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- PDB-1hx1: CRYSTAL STRUCTURE OF A BAG DOMAIN IN COMPLEX WITH THE HSC70 ATPAS... -

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Basic information

Entry
Database: PDB / ID: 1hx1
TitleCRYSTAL STRUCTURE OF A BAG DOMAIN IN COMPLEX WITH THE HSC70 ATPASE DOMAIN
Components
  • BAG family molecular chaperone regulator 1
  • Heat shock 70 kDa protein 8
KeywordsCHAPERONE/CHAPERONE INHIBITOR / PROTEIN-PROTEIN COMPLEX / APOPTOSIS / PROTEIN FOLDING / MOLECULAR CHAPERONE / NUCLEOTIDE EXCHANGE FACTOR / CHAPERONE-CHAPERONE INHIBITOR COMPLEX
Function / homology
Function and homology information


synaptic vesicle uncoating / adenyl-nucleotide exchange factor activity / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / misfolded protein binding ...synaptic vesicle uncoating / adenyl-nucleotide exchange factor activity / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / presynaptic cytosol / Prp19 complex / misfolded protein binding / postsynaptic cytosol / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / autophagosome / Regulation of HSF1-mediated heat shock response / cellular response to unfolded protein / heat shock protein binding / protein folding chaperone / RNA splicing / vesicle-mediated transport / spliceosomal complex / terminal bouton / mRNA processing / melanosome / unfolded protein binding / ribonucleoprotein complex / protein refolding / chaperone binding / protein stabilization / lysosome / cell surface receptor signaling pathway / dendrite / apoptotic process / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / negative regulation of apoptotic process / ATP hydrolysis activity / membrane / nucleoplasm / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Molecular chaperone regulator BAG-1 / BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domains, present in regulator of Hsp70 proteins / BAG domain profile. / BAG domain / Defensin A-like - #30 / Heat shock hsp70 proteins family signature 1. ...Molecular chaperone regulator BAG-1 / BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domains, present in regulator of Hsp70 proteins / BAG domain profile. / BAG domain / Defensin A-like - #30 / Heat shock hsp70 proteins family signature 1. / Heat shock hsp70 proteins family signature 2. / Heat shock hsp70 proteins family signature 3. / Heat shock protein 70, conserved site / Heat shock protein 70kD, peptide-binding domain superfamily / Defensin A-like / 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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Nucleotidyltransferase; domain 5 / Ubiquitin-like domain superfamily / 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 speciesBos taurus (cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSondermann, H. / Scheufler, C. / Moarefi, I.
CitationJournal: Science / Year: 2001
Title: Structure of a Bag/Hsc70 complex: convergent functional evolution of Hsp70 nucleotide exchange factors.
Authors: Sondermann, H. / Scheufler, C. / Schneider, C. / Hohfeld, J. / Hartl, F.U. / Moarefi, I.
History
DepositionJan 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2012Group: Database references / Structure summary
Revision 1.4Dec 18, 2019Group: Data collection / Database references / Category: diffrn_source / struct_ref_seq_dif
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type / _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 70 kDa protein 8
B: BAG family molecular chaperone regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7883
Polymers57,6662
Non-polymers1221
Water6,467359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.570, 40.780, 129.260
Angle α, β, γ (deg.)90.00, 114.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Heat shock 70 kDa protein 8 / HSC70 / Heat shock cognate 71 kDa protein


Mass: 44509.086 Da / Num. of mol.: 1 / Fragment: ATPASE DOMAIN
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
#2: Protein BAG family molecular chaperone regulator 1 / BAG-1 / Bcl-2-associated athanogene 1


Mass: 13157.168 Da / Num. of mol.: 1 / Fragment: BAG DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG1, HAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q99933
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG3350, Tris, Na-K-tartrate, glycerol, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
210 mMHEPES1drop
350-100 mMsodium potassium tartrate1reservoir
412-16 %PEG33501reservoir
50.1 MTris1reservoir
625 %(w/v)glycerol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONMPG/DESY, HAMBURG BW610.9786, 0.9792, 0.9500
SYNCHROTRONESRF ID14-420.9287
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJun 21, 2000
ADSC QUANTUM 42CCDOct 24, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DiamondMADMx-ray1
2DiamondSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.97921
30.951
40.92871
ReflectionResolution: 1.9→15 Å / Num. all: 43748 / Num. obs: 43748 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 21
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.27
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.27

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
DMmodel building
CNS1refinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→14.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1785682.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH and HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.279 3149 7.2 %RANDOM
Rwork0.234 ---
all-43748 --
obs-43748 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.29 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.21 Å20 Å23.63 Å2
2--0.06 Å20 Å2
3----12.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 8 359 4143
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 509 7.1 %
Rwork0.351 6708 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3TRIS.PARTRIS.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.2 % / Rfactor obs: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.399 / % reflection Rfree: 7.1 % / Rfactor Rwork: 0.351

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