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- PDB-4h5r: HSC70 NBD with Na, Cl and glycerol -

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Basic information

Entry
Database: PDB / ID: 4h5r
TitleHSC70 NBD with Na, Cl and glycerol
ComponentsHeat shock cognate 71 kDa protein
KeywordsTRANSCRIPTION / HSC70 NBD domain
Function / homology
Function and homology information


lumenal side of lysosomal membrane / regulation of protein import / protein transmembrane import into intracellular organelle / positive regulation of lysosomal membrane permeability / 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 ...lumenal side of lysosomal membrane / regulation of protein import / protein transmembrane import into intracellular organelle / positive regulation of lysosomal membrane permeability / 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 / lysosomal matrix / A1 adenosine receptor binding / late endosomal microautophagy / protein carrier chaperone / response to nickel cation / Respiratory syncytial virus genome transcription / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Lipophagy / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / response to odorant / C3HC4-type RING finger domain binding / synaptic vesicle uncoating / positive regulation by host of viral genome replication / clathrin coat disassembly / CHL1 interactions / ATP-dependent protein disaggregase activity / negative regulation of NLRP3 inflammasome complex assembly / regulation of protein complex stability / photoreceptor ribbon synapse / maintenance of postsynaptic specialization structure / membrane organization / glycinergic synapse / Prp19 complex / presynaptic cytosol / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic specialization membrane / intermediate filament / regulation of postsynapse organization / Lysosome Vesicle Biogenesis / negative regulation of cardiac muscle cell apoptotic process / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / postsynaptic cytosol / Golgi Associated Vesicle Biogenesis / non-chaperonin molecular chaperone ATPase / phosphatidylserine binding / positive regulation of proteolysis / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / regulation of protein-containing complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / estrous cycle / Protein methylation / ATP metabolic process / positive regulation of phagocytosis / forebrain development / skeletal muscle tissue development / heat shock protein binding / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to cadmium ion / photoreceptor inner segment / autophagosome / lysosomal lumen / cellular response to starvation / mRNA Splicing - Major Pathway / cerebellum development / dendritic shaft / kidney development / response to activity / response to progesterone / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / spliceosomal complex / peptide binding / ADP binding / Late endosomal microautophagy / regulation of protein stability / PKR-mediated signaling / terminal bouton / mRNA splicing, via spliceosome / cellular response to hydrogen peroxide / Chaperone Mediated Autophagy / positive regulation of T cell mediated cytotoxicity / protein import into nucleus / G1/S transition of mitotic cell cycle / unfolded protein binding / melanosome / late endosome / protein folding / synaptic vesicle / MHC class II protein complex binding / response to estradiol / Clathrin-mediated endocytosis / protein-folding chaperone 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
PHOSPHATE ION / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 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
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)85,77020
Polymers84,3312
Non-polymers1,43818
Water13,637757
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A: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,97911
Polymers42,1661
Non-polymers81410
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)42,7909
Polymers42,1661
Non-polymers6258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-128 kcal/mol
Surface area31090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.637, 102.462, 77.776
Angle α, β, γ (deg.)90.00, 119.80, 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 , 6 types, 775 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 757 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M KCl in Tris, 30%PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP

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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: Jul 12, 2007
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.64→48 Å / Num. all: 97171 / Num. obs: 97171 / % possible obs: 88 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 25
Reflection shellResolution: 1.64→1.71 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.8 / % possible all: 70

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2bup
Resolution: 1.64→48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.951 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23855 5111 5 %RANDOM
Rwork0.20501 ---
obs0.20668 97171 88.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.361 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å21.44 Å2
2---0.89 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.64→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5916 0 78 757 6751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226068
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9668190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2835762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15724.317278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.619151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2911544
X-RAY DIFFRACTIONr_chiral_restr0.0840.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024516
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.23091
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24226
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2612
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3450.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7351.53782
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26826092
X-RAY DIFFRACTIONr_scbond_it2.09432316
X-RAY DIFFRACTIONr_scangle_it3.3444.52098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.681 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.727 94 -
Rwork0.54 2140 -
obs--26.21 %

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