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- PDB-3m3z: Crystal structure of HSC70/BAG1 in complex with small molecule in... -

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Basic information

Entry
Database: PDB / ID: 3m3z
TitleCrystal structure of HSC70/BAG1 in complex with small molecule inhibitor
Components
  • BAG family molecular chaperone regulator 1
  • Heat shock cognate 71 kDa protein
KeywordsPROTEIN BINDING / GRP78 / HSP70 / HSC70 / CHAPERONE / HEAT SHOCK / PROTEIN FOLDING / ATP-BINDING / ADENOSINE / NUCLEOSIDE / NUCLEOTIDE-BINDING / STRESS RESPONSE / ENDOPLASMATIC RETICULUM / SMALL MOLECULE INHIBITOR / SELECTIVITY / HOST-VIRUS INTERACTION / PHOSPHOPROTEIN / ALTERNATIVE INITIATION / APOPTOSIS / NUCLEUS
Function / homology
Function and homology information


lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / chaperone-mediated autophagy translocation complex disassembly / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Lipophagy / Respiratory syncytial virus genome transcription / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / protein carrier chaperone ...lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / chaperone-mediated autophagy translocation complex disassembly / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Lipophagy / Respiratory syncytial virus genome transcription / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / protein carrier chaperone / adenyl-nucleotide exchange factor activity / positive regulation of smooth muscle cell apoptotic process / clathrin coat disassembly / C3HC4-type RING finger domain binding / CHL1 interactions / regulation of protein complex stability / negative regulation of NLRP3 inflammasome complex assembly / ATP-dependent protein disaggregase activity / membrane organization / protein folding chaperone complex / Lysosome Vesicle Biogenesis / cellular response to steroid hormone stimulus / chaperone-mediated autophagy / Golgi Associated Vesicle Biogenesis / non-chaperonin molecular chaperone ATPase / : / Prp19 complex / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / response to unfolded protein / regulation of protein-containing complex assembly / Attenuation phase / ATP metabolic process / Protein methylation / heat shock protein binding / protein folding chaperone / mRNA Splicing - Major Pathway / lysosomal lumen / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to starvation / AUF1 (hnRNP D0) binds and destabilizes mRNA / spliceosomal complex / ATP-dependent protein folding chaperone / Late endosomal microautophagy / G protein-coupled receptor binding / mRNA splicing, via spliceosome / PKR-mediated signaling / regulation of protein stability / Chaperone Mediated Autophagy / MHC class II protein complex binding / unfolded protein binding / melanosome / protein folding / Clathrin-mediated endocytosis / protein-folding chaperone binding / protein refolding / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / protein-macromolecule adaptor activity / blood microparticle / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / protein stabilization / positive regulation of cell migration / cadherin binding / receptor ligand activity / ribonucleoprotein complex / lysosomal membrane / focal adhesion / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / negative regulation of apoptotic process / nucleolus / enzyme binding / ATP hydrolysis activity / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
BAG domain / Molecular chaperone regulator BAG / BAG domain superfamily / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. ...BAG domain / Molecular chaperone regulator BAG / BAG domain superfamily / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Defensin A-like - #30 / 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 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3F5 / Heat shock cognate 71 kDa protein / BAG family molecular chaperone regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDokurno, P. / Surgenor, A.E. / Shaw, T. / Macias, A.T. / Massey, A.J. / Williamson, D.S.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Adenosine-Derived Inhibitors of 78 kDa Glucose Regulated Protein (Grp78) ATPase: Insights into Isoform Selectivity.
Authors: Macias, A.T. / Williamson, D.S. / Allen, N. / Borgognoni, J. / Clay, A. / Daniels, Z. / Dokurno, P. / Drysdale, M.J. / Francis, G.L. / Graham, C.J. / Howes, R. / Matassova, N. / Murray, J.B. ...Authors: Macias, A.T. / Williamson, D.S. / Allen, N. / Borgognoni, J. / Clay, A. / Daniels, Z. / Dokurno, P. / Drysdale, M.J. / Francis, G.L. / Graham, C.J. / Howes, R. / Matassova, N. / Murray, J.B. / Parsons, R. / Shaw, T. / Surgenor, A.E. / Terry, L. / Wang, Y. / Wood, M. / Massey, A.J.
History
DepositionMar 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock cognate 71 kDa protein
B: BAG family molecular chaperone regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5973
Polymers55,2442
Non-polymers3531
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint1 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.776, 120.969, 53.537
Angle α, β, γ (deg.)90.00, 106.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42086.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA8, HSC70, HSP73, HSPA10 / Plasmid: PET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11142
#2: Protein BAG family molecular chaperone regulator 1 / BAG-1 / Bcl-2-associated athanogene 1


Mass: 13157.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG1, HAP / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q99933
#3: Chemical ChemComp-3F5 / 5'-O-(2-amino-2-oxoethyl)-8-(methylamino)adenosine


Mass: 353.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG3350, 0.1M TRIS BUFFER, 25MM SODIUM-POTASSIUM TARTRATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 20, 2007 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 29699 / Num. obs: 29699 / % possible obs: 88.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 4.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 1.4 / Num. unique all: 2084 / % possible all: 83.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HX1

1hx1


Resolution: 2.1→25 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.535 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.276 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29305 2003 7.8 %RANDOM
Rwork0.19801 ---
obs0.20547 23702 88.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.815 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.61 Å2
2---0.47 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3811 0 25 349 4185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223893
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.9615252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4245486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.03724.917181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.91515717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5591526
X-RAY DIFFRACTIONr_chiral_restr0.1270.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022896
X-RAY DIFFRACTIONr_nbd_refined0.2350.22001
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22626
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2333
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.224
X-RAY DIFFRACTIONr_mcbond_it0.941.52506
X-RAY DIFFRACTIONr_mcangle_it1.53223906
X-RAY DIFFRACTIONr_scbond_it2.50131564
X-RAY DIFFRACTIONr_scangle_it3.6374.51346
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 140 -
Rwork0.278 1673 -
obs--84.96 %

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