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- PDB-2qwr: Crystal structure of disulfide-bond-crosslinked complex of bovine... -

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Basic information

Entry
Database: PDB / ID: 2qwr
TitleCrystal structure of disulfide-bond-crosslinked complex of bovine hsc70 (1-394aa)R171C and bovine Auxilin (810-910aa)D876C in the AMPPNP intact form
Components
  • Heat shock cognate 71 kDa protein
  • Putative tyrosine-protein phosphatase auxilin
KeywordsCHAPERONE / chaperone-cochaperone complex / ATP-binding / Nucleotide-binding / Nucleus / Phosphorylation / Stress response / Hydrolase / Protein phosphatase / SH3-binding
Function / homology
Function and homology information


regulation of clathrin coat assembly / 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 recycling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand ...regulation of clathrin coat assembly / 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 recycling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein targeting to lysosome involved in chaperone-mediated autophagy / clathrin heavy chain binding / synaptic vesicle uncoating / AUF1 (hnRNP D0) binds and destabilizes mRNA / clathrin coat disassembly / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / Prp19 complex / clathrin-coated vesicle / Neutrophil degranulation / clathrin binding / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / intracellular transport / heat shock protein binding / protein folding chaperone / RNA splicing / protein tyrosine phosphatase activity / ATP-dependent protein folding chaperone / spliceosomal complex / SH3 domain binding / mRNA processing / melanosome / presynapse / protein-macromolecule adaptor activity / protein refolding / vesicle / molecular adaptor activity / postsynaptic density / ribonucleoprotein complex / protein domain specific binding / lysosomal membrane / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DnaJ domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Defensin A-like - #30 / DnaJ molecular chaperone homology domain / dnaJ domain profile. ...DnaJ domain / Tensin phosphatase, C2 domain / Tensin-type phosphatase domain / C2 domain of PTEN tumour-suppressor protein / Phosphatase tensin-type domain profile. / C2 tensin-type domain profile. / C2 domain of PTEN tumour-suppressor protein / Defensin A-like - #30 / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / 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 / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / C2 domain superfamily / ATPase, nucleotide binding domain / Helix Hairpins / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Heat shock cognate 71 kDa protein / Auxilin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 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 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Heat shock cognate 71 kDa protein
B: Putative tyrosine-protein phosphatase auxilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8666
Polymers54,1162
Non-polymers7504
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.797, 56.494, 225.878
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 43368.059 Da / Num. of mol.: 1 / Mutation: R171C
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
#2: Protein Putative tyrosine-protein phosphatase auxilin / DnaJ homolog subfamily C member 6


Mass: 10747.485 Da / Num. of mol.: 1 / Mutation: D876C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: DNAJC6 / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q27974, protein-tyrosine-phosphatase

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Non-polymers , 4 types, 109 molecules

#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: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 289 K / Method: microbatch under oil / pH: 8.5
Details: PEG3350, Ammonium Acetate, pH 8.5, 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: Apr 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 25924 / % possible obs: 99.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Χ2: 1.038 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.283.30.55625611.0671100
2.28-2.373.40.48925071.065199.9
2.37-2.483.40.3825441.0511100
2.48-2.613.40.29625511.0761100
2.61-2.773.40.21425681.0471100
2.77-2.993.40.14725951.0441100
2.99-3.293.40.09525631.032199.9
3.29-3.763.30.05726080.974199.7
3.76-4.743.30.04426310.976199.5
4.74-503.20.03927961.048198.9

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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: 2.21→31.67 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 20.977 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 1310 5.1 %RANDOM
Rwork0.23 ---
obs0.233 25852 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.339 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å20 Å2
2--1.06 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.21→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3713 0 45 105 3863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223823
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9685168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22824.566173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49615677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0091524
X-RAY DIFFRACTIONr_chiral_restr0.0950.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022841
X-RAY DIFFRACTIONr_nbd_refined0.2120.21675
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22612
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2161
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.24
X-RAY DIFFRACTIONr_mcbond_it0.6641.52431
X-RAY DIFFRACTIONr_mcangle_it0.92723800
X-RAY DIFFRACTIONr_scbond_it1.59931580
X-RAY DIFFRACTIONr_scangle_it2.4234.51368
LS refinement shellResolution: 2.21→2.266 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 87 -
Rwork0.325 1774 -
all-1861 -
obs--98.57 %

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