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- PDB-4h5n: HSC70 NBD with PO4, Na, Cl -

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Basic information

Entry
Database: PDB / ID: 4h5n
TitleHSC70 NBD with PO4, Na, Cl
ComponentsHeat shock cognate 71 kDa protein
KeywordsTRANSCRIPTION / Nucleotide Binding Domain
Function / homology
Function and homology information


regulation of protein import / lumenal side of lysosomal membrane / negative regulation of supramolecular fiber organization / protein carrier chaperone / positive regulation by host of viral genome replication / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / postsynaptic specialization membrane / Lipophagy / GABA synthesis, release, reuptake and degradation / slow axonal transport ...regulation of protein import / lumenal side of lysosomal membrane / negative regulation of supramolecular fiber organization / protein carrier chaperone / positive regulation by host of viral genome replication / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / postsynaptic specialization membrane / Lipophagy / GABA synthesis, release, reuptake and degradation / slow axonal transport / chaperone-mediated autophagy translocation complex disassembly / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / glycinergic synapse / late endosomal microautophagy / regulation of postsynapse organization / CHL1 interactions / regulation of protein complex stability / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / photoreceptor ribbon synapse / membrane organization / presynaptic cytosol / chaperone complex / Prp19 complex / positive regulation of mRNA splicing, via spliceosome / Lysosome Vesicle Biogenesis / misfolded protein binding / postsynaptic cytosol / Golgi Associated Vesicle Biogenesis / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / phosphatidylserine binding / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / autophagosome / Protein methylation / HSF1-dependent transactivation / response to unfolded protein / ATP metabolic process / Regulation of HSF1-mediated heat shock response / regulation of protein-containing complex assembly / Attenuation phase / cellular response to unfolded protein / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein folding chaperone / mRNA Splicing - Major Pathway / lysosomal lumen / cellular response to starvation / vesicle-mediated transport / spliceosomal complex / G protein-coupled receptor binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / Late endosomal microautophagy / mRNA splicing, via spliceosome / terminal bouton / protein-macromolecule adaptor activity / regulation of protein stability / Chaperone Mediated Autophagy / melanosome / unfolded protein binding / Clathrin-mediated endocytosis / protein folding / ribonucleoprotein complex / late endosome / MHC class II protein complex binding / protein refolding / lysosomal membrane / chaperone binding / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / blood microparticle / ficolin-1-rich granule lumen / lysosome / regulation of cell cycle / cadherin binding / glutamatergic synapse / focal adhesion / dendrite / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / Neutrophil degranulation / ATP hydrolysis activity / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular space / extracellular exosome / extracellular region / membrane / nucleoplasm / ATP binding / plasma membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
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 ...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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsStec, B.
CitationJournal: Biochimie / Year: 2015
Title: New crystal structures of HSC-70 ATP binding domain confirm the role of individual binding pockets and suggest a new method of inhibition.
Authors: Zhang, Z. / Cellitti, J. / Teriete, P. / Pellecchia, M. / Stec, B.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Database references

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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)85,86121
Polymers84,3312
Non-polymers1,53019
Water14,556808
1
A: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,88310
Polymers42,1661
Non-polymers7179
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,97811
Polymers42,1661
Non-polymers81210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-119 kcal/mol
Surface area30290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.802, 101.693, 77.421
Angle α, β, γ (deg.)90.00, 119.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 42165.648 Da / Num. of mol.: 2
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) / Strain (production host): BL21 / References: UniProt: P11142

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Non-polymers , 5 types, 827 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 808 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE MATCHES WITH ISOFORM 2 OF UNIPROT ENTRY P11142 WITH IDENTIFIER P11142-2.

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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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M KCl in Tris, 30%PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Aug 23, 2007 / Details: Osmic
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→48 Å / Num. all: 62313 / Num. obs: 62313 / % possible obs: 89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.1
Reflection shellResolution: 1.86→1.9 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.2 / % possible all: 77

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2bup
Resolution: 1.86→48 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.486 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24751 3292 5 %RANDOM
Rwork0.19033 ---
obs0.19325 62313 86.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.868 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å21.21 Å2
2---0.69 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.86→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5916 0 83 808 6807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226072
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9678196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8235762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70724.317278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.834151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5831544
X-RAY DIFFRACTIONr_chiral_restr0.0930.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024516
X-RAY DIFFRACTIONr_nbd_refined0.2190.23785
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24317
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2958
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.231
X-RAY DIFFRACTIONr_mcbond_it0.8081.53782
X-RAY DIFFRACTIONr_mcangle_it1.426092
X-RAY DIFFRACTIONr_scbond_it2.53232319
X-RAY DIFFRACTIONr_scangle_it3.9054.52104
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 59 -
Rwork0.333 1278 -
obs--24.04 %

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