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- PDB-6h54: CRYSTAL STRUCTURE OF BOVINE HSC70(AA1-554)E213A/D214A IN COMPLEX ... -

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Basic information

Entry
Database: PDB / ID: 6h54
TitleCRYSTAL STRUCTURE OF BOVINE HSC70(AA1-554)E213A/D214A IN COMPLEX WITH INHIBITOR VER155008
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE / Hsc70 / Vernalis inhibitor
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 / chaperone-mediated autophagy translocation complex disassembly ...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 / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Prp19 complex / presynaptic cytosol / Neutrophil degranulation / postsynaptic cytosol / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / autophagosome / protein folding chaperone / heat shock protein binding / RNA splicing / spliceosomal complex / ATP-dependent protein folding chaperone / terminal bouton / mRNA processing / melanosome / protein-macromolecule adaptor activity / protein refolding / lysosome / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / dendrite / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 ...Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-3FD / trimethylamine oxide / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPlank, C. / Zehe, M. / Grimm, C. / Sotriffer, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRU 216 Germany
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
DepositionJul 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rrim_I_all
Revision 2.0Jul 8, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / audit_author / cell / chem_comp / citation / citation_author / computing / diffrn / entity / entity_src_gen / pdbx_audit_support / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_mon_prot_cis / struct_site / struct_site_gen / symmetry
Item: _cell.angle_beta / _cell.volume ..._cell.angle_beta / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.title / _diffrn.pdbx_serial_crystal_experiment / _entity_src_gen.gene_src_common_name / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_method_to_determine_struct / _refine.pdbx_overall_phase_error / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _struct_mon_prot_cis.pdbx_omega_angle / _symmetry.space_group_name_Hall
Description: Ligand geometry / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Feb 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)61,9415
Polymers60,9791
Non-polymers9624
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint5 kcal/mol
Surface area24470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.190, 49.340, 86.960
Angle α, β, γ (deg.)90.000, 99.801, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: HSPA8, HSC70 / Production host: Escherichia coli (E. coli) / References: UniProt: P19120

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Non-polymers , 5 types, 233 molecules

#2: Chemical ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9NO
#3: Chemical ChemComp-3FD / 4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile


Mass: 556.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23Cl2N7O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 229 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 291 K / Method: batch mode / Details: PEG 4000, TMAO, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.02→56.765 Å / Num. obs: 34413 / % possible obs: 94.1 % / Redundancy: 3.09 % / Biso Wilson estimate: 36.24 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.093 / Net I/σ(I): 9.49
Reflection shellResolution: 2.02→2.07 Å / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fl9

4fl9


Resolution: 2.02→56.765 Å / SU ML: 0.3347 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.0432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 1715 4.99 %
Rwork0.2205 32671 -
obs0.2224 34386 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.69 Å2
Refinement stepCycle: LAST / Resolution: 2.02→56.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4225 0 0 229 4454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00174287
X-RAY DIFFRACTIONf_angle_d0.4795792
X-RAY DIFFRACTIONf_chiral_restr0.0431663
X-RAY DIFFRACTIONf_plane_restr0.0028749
X-RAY DIFFRACTIONf_dihedral_angle_d12.24362627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.080.42651470.37362729X-RAY DIFFRACTION95.48
2.08-2.150.4111470.35842715X-RAY DIFFRACTION95.21
2.15-2.230.32831670.32442629X-RAY DIFFRACTION91.34
2.23-2.310.39971520.30392632X-RAY DIFFRACTION92.95
2.31-2.420.35571300.28062775X-RAY DIFFRACTION95.62
2.42-2.550.33131430.27262738X-RAY DIFFRACTION95.52
2.55-2.710.29831330.24432674X-RAY DIFFRACTION92.24
2.71-2.920.32881210.23982746X-RAY DIFFRACTION94.28
2.92-3.210.25981440.22892780X-RAY DIFFRACTION96.09
3.21-3.670.23921440.20442667X-RAY DIFFRACTION92.28
3.67-4.630.19431310.16762831X-RAY DIFFRACTION96.29
4.63-56.7650.19641560.17392755X-RAY DIFFRACTION91.95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3188118359-0.412094774408-0.230685897220.307356943604-0.4859500095410.9509725627430.125817603431-0.31047048640.171810690454-0.7871012763510.0898597319402-0.06900233035830.6795535742230.02520623239290.1769651321580.560761387741-0.0425888493951-0.06384483957510.2021251207070.07852956274420.240879395181-12.4972235729-20.9925047193-7.54392468828
20.527060145924-0.1731014033360.309877294431-0.0890524862704-0.1849955837590.7356180630460.02015035540890.02517156899140.00922105389055-0.100964397403-0.01167186503680.0311528400110.06376676960070.020567045361.83187618106E-50.257865945313-0.07951206112470.00406351844940.2029701489640.01766566661490.259149161645-10.2332907675-9.82836088772-19.3141674497
30.318698375051-0.2704063701710.0178056391850.191779554443-0.08039244478460.2221522646580.09891540700130.128952360695-0.02422876037060.0210288364626-0.158103057469-0.0330917844227-0.1352499465940.257252789649-8.8879078333E-60.272708594195-0.01491625683080.01190765014520.326866973650.02979738723140.289425746098-46.6205697031-4.59196379234-38.5637794097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 408 )
3X-RAY DIFFRACTION3chain 'A' and (resid 409 through 553 )

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