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- PDB-3fzf: Crystal Structure of Hsc70/Bag1 in complex with ATP -

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Basic information

Entry
Database: PDB / ID: 3fzf
TitleCrystal Structure of Hsc70/Bag1 in complex with ATP
Components
  • BAG family molecular chaperone regulator 1
  • Heat shock cognate 71 kDa protein
KeywordsCHAPERONE / HSP70 / HSC70 / BAG1 / heat shock / protein folding / adenosine / nucleoside / nucleotide exchange factor / small molecule inhibitor / ATP-binding / nucleotide-binding / stress response / apoptosis
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 / adenyl-nucleotide exchange factor activity / response to odorant / C3HC4-type RING finger domain binding / synaptic vesicle uncoating / positive regulation by host of viral genome replication / positive regulation of smooth muscle cell apoptotic process / 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 / cellular response to starvation / autophagosome / photoreceptor inner segment / lysosomal lumen / mRNA Splicing - Major Pathway / cerebellum development / kidney development / dendritic shaft / 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 / late endosome / melanosome / protein folding / synaptic vesicle / MHC class II protein complex binding / response to estradiol
Similarity search - Function
BAG domain / Molecular chaperone regulator BAG / BAG domain superfamily / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. ...BAG domain / Molecular chaperone regulator BAG / BAG domain superfamily / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Ubiquitin family / Nucleotidyltransferase; domain 5 / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Heat shock cognate 71 kDa protein / BAG family molecular chaperone regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDokurno, P. / Williamson, D.S. / Murray, J.B. / Surgenor, A.E.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Novel adenosine-derived inhibitors of 70 kDa heat shock protein, discovered through structure-based design
Authors: Williamson, D.S. / Borgognoni, J. / Clay, A. / Daniels, Z. / Dokurno, P. / Drysdale, M.J. / Foloppe, N. / Francis, G.L. / Graham, C.J. / Howes, R. / Macias, A.T. / Murray, J.B. / Parsons, R. ...Authors: Williamson, D.S. / Borgognoni, J. / Clay, A. / Daniels, Z. / Dokurno, P. / Drysdale, M.J. / Foloppe, N. / Francis, G.L. / Graham, C.J. / Howes, R. / Macias, A.T. / Murray, J.B. / Parsons, R. / Shaw, T. / Surgenor, A.E. / Terry, L. / Wang, Y. / Wood, M. / Massey, A.J.
History
DepositionJan 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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

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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: BAG family molecular chaperone regulator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7513
Polymers55,2442
Non-polymers5071
Water5,260292
1
A: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5942
Polymers42,0871
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BAG family molecular chaperone regulator 1


Theoretical massNumber of molelcules
Total (without water)13,1571
Polymers13,1571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.289, 121.123, 52.773
Angle α, β, γ (deg.)90.00, 106.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42086.547 Da / Num. of mol.: 1 / Fragment: UNP residues 4-381
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA8, HSC70, HSP73, HSPA10 / Plasmid: pET101 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11142
#2: Protein BAG family molecular chaperone regulator 1 / BAG-1 / Bcl-2-associated athanogene 1 / Glucocorticoid receptor-associated protein RAP46


Mass: 13157.168 Da / Num. of mol.: 1 / Fragment: UNP residues 222-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAG1, HAP / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99933
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG3350, 0.1M Tris buffer, 25mM sodium-potassium tartrate, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 14, 2006 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→24.87 Å / Num. all: 32145 / Num. obs: 32145 / % possible obs: 98.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 3.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.96 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.2 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HX1

1hx1


Resolution: 2.2→24.87 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.906 / SU B: 10.215 / SU ML: 0.243 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.382 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29235 1859 7.7 %RANDOM
Rwork0.20049 ---
obs0.2074 22350 98.38 %-
all-22350 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.924 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å20 Å2-1.22 Å2
2---1.48 Å20 Å2
3---3.23 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 31 292 4121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223884
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.9775244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3565486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49724.888178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.15715713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9481526
X-RAY DIFFRACTIONr_chiral_restr0.1050.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022869
X-RAY DIFFRACTIONr_nbd_refined0.2340.21882
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22667
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.220
X-RAY DIFFRACTIONr_mcbond_it0.7531.52498
X-RAY DIFFRACTIONr_mcangle_it1.29323899
X-RAY DIFFRACTIONr_scbond_it2.08131547
X-RAY DIFFRACTIONr_scangle_it3.3564.51345
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 128 -
Rwork0.305 1615 -
obs-1785 96.99 %

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