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- PDB-2bup: T13G Mutant of the ATPASE fragment of Bovine HSC70 -

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Basic information

Entry
Database: PDB / ID: 2bup
TitleT13G Mutant of the ATPASE fragment of Bovine HSC70
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE / MOLECULAR CHAPERONE / ATPASE / HYDROLASE (ACTING ON ACID ANHYDRIDES)
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly ...Regulation of HSF1-mediated heat shock response / Attenuation phase / HSF1-dependent transactivation / Protein methylation / GABA synthesis, release, reuptake and degradation / PKR-mediated signaling / mRNA Splicing - Major Pathway / synaptic vesicle uncoating / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / protein targeting to lysosome involved in chaperone-mediated autophagy / late endosomal microautophagy / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Prp19 complex / presynaptic cytosol / Neutrophil degranulation / postsynaptic cytosol / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / autophagosome / protein folding chaperone / heat shock protein binding / RNA splicing / ATP-dependent protein folding chaperone / spliceosomal complex / terminal bouton / mRNA processing / melanosome / protein-macromolecule adaptor activity / protein refolding / lysosome / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / dendrite / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytoplasm
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 / ADENOSINE-5'-TRIPHOSPHATE / : / PHOSPHATE ION / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.7 Å
AuthorsSousa, M.C. / Mckay, D.B.
Citation
Journal: Biochemistry / Year: 1998
Title: The hydroxyl of threonine 13 of the bovine 70-kDa heat shock cognate protein is essential for transducing the ATP-induced conformational change.
Authors: Sousa, M.C. / McKay, D.B.
#1: Journal: J.Biol.Chem. / Year: 1995
Title: How Potassium Affects the Activity of the Molecular Chaperone Hsc70. II. Potassium Binds Specifically in the ATPase Active Site
Authors: Wilbanks, S.M. / McKay, D.B.
#2: Journal: J.Biol.Chem. / Year: 1995
Title: How Potassium Affects the Activity of the Molecular Chaperone Hsc70. I. Potassium is Required for Optimal ATPase Activity
Authors: O'Brien, M.C. / McKay, D.B.
#3: Journal: J.Biol.Chem. / Year: 1994
Title: Structural Basis of the 70-kilodalton Heat Shock Cognate Protein ATP Hydrolytic Activity. II. Structure of the Active Site with ADP or ATP Bound to Wild Type and Mutant ATPase Fragment.
Authors: Flaherty, K.M. / Wilbanks, S.M. / Deluca-Flaherty, C. / McKay, D.B.
#4: Journal: Nature / Year: 1990
Title: Three-Dimensional Structure of the ATPase Fragment of a 70K Heat-Shock Cognate Protein
Authors: Flaherty, K.M. / Deluca-Flaherty, C. / McKay, D.B.
History
DepositionSep 8, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1549
Polymers41,9511
Non-polymers1,2038
Water7,837435
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.350, 64.300, 46.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Heat shock cognate 71 kDa protein / HSP70 / HEAT SHOCK PROTEIN / Heat shock 70 kDa protein 8


Mass: 41951.473 Da / Num. of mol.: 1 / Fragment: ATPASE / Mutation: T13G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19120

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Non-polymers , 7 types, 443 molecules

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


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ACTIVE SITE CONTAINS A MIXTURE OF TWO GROUPS OF ATOMS. GROUP 1 IS FORMED BY ADP 486, PI 488 AND ...THE ACTIVE SITE CONTAINS A MIXTURE OF TWO GROUPS OF ATOMS. GROUP 1 IS FORMED BY ADP 486, PI 488 AND HOH 545 AND HAS AN ACCOPANCY OF 0.6. GROUP TWO IS ATP 489 AND HOH 1119 WITH AN OCCUPANCY OF 0.4

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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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growpH: 9 / Details: pH 9.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMMgATP1reservoir
250 mMCHES1reservoir
31 M1reservoirKCl
420 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MACSCIENCE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 46807 / % possible obs: 97.4 % / Redundancy: 4 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058
Reflection shellResolution: 1.7→1.76 Å / Rsym value: 0.14 / % possible all: 89.5
Reflection
*PLUS
Num. measured all: 167988
Reflection shell
*PLUS
% possible obs: 89.5 % / Rmerge(I) obs: 0.14

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.7→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 1007200.37 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4701 10 %RANDOM
Rwork0.195 ---
obs0.195 46807 97.5 %-
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.41 Å20 Å20 Å2
2---3.6 Å20 Å2
3---1.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2901 0 68 435 3404
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.981.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 724 10 %
Rwork0.222 6532 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TOPPAR_MCS:BILL_DNA-RNA-ATOPPAR_MCS:ADP+PI.TOP
X-RAY DIFFRACTION3TOPPAR_MCS:ADP+PI.PARTOPPAR_MCS:BILL_ATP.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.264 / % reflection Rfree: 10 % / Rfactor Rwork: 0.222

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