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- PDB-4hwi: Crystal structure of ATBAG1 in complex with HSP70 -

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Basic information

Entry
Database: PDB / ID: 4hwi
TitleCrystal structure of ATBAG1 in complex with HSP70
Components
  • BAG family molecular chaperone regulator 1
  • Heat shock cognate 71 kDa protein
KeywordsCHAPERONE/APOPTOSIS / BAG domain / ubiquitin-like domain / co-chaperone / complex with molecular chaperone / CHAPERONE-APOPTOSIS complex
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 / protein carrier chaperone / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Respiratory syncytial virus genome transcription / Lipophagy / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy ...lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / chaperone-mediated autophagy translocation complex disassembly / protein carrier chaperone / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Respiratory syncytial virus genome transcription / Lipophagy / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / cytoplasm protein quality control by the ubiquitin-proteasome system / clathrin coat disassembly / C3HC4-type RING finger domain binding / negative regulation of NLRP3 inflammasome complex assembly / CHL1 interactions / regulation of protein complex stability / ATP-dependent protein disaggregase activity / membrane organization / protein folding chaperone complex / Lysosome Vesicle Biogenesis / cellular response to steroid hormone stimulus / Golgi Associated Vesicle Biogenesis / chaperone-mediated autophagy / 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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mRNA Splicing - Major Pathway / lysosomal lumen / cellular response to starvation / AUF1 (hnRNP D0) binds and destabilizes mRNA / spliceosomal complex / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / Late endosomal microautophagy / regulation of protein stability / PKR-mediated signaling / mRNA splicing, via spliceosome / Chaperone Mediated Autophagy / MHC class II protein complex binding / unfolded protein binding / melanosome / protein folding / Clathrin-mediated endocytosis / protein-folding chaperone binding / protein refolding / protein-macromolecule adaptor activity / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / blood microparticle / ficolin-1-rich granule lumen / positive regulation of cell migration / cadherin binding / receptor ligand activity / ribonucleoprotein complex / lysosomal membrane / focal adhesion / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation / nucleolus / enzyme binding / ATP hydrolysis activity / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Ubiquitin-like (UB roll) / Nucleotidyltransferase; domain 5 / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Heat shock cognate 71 kDa protein / BAG family molecular chaperone regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.273 Å
AuthorsShen, Y. / Fang, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural insight into plant programmed cell death mediated by BAG proteins in Arabidopsis thaliana.
Authors: Fang, S. / Li, L. / Cui, B. / Men, S. / Shen, Y. / Yang, X.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)61,7772
Polymers61,7772
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.928, 87.360, 65.070
Angle α, β, γ (deg.)90.00, 109.18, 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: 41591.020 Da / Num. of mol.: 1 / Fragment: HSP70 ATPase domain (UNP residues 5-381)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSC70, HSP73, HSPA10, HSPA8 / Production host: Escherichia coli (E. coli) / References: UniProt: P11142
#2: Protein BAG family molecular chaperone regulator 1 / Bcl-2-associated athanogene 1


Mass: 20185.732 Da / Num. of mol.: 1 / Fragment: BAG domain (UNP residues 66-242)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g52060, BAG1, MSG15.15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WUQ1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 0.02 M citric acid / 0.08 M Bis-Tris propane, pH 8.8, 20% PEG3350, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97921
ReflectionResolution: 2.273→35.604 Å / Num. all: 30237 / Num. obs: 29495 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.273→2.34 Å / % possible all: 90.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(PHENIX.REFINE: 1.6.4_486)model building
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.6.4_486phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1HX1 AND 4HWC

1hx1

4hwc


Resolution: 2.273→35.604 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 1487 5.08 %
Rwork0.2026 --
obs0.2055 29291 96.95 %
all-29513 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.363 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.9987 Å2-0 Å2-3.0264 Å2
2---10.1306 Å20 Å2
3----0.8681 Å2
Refinement stepCycle: LAST / Resolution: 2.273→35.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4307 0 0 114 4421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074365
X-RAY DIFFRACTIONf_angle_d1.0085875
X-RAY DIFFRACTIONf_dihedral_angle_d14.8321656
X-RAY DIFFRACTIONf_chiral_restr0.065677
X-RAY DIFFRACTIONf_plane_restr0.005759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.273-2.34680.3007990.20742055X-RAY DIFFRACTION79
2.3468-2.43060.28731380.21782563X-RAY DIFFRACTION98
2.4306-2.52790.32311350.21632548X-RAY DIFFRACTION98
2.5279-2.64290.27771390.21062559X-RAY DIFFRACTION99
2.6429-2.78220.27371300.21782575X-RAY DIFFRACTION99
2.7822-2.95650.31221330.23122615X-RAY DIFFRACTION99
2.9565-3.18460.31381480.23762538X-RAY DIFFRACTION99
3.1846-3.50480.29031350.22992606X-RAY DIFFRACTION100
3.5048-4.01140.24651390.19762601X-RAY DIFFRACTION100
4.0114-5.05170.17851580.14712595X-RAY DIFFRACTION100
5.0517-35.6080.2251330.18982549X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -3.9841 Å / Origin y: 11.2972 Å / Origin z: -12.5329 Å
111213212223313233
T0.0613 Å2-0.0121 Å20.0117 Å2-0.045 Å20.0205 Å2--0.0346 Å2
L0.2685 °2-0.0739 °20.1816 °2-0.1791 °20.0225 °2--0.1589 °2
S0.0824 Å °0.0434 Å °-0.0354 Å °-0.0477 Å °-0.0629 Å °0.0212 Å °0.0341 Å °0.014 Å °-0.0179 Å °
Refinement TLS groupSelection details: all

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