[English] 日本語
Yorodumi
- PDB-6h54: CRYSTAL STRUCTURE OF BOVINE HSC70(AA1-554)E213A/D214A IN COMPLEX ... -

+
Open data


ID or keywords:

Loading...

-
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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / synaptic vesicle uncoating ...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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / synaptic vesicle uncoating / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Prp19 complex / Neutrophil degranulation / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / heat shock protein binding / protein folding chaperone / RNA splicing / ATP-dependent protein folding chaperone / spliceosomal complex / mRNA processing / melanosome / presynapse / protein-macromolecule adaptor activity / protein refolding / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 5 types, 233 molecules

#2: Chemical ChemComp-TMO / trimethylamine 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


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


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.: 229 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 291 K / Method: batch mode / Details: PEG 4000, TMAO, Glycerol

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more