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- PDB-1ngj: STRUCTURAL BASIS OF THE 70-KILODALTON HEAT SHOCK COGNATE PROTEIN ... -

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Basic information

Entry
Database: PDB / ID: 1ngj
TitleSTRUCTURAL 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
ComponentsHEAT-SHOCK COGNATE 70 kD PROTEIN
KeywordsHYDROLASE(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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / synaptic vesicle uncoating ...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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / synaptic vesicle uncoating / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Clathrin-mediated endocytosis / Prp19 complex / Neutrophil degranulation / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / heat shock protein binding / protein folding chaperone / RNA splicing / ATP-dependent protein folding chaperone / spliceosomal complex / mRNA processing / melanosome / presynapse / protein-macromolecule adaptor activity / protein refolding / ribonucleoprotein complex / lysosomal membrane / negative regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytosol / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsFlaherty, K.M. / Wilbanks, S.M. / Deluca-Flaherty, C. / Mckay, D.B.
Citation
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.
#1: 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
DepositionMay 17, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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

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Assembly

Deposited unit
A: HEAT-SHOCK COGNATE 70 kD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0443
Polymers42,5131
Non-polymers5312
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.300, 65.000, 46.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HEAT-SHOCK COGNATE 70 kD PROTEIN


Mass: 42513.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: BRAIN / References: UniProt: P19120, adenosinetriphosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal grow
*PLUS
pH: 9.5 / Method: unknown / Details: pH is adjusted to 9.5 with NaOH
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG800011
21.0 M11NaCl
350 mMCAPS11
41 mMMgAMPPNP11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.194 -
obs0.194 17071
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 32 163 3153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.194 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.7

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