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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


Attenuation phase / PKR-mediated signaling / protein transmembrane import into intracellular organelle / positive regulation of lysosomal membrane permeability / positive regulation of protein refolding / prostaglandin binding / slow axonal transport / clathrin-uncoating ATPase activity / lysosomal matrix / Protein methylation ...Attenuation phase / PKR-mediated signaling / protein transmembrane import into intracellular organelle / positive regulation of lysosomal membrane permeability / positive regulation of protein refolding / prostaglandin binding / slow axonal transport / clathrin-uncoating ATPase activity / lysosomal matrix / Protein methylation / mRNA Splicing - Major Pathway / A1 adenosine receptor binding / late endosomal microautophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / HSF1-dependent transactivation / response to nickel cation / negative regulation of supramolecular fiber organization / chaperone-mediated autophagy translocation complex disassembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to odorant / GABA synthesis, release, reuptake and degradation / Lysosome Vesicle Biogenesis / protein targeting to lysosome involved in chaperone-mediated autophagy / Golgi Associated Vesicle Biogenesis / positive regulation by host of viral genome replication / Regulation of HSF1-mediated heat shock response / protein-containing complex disassembly / clathrin coat disassembly / C3HC4-type RING finger domain binding / photoreceptor ribbon synapse / negative regulation of NLRP3 inflammasome complex assembly / modulation by host of viral process / regulation of protein complex stability / maintenance of postsynaptic specialization structure / ATP-dependent protein disaggregase activity / Clathrin-mediated endocytosis / neuron spine / glycinergic synapse / positive regulation of mRNA splicing, via spliceosome / axo-dendritic transport / regulation of postsynapse organization / protein folding chaperone complex / intermediate filament / Neutrophil degranulation / negative regulation of cardiac muscle cell apoptotic process / postsynaptic specialization membrane / chaperone-mediated autophagy / phosphatidylserine binding / cellular response to cadmium ion / response to starvation / non-chaperonin molecular chaperone ATPase / positive regulation of proteolysis / : / asymmetric synapse / Prp19 complex / ATP metabolic process / skeletal muscle tissue development / forebrain development / positive regulation of phagocytosis / estrous cycle / : / heat shock protein binding / photoreceptor inner segment / protein folding chaperone / cerebellum development / peptide binding / lysosomal lumen / autophagosome / RNA splicing / dendritic shaft / response to progesterone / response to activity / kidney development / spliceosomal complex / ATP-dependent protein folding chaperone / G protein-coupled receptor binding / terminal bouton / regulation of protein stability / ADP binding / positive regulation of T cell mediated cytotoxicity / cellular response to hydrogen peroxide / G1/S transition of mitotic cell cycle / mRNA processing / protein import into nucleus / unfolded protein binding / late endosome / synaptic vesicle / melanosome / protein folding / response to estradiol / presynapse / protein-folding chaperone binding / cellular response to heat / protein refolding / protein-macromolecule adaptor activity / dendritic spine / perikaryon / microtubule / response to ethanol / postsynapse
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

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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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