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- PDB-2qwm: Crystal structure of bovine hsc70 (1-394aa)in the ADP*Vi state -

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Basic information

Entry
Database: PDB / ID: 2qwm
TitleCrystal structure of bovine hsc70 (1-394aa)in the ADP*Vi state
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE / ATP-binding / Nucleotide-binding / Nucleus / Phosphorylation / Stress response
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 / VANADATE ION / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å
AuthorsJiang, J. / Maes, E.G. / Wang, L. / Taylor, A.B. / Hinck, A.P. / Lafer, E.M. / Sousa, R.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural basis of J cochaperone binding and regulation of Hsp70.
Authors: Jiang, J. / Maes, E.G. / Taylor, A.B. / Wang, L. / Hinck, A.P. / Lafer, E.M. / Sousa, R.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_asym_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_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)88,16113
Polymers86,8442
Non-polymers1,31711
Water6,467359
1
A: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0356
Polymers43,4221
Non-polymers6125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock cognate 71 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1277
Polymers43,4221
Non-polymers7056
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.336, 77.841, 75.793
Angle α, β, γ (deg.)90.000, 101.530, 90.000
Int Tables number4
Space group name H-MP1211

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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: 43422.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: HSPA8, HSC70 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P19120

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Non-polymers , 6 types, 370 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 289 K / Method: microbatch under oil / pH: 8
Details: PEG3350, Calcium Acetate, pH 8.0, microbatch under oil, temperature 289K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 70267 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.061 / Χ2: 1.058 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.86-1.933.50.41569811.12199.8
1.93-23.60.30969891.0721100
2-2.093.60.22770171.0561100
2.09-2.213.60.16869621.1141100
2.21-2.343.60.13270081.0321100
2.34-2.523.70.10270331.051100
2.52-2.783.70.07570211.0631100
2.78-3.183.70.05170211.0421100
3.18-4.013.80.02970601.0211100
4.01-503.70.0271751.021199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→36.06 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.135 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3541 5 %RANDOM
Rwork0.188 ---
obs0.19 70206 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.398 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.86→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 76 359 6333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226063
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.978199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9175760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63124.317278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.226151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6791544
X-RAY DIFFRACTIONr_chiral_restr0.0750.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024538
X-RAY DIFFRACTIONr_nbd_refined0.1930.22763
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24215
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.2425
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.221
X-RAY DIFFRACTIONr_mcbond_it0.4541.53774
X-RAY DIFFRACTIONr_mcangle_it0.83926080
X-RAY DIFFRACTIONr_scbond_it1.72832327
X-RAY DIFFRACTIONr_scangle_it2.744.52119
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 257 -
Rwork0.246 4913 -
all-5170 -
obs--99.69 %

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