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- PDB-2v7z: Crystal structure of the 70-kDa heat shock cognate protein from R... -

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Basic information

Entry
Database: PDB / ID: 2v7z
TitleCrystal structure of the 70-kDa heat shock cognate protein from Rattus norvegicus in post-ATP hydrolysis state
ComponentsHEAT SHOCK COGNATE 71 KDA PROTEIN
KeywordsCHAPERONE / DOMAIN REARRANGEMENT / HSP70 / HSC70 / ATPASE / NUCLEUS / CYTOPLASM / NUCLEOTIDE-BINDING / HEAT SHOCK PROTEIN / ATP-BINDING / PHOSPHORYLATION / STRESS RESPONSE
Function / homology
Function and homology information


protein-containing complex disassembly => GO:0032984 / : / : / Attenuation phase / PKR-mediated signaling / Protein methylation / mRNA Splicing - Major Pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / HSF1-dependent transactivation / : ...protein-containing complex disassembly => GO:0032984 / : / : / Attenuation phase / PKR-mediated signaling / Protein methylation / mRNA Splicing - Major Pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / HSF1-dependent transactivation / : / protein transmembrane import into intracellular organelle / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of lysosomal membrane permeability / lysosomal matrix / A1 adenosine receptor binding / late endosomal microautophagy / Lysosome Vesicle Biogenesis / response to nickel cation / protein-containing complex disassembly / GABA synthesis, release, reuptake and degradation / : / Golgi Associated Vesicle Biogenesis / Regulation of HSF1-mediated heat shock response / protein targeting to lysosome involved in chaperone-mediated autophagy / response to odorant / response to xenobiotic stimulus => GO:0009410 / positive regulation by host of viral genome replication / synaptic vesicle uncoating / modulation by host of viral process / C3HC4-type RING finger domain binding / clathrin coat disassembly / negative regulation of NLRP3 inflammasome complex assembly / ATP-dependent protein disaggregase activity / regulation of protein complex stability / Clathrin-mediated endocytosis / photoreceptor ribbon synapse / maintenance of postsynaptic specialization structure / misfolded protein binding / neuron spine / glycinergic synapse / Prp19 complex / presynaptic cytosol / axo-dendritic transport / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic specialization membrane / intermediate filament / Neutrophil degranulation / regulation of postsynapse organization / negative regulation of cardiac muscle cell apoptotic process / chaperone-mediated autophagy / postsynaptic cytosol / positive regulation of catalytic activity / response to starvation / phosphatidylserine binding / non-chaperonin molecular chaperone ATPase / transcription factor binding / positive regulation of proteolysis / chaperone cofactor-dependent protein refolding / response to unfolded protein / estrous cycle / autophagosome / asymmetric synapse / cellular response to unfolded protein / ATP metabolic process / positive regulation of phagocytosis / chaperone-mediated protein folding / skeletal muscle tissue development / forebrain development / vesicle-mediated transport / protein folding chaperone / heat shock protein binding / cellular response to cadmium ion / photoreceptor inner segment / lysosomal lumen / cerebellum development / RNA splicing / response to activity / dendritic shaft / kidney development / response to progesterone / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / spliceosomal complex / peptide binding / regulation of protein stability / terminal bouton / ADP binding / cellular response to hydrogen peroxide / mRNA processing / positive regulation of T cell mediated cytotoxicity / G1/S transition of mitotic cell cycle / protein import into nucleus / unfolded protein binding
Similarity search - Function
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 ...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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Heat shock cognate 71 kDa protein / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsChang, Y.-W. / Sun, Y.-J. / Wang, C. / Hsiao, C.-D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structures of the 70-kDa Heat Shock Proteins in Domain Disjoining Conformation.
Authors: Chang, Y.-W. / Sun, Y.-J. / Wang, C. / Hsiao, C.-D.
History
DepositionAug 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8356
Polymers119,7912
Non-polymers1,0444
Water1,69394
1
A: HEAT SHOCK COGNATE 71 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4183
Polymers59,8961
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HEAT SHOCK COGNATE 71 KDA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4183
Polymers59,8961
Non-polymers5222
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)179.851, 94.792, 78.234
Angle α, β, γ (deg.)90.00, 93.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HEAT SHOCK COGNATE 71 KDA PROTEIN / HEAT SHOCK 70 KDA PROTEIN 8


Mass: 59895.559 Da / Num. of mol.: 2
Fragment: NUCLEOTIDE-BINDING DOMAIN AND SUBSTRATE-BINDING DOMAIN (RESIDUES 1-543)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4FZY7, UniProt: P63018*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 9.5
Details: 100 MM CHES, PH 9.5, 23% (W/V) PEG2000, 2% (W/V) PEG8000, 10 MM THREONINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1.0229
DetectorType: ADSC CCD / Detector: CCD
Details: VERTICALLY COLLIMATING PREMIRROR, LN2-COOLED FIXED-EXIT DOUBLE CRYSTAL SI(111) MONOCHROMATOR , TOROIDAL FOCUSING MIRROR
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0229 Å / Relative weight: 1
ReflectionResolution: 3.5→29.01 Å / Num. obs: 15130 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.4
Reflection shellResolution: 3.5→3.62 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
Blu-IceCONTROL SOFTWAREdata reduction
SCALEPACKHKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HSC

3hsc


Resolution: 3.5→29.01 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 205631.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 746 4.9 %RANDOM
Rwork0.257 ---
obs0.257 15130 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9485 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 71.4 Å2
Baniso -1Baniso -2Baniso -3
1-76.66 Å20 Å210.58 Å2
2---36.4 Å20 Å2
3----40.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.89 Å0.98 Å
Refinement stepCycle: LAST / Resolution: 3.5→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 64 94 6062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
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_deg2.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.031.5
X-RAY DIFFRACTIONc_mcangle_it17.092
X-RAY DIFFRACTIONc_scbond_it17.352
X-RAY DIFFRACTIONc_scangle_it24.182.5
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.415 115 4.8 %
Rwork0.388 2271 -
obs--86.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ADP.PARADP.TOP
X-RAY DIFFRACTION5PO4.PARPO4.TOP

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