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- PDB-7o6r: Crystal structure of bovine Hsc70(aa1-554)E213A/D214A in complex ... -

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Basic information

Entry
Database: PDB / ID: 7o6r
TitleCrystal structure of bovine Hsc70(aa1-554)E213A/D214A in complex with 1H-Indazole
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy ...Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Neutrophil degranulation / non-chaperonin molecular chaperone ATPase / : / Prp19 complex / heat shock protein binding / protein folding chaperone / RNA splicing / spliceosomal complex / ATP-dependent protein folding chaperone / mRNA processing / melanosome / presynapse / protein refolding / protein-macromolecule adaptor activity / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein ...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 70kD, C-terminal domain superfamily / Heat shock protein 70 family / Hsp70 protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Alpha-Beta Complex / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / 1H-indazole / trimethylamine oxide / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZehe, M. / Grimm, C. / Sotriffer, C.
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Combined In-Solution Fragment Screening and Crystallographic Binding-Mode Analysis with a Two-Domain Hsp70 Construct.
Authors: Zehe, M. / Kehrein, J. / Schollmayer, C. / Plank, C. / Kovacs, H. / Merino Asumendi, E. / Holzgrabe, U. / Grimm, C. / Sotriffer, C.
History
DepositionApr 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6598
Polymers60,9791
Non-polymers6807
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint6 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.589, 50.466, 86.958
Angle α, β, γ (deg.)90.000, 99.879, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Heat shock cognate 71 kDa protein / Heat shock 70 kDa protein 8


Mass: 60978.867 Da / Num. of mol.: 1 / Mutation: E213A, D214A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: HSPA8, HSC70 / Production host: Escherichia coli (E. coli) / References: UniProt: P19120

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Non-polymers , 7 types, 193 molecules

#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-LZ1 / 1H-indazole


Mass: 118.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*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: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-TMO / trimethylamine oxide


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: PEG 8000, TMAO, potassium chloride, HEPES-NaOH, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→24.92 Å / Num. obs: 37394 / % possible obs: 97.9 % / Redundancy: 3 % / Biso Wilson estimate: 34.25 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.086 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2775 / CC1/2: 0.574

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Processing

Software
NameVersionClassification
MxCuBEdata collection
Cootmodel building
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FL9

4fl9


Resolution: 2→24.92 Å / SU ML: 0.2988 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8276 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2445 1868 5 %
Rwork0.1862 35468 -
obs0.189 37336 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.62 Å2
Refinement stepCycle: LAST / Resolution: 2→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4139 0 41 186 4366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714248
X-RAY DIFFRACTIONf_angle_d0.80925734
X-RAY DIFFRACTIONf_chiral_restr0.0567654
X-RAY DIFFRACTIONf_plane_restr0.0049746
X-RAY DIFFRACTIONf_dihedral_angle_d21.37071598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.33851540.29572719X-RAY DIFFRACTION98.76
2.05-2.110.33461600.2712766X-RAY DIFFRACTION99.19
2.11-2.180.33441560.25982742X-RAY DIFFRACTION99.01
2.18-2.260.33161380.252714X-RAY DIFFRACTION99.2
2.26-2.350.37781260.28882611X-RAY DIFFRACTION93.48
2.35-2.460.31351450.2372716X-RAY DIFFRACTION98.08
2.46-2.590.2921450.22482635X-RAY DIFFRACTION94.98
2.59-2.750.25811540.22762X-RAY DIFFRACTION99.42
2.75-2.960.21621350.19162784X-RAY DIFFRACTION98.98
2.96-3.260.26561540.18962658X-RAY DIFFRACTION96.17
3.26-3.730.21161350.16432767X-RAY DIFFRACTION98.44
3.73-4.690.20481170.13972757X-RAY DIFFRACTION96.57
4.69-24.920.18691490.15062837X-RAY DIFFRACTION97.93

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