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- PDB-3a8y: Crystal structure of the complex between the BAG5 BD5 and Hsp70 NBD -

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Basic information

Entry
Database: PDB / ID: 3a8y
TitleCrystal structure of the complex between the BAG5 BD5 and Hsp70 NBD
Components
  • BAG family molecular chaperone regulator 5
  • Heat shock 70 kDa protein 1
KeywordsHYDROLASE / BAG domain / Hsp70 / ATPase domain / PROTEIN COMPLEX / TRIPLE HELIX / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


regulation of inclusion body assembly / : / junctional membrane complex / negative regulation of protein refolding / regulation of ubiquitin-protein transferase activity / : / : / denatured protein binding / adenyl-nucleotide exchange factor activity / cellular heat acclimation ...regulation of inclusion body assembly / : / junctional membrane complex / negative regulation of protein refolding / regulation of ubiquitin-protein transferase activity / : / : / denatured protein binding / adenyl-nucleotide exchange factor activity / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / death receptor agonist activity / C3HC4-type RING finger domain binding / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / regulation of mitotic spindle assembly / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / Golgi organization / mRNA catabolic process / : / ubiquitin ligase inhibitor activity / regulation of protein ubiquitination / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Mitochondrial unfolded protein response (UPRmt) / Attenuation phase / chaperone-mediated protein complex assembly / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / transcription regulator inhibitor activity / vesicle-mediated transport / heat shock protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / inclusion body / negative regulation of protein ubiquitination / protein folding chaperone / centriole / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of erythrocyte differentiation / positive regulation of RNA splicing / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / negative regulation of cell growth / G protein-coupled receptor binding / PKR-mediated signaling / histone deacetylase binding / disordered domain specific binding / transcription corepressor activity / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / negative regulation of neuron projection development / protein-folding chaperone binding / cellular response to heat / virus receptor activity / protein refolding / cellular response to oxidative stress / blood microparticle / vesicle / ficolin-1-rich granule lumen / protein stabilization / nuclear speck / cadherin binding / receptor ligand activity / ribonucleoprotein complex / signaling receptor binding / negative regulation of cell population proliferation / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / centrosome / positive regulation of gene expression / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm
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 / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Heat shock 70 kDa protein 1B / Heat shock 70 kDa protein 1A / BAG family molecular chaperone regulator 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsArakawa, A. / Handa, N. / Ohsawa, N. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2010
Title: The C-terminal BAG domain of BAG5 induces conformational changes of the Hsp70 nucleotide-binding domain for ADP-ATP exchange
Authors: Arakawa, A. / Handa, N. / Ohsawa, N. / Shida, M. / Kigawa, T. / Hayashi, F. / Shirouzu, M. / Yokoyama, S.
History
DepositionOct 13, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Oct 16, 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 70 kDa protein 1
B: Heat shock 70 kDa protein 1
C: BAG family molecular chaperone regulator 5
D: BAG family molecular chaperone regulator 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,8866
Polymers118,6424
Non-polymers2442
Water9,404522
1
A: Heat shock 70 kDa protein 1
C: BAG family molecular chaperone regulator 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4433
Polymers59,3212
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock 70 kDa protein 1
D: BAG family molecular chaperone regulator 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4433
Polymers59,3212
Non-polymers1221
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-12 kcal/mol
Surface area11350 Å2
Unit cell
Length a, b, c (Å)64.108, 84.266, 96.632
Angle α, β, γ (deg.)90.00, 100.73, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a heterodimer of BD5 (BAG domain 5) and NBD (nucleotide-binding domain), which was confirmed by gel filtration chromatography.

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Components

#1: Protein Heat shock 70 kDa protein 1 / HSP70.1 / HSP70-1/HSP70-2


Mass: 43150.766 Da / Num. of mol.: 2 / Fragment: Nucleotide-binding domain, UNP residues 1-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Hsp70 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P08107, UniProt: P0DMV8*PLUS
#2: Protein BAG family molecular chaperone regulator 5 / BAG-5 / Bcl-2-associated athanogene 5


Mass: 16170.274 Da / Num. of mol.: 2 / Fragment: BAG domain 5, UNP residues 341-447
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG5 / Plasmid: pCR2.1 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q9UL15
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCL, 0.25M Trimethylamine n-oxide, 20% PEG MME 2000, 3% Hexanediol , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 118991 / Num. obs: 42589 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 2.79 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.047 / Net I/σ(I): 21.2
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.181 / % possible all: 85.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HX1

1hx1


Resolution: 2.3→19.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1676279.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2134 5 %RANDOM
Rwork0.218 ---
obs0.218 42522 94.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.5285 Å2 / ksol: 0.303158 e/Å3
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.36 Å20 Å210.37 Å2
2---3.88 Å20 Å2
3----4.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7519 0 16 522 8057
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 332 5.2 %
Rwork0.288 6078 -
obs--86.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2trs.paramtrs.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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