrin-mediated endocytosis / protein-folding chaperone binding
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 70 family / Hsp70 protein / Heat shock protein 70kD, C-terminal domain superfamily / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock cognate 71 kDa protein
B: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,01011
Polymers83,7852
Non-polymers1,2259
Water7,044391
1
A: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4595
Polymers41,8921
Non-polymers5664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5516
Polymers41,8921
Non-polymers6585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.677, 78.039, 75.377
Angle α, β, γ (deg.)90.000, 101.260, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Heat shock cognate 71 kDa protein / Heat shock 70 kDa protein 8 / Lipopolysaccharide-associated protein 1 / LPS-associated protein 1


Mass: 41892.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA8, HSC70, HSP73, HSPA10 / Production host: Escherichia coli (E. coli) / References: UniProt: P11142

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Non-polymers , 5 types, 400 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 24% PEG3350, 0.2M Ca acetate

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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: 1.85→73.94 Å / Num. obs: 71566 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.9
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 1.005 / Num. unique obs: 4400 / CC1/2: 0.633

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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: 1.85→73.71 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.291 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 3597 5 %RANDOM
Rwork0.2177 ---
obs0.2192 67947 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.82 Å2 / Biso mean: 22.919 Å2 / Biso min: 10.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å2-1.96 Å2
2---0.65 Å2-0 Å2
3---1.82 Å2
Refinement stepCycle: final / Resolution: 1.85→73.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5876 0 72 391 6339
Biso mean--20.42 27.04 -
Num. residues----760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0136105
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175707
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.6478267
X-RAY DIFFRACTIONr_angle_other_deg1.1171.58413220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6315774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60422.331326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.002151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7121545
X-RAY DIFFRACTIONr_chiral_restr0.0390.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021279
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 250 -
Rwork0.302 5018 -
all-5268 -
obs--99.96 %

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