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- PDB-1xqs: Crystal structure of the HspBP1 core domain complexed with the fr... -

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Basic information

Entry
Database: PDB / ID: 1xqs
TitleCrystal structure of the HspBP1 core domain complexed with the fragment of Hsp70 ATPase domain
Components
  • HSPBP1 protein
  • Heat shock 70 kDa protein 1
KeywordsCHAPERONE / armadillo repeat / superhelical twist
Function / homology
Function and homology information


: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / adenyl-nucleotide exchange factor activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / : / death receptor agonist activity ...: / positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / adenyl-nucleotide exchange factor activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / : / death receptor agonist activity / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation / molecular sequestering activity / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / enzyme inhibitor activity / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein complex assembly / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / inclusion body / protein folding chaperone / vesicle-mediated transport / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / positive regulation of protein ubiquitination / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / positive regulation of interleukin-8 production / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding / virus receptor activity / cellular response to oxidative stress / cellular response to heat / positive regulation of NF-kappaB transcription factor activity / protein refolding / blood microparticle / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / protein stabilization / nuclear speck / cadherin binding / ribonucleoprotein complex / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Nucleotide exchange factor Fes1 / Nucleotide exchange factor Fes1 / 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 ...Nucleotide exchange factor Fes1 / Nucleotide exchange factor Fes1 / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Armadillo-like helical / Alpha Horseshoe / Nucleotidyltransferase; domain 5 / Armadillo-type fold / Alpha-Beta Complex / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Heat shock 70 kDa protein 1B / Heat shock 70 kDa protein 1A / Hsp70-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShomura, Y. / Dragovic, Z. / Chang, H.C. / Tzvetkov, N. / Young, J.C. / Brodsky, J.L. / Guerriero, V. / Hartl, F.U. / Bracher, A.
CitationJournal: Mol.Cell / Year: 2005
Title: Regulation of Hsp70 Function by HspBP1; Structural Analysis Reveals an Alternate Mechanism for Hsp70 Nucleotide Exchange
Authors: Shomura, Y. / Dragovic, Z. / Chang, H.C. / Tzvetkov, N. / Young, J.C. / Brodsky, J.L. / Guerriero, V. / Hartl, F.U. / Bracher, A.
History
DepositionOct 13, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HSPBP1 protein
B: HSPBP1 protein
C: Heat shock 70 kDa protein 1
D: Heat shock 70 kDa protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,1816
Polymers105,4874
Non-polymers6942
Water88349
1
A: HSPBP1 protein
C: Heat shock 70 kDa protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0903
Polymers52,7432
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HSPBP1 protein
D: Heat shock 70 kDa protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0903
Polymers52,7432
Non-polymers3471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.484, 94.809, 155.704
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HSPBP1 protein


Mass: 31302.049 Da / Num. of mol.: 2 / Fragment: core domain (84-359) / Mutation: E88G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPROExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus RIL / References: UniProt: Q9NZL4
#2: Protein Heat shock 70 kDa protein 1 / Hsp70 / HSP70.1 / HSP70-1/HSP70-2


Mass: 21441.225 Da / Num. of mol.: 2 / Fragment: LOBE II OF ATPASE DOMAIN (184-371)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPROExHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon plus RIL / References: UniProt: P08107, UniProt: P0DMV8*PLUS
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.57 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, Potassium chloride, Magnesium chloride, AMP-PNP, DTT, HEPES KOH, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2004
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.9→46.6 Å / Num. all: 24763 / Num. obs: 24763 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 90.8 Å2 / Rsym value: 0.075 / Net I/σ(I): 6.5
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 3574 / Rsym value: 0.456 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
BEASTmodel building
AMoREphasing
MOLREPphasing
CNS1refinement
CCP4(SCALA)data scaling
BEASTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.6 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.296 1258 RANDOM
Rwork0.237 --
all-24763 -
obs-24730 -
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.169 Å20 Å20 Å2
2--4.768 Å20 Å2
3---1.599 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 0 46 49 6795
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 2.9→2.94 Å /
RfactorNum. reflection
Rfree0.367 51
Rwork0.457 -
obs-942

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