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- PDB-3cqx: Chaperone Complex -

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Basic information

Entry
Database: PDB / ID: 3cqx
TitleChaperone Complex
Components
  • BAG family molecular chaperone regulator 2
  • Heat shock cognate 71 kDa protein
KeywordsCHAPERONE / protein-protein complex / ATP-binding / Cytoplasm / Nucleotide-binding / Nucleus / Phosphoprotein / Stress response / Coiled coil
Function / homology
Function and homology information


protein-containing complex disassembly => GO:0032984 / : / GABA synthesis, release, reuptake and degradation / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / Protein methylation / AUF1 (hnRNP D0) binds and destabilizes mRNA / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding ...protein-containing complex disassembly => GO:0032984 / : / GABA synthesis, release, reuptake and degradation / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / Protein methylation / AUF1 (hnRNP D0) binds and destabilizes mRNA / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / mRNA Splicing - Major Pathway / positive regulation of lysosomal membrane permeability / lysosomal matrix / Attenuation phase / A1 adenosine receptor binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / : / Lysosome Vesicle Biogenesis / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / adenyl-nucleotide exchange factor activity / late endosomal microautophagy / positive regulation by host of viral genome replication / modulation by host of viral process / C3HC4-type RING finger domain binding / Golgi Associated Vesicle Biogenesis / clathrin coat disassembly / positive regulation of protein processing / regulation of protein complex stability / Clathrin-mediated endocytosis / photoreceptor ribbon synapse / maintenance of postsynaptic specialization structure / neuron spine / positive regulation of proteasomal protein catabolic process / misfolded protein binding / Prp19 complex / glycinergic synapse / protein metabolic process / presynaptic cytosol / axo-dendritic transport / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic cytosol / regulation of postsynapse organization / negative regulation of cardiac muscle cell apoptotic process / intermediate filament / chaperone-mediated autophagy / positive regulation of catalytic activity / phosphatidylserine binding / positive regulation of proteolysis / transcription factor binding / chaperone cofactor-dependent protein refolding / response to unfolded protein / asymmetric synapse / autophagosome / cellular response to unfolded protein / chaperone-mediated protein folding / ATP metabolic process / protein folding chaperone / vesicle-mediated transport / positive regulation of phagocytosis / negative regulation of protein ubiquitination / heat shock protein binding / Neutrophil degranulation / photoreceptor inner segment / RNA splicing / dendritic shaft / G protein-coupled receptor binding / peptide binding / spliceosomal complex / regulation of protein stability / tau protein binding / terminal bouton / mRNA processing / ADP binding / positive regulation of T cell mediated cytotoxicity / protein import into nucleus / unfolded protein binding / melanosome / synaptic vesicle / late endosome / protein folding / presynapse / myelin sheath / protein-macromolecule adaptor activity / protein-folding chaperone binding / protein refolding / postsynapse / perikaryon / microtubule / transmembrane transporter binding / protein autophosphorylation / dendritic spine / postsynaptic density / lysosome / protein stabilization / regulation of cell cycle / ribonucleoprotein complex
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #890 / BAG family molecular chaperone regulator 2 / 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. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #890 / BAG family molecular chaperone regulator 2 / 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 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THIOCYANATE ION / Heat shock cognate 71 kDa protein / BAG family molecular chaperone regulator 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsXu, Z. / Nix, J.C. / Misra, S.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis of nucleotide exchange and client binding by the Hsp70 cochaperone Bag2
Authors: Xu, Z. / Page, R.C. / Gomes, M.M. / Kohli, E. / Nix, J.C. / Herr, A.B. / Patterson, C. / Misra, S.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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

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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
C: BAG family molecular chaperone regulator 2
D: BAG family molecular chaperone regulator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,58313
Polymers104,2004
Non-polymers3829
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-97 kcal/mol
Surface area40410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.846, 105.808, 210.683
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 42398.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hspa8, Hsc70, Hsc73 / Plasmid: pHis-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta2(DE3) / References: UniProt: P63017
#2: Protein BAG family molecular chaperone regulator 2 / Bcl-2-associated athanogene 2 / BAG-2


Mass: 9701.124 Da / Num. of mol.: 2 / Fragment: BAG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bag2 / Plasmid: pHis-parallel / Production host: Escherichia coli (E. coli) / Strain (production host): Roseta2(DE3) / References: UniProt: Q91YN9
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Nov 8, 2007
Details: Rosenbaum-Rock monochromator 1:high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator 2:double crystal, Rosenbaum-rock vertical focusing mirror
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.3→43.13 Å / Num. all: 53515 / Num. obs: 53515 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 6.96 % / Biso Wilson estimate: 40.418 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Χ2: 0.92 / Net I/σ(I): 18.1 / Scaling rejects: 11520
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.11 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 8 / Num. measured all: 38704 / Num. unique all: 5236 / Rsym value: 0.179 / Χ2: 1.13 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HX1

1hx1


Resolution: 2.3→43.13 Å / FOM work R set: 0.827 / Isotropic thermal model: anisotorpic / Cross valid method: thoughtout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 2679 5 %random
Rwork0.222 ---
all-53545 --
obs-52903 98.8 %-
Solvent computationBsol: 21.638 Å2
Displacement parametersBiso mean: 34.074 Å2
Baniso -1Baniso -2Baniso -3
1--1.588 Å20 Å20 Å2
2--2.542 Å20 Å2
3----0.954 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→43.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7126 0 19 240 7385
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.153
X-RAY DIFFRACTIONc_mcbond_it1.3831.5
X-RAY DIFFRACTIONc_scbond_it2.5052
X-RAY DIFFRACTIONc_mcangle_it2.1662
X-RAY DIFFRACTIONc_scangle_it3.742.5
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection
Rfree0.339 271
Rwork0.267 -
obs-5124
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5SCN.paraSCN.top

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