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- PDB-4fl9: Crystal Structure of bovine hsc70(aa1-554)E213A/D214A at 1.9A Res... -

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Basic information

Entry
Database: PDB / ID: 4fl9
TitleCrystal Structure of bovine hsc70(aa1-554)E213A/D214A at 1.9A Resolution
ComponentsHeat shock cognate 71 kDa protein
KeywordsTRANSCRIPTION / heat shock protein
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
Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 ...Substrate Binding Domain Of DNAk; Chain A, domain 1 / Defensin A-like - #30 / Substrate Binding Domain Of DNAk; Chain A, domain 1 / 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 / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / trimethylamine oxide / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsGrimm, C.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of bovine hsc70(aa1-554)E213A/D214A at 1.9A Resolution
Authors: Grimm, C.
History
DepositionJun 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2834
Polymers60,9791
Non-polymers3043
Water6,648369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.255, 50.380, 86.638
Angle α, β, γ (deg.)90.00, 99.65, 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: 60978.867 Da / Num. of mol.: 1 / Fragment: UNP residues 1-554 / Mutation: E213A, D214A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: HSPA8, HSC70 / Production host: Escherichia coli (E. coli) / References: UniProt: P19120
#2: Chemical ChemComp-TMO / trimethylamine oxide / Trimethylamine N-oxide


Mass: 75.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9NO
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: PEG8000,TRIMETHYL AMINE OXIDE , pH 7.5, Microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 44720 / Num. obs: 44250 / % possible obs: 98.9 % / Redundancy: 3.46 % / Rsym value: 0.072 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 1.84 / Num. unique all: 7204 / % possible all: 95.5

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→38.85 Å / SU ML: 0.66 / σ(F): 1.22 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 4097 5.03 %
Rwork0.1921 --
obs0.1941 44248 93.71 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.949 Å2 / ksol: 0.393 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.5671 Å2-0 Å2-3.8961 Å2
2---2.204 Å2-0 Å2
3----3.3632 Å2
Refinement stepCycle: LAST / Resolution: 1.901→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 18 369 4548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084288
X-RAY DIFFRACTIONf_angle_d1.3195803
X-RAY DIFFRACTIONf_dihedral_angle_d13.8391623
X-RAY DIFFRACTIONf_chiral_restr0.085668
X-RAY DIFFRACTIONf_plane_restr0.007760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-1.92330.41141250.34742115X-RAY DIFFRACTION73
1.9233-1.94680.34161040.31892307X-RAY DIFFRACTION81
1.9468-1.97140.33321250.30172499X-RAY DIFFRACTION88
1.9714-1.99740.33661420.2752631X-RAY DIFFRACTION91
1.9974-2.02470.34431550.27132629X-RAY DIFFRACTION93
2.0247-2.05370.34671310.242616X-RAY DIFFRACTION94
2.0537-2.08430.2521480.21982740X-RAY DIFFRACTION93
2.0843-2.11690.22251190.21142602X-RAY DIFFRACTION93
2.1169-2.15160.26071280.22182706X-RAY DIFFRACTION94
2.1516-2.18870.28511330.22592700X-RAY DIFFRACTION93
2.1887-2.22850.25891390.21362652X-RAY DIFFRACTION95
2.2285-2.27130.26441330.20072708X-RAY DIFFRACTION94
2.2713-2.31770.30811290.21452688X-RAY DIFFRACTION95
2.3177-2.36810.26041220.20882760X-RAY DIFFRACTION95
2.3681-2.42320.26021360.19262658X-RAY DIFFRACTION95
2.4232-2.48370.24671730.20072657X-RAY DIFFRACTION96
2.4837-2.55090.26181530.19522758X-RAY DIFFRACTION95
2.5509-2.62590.28541730.19432698X-RAY DIFFRACTION96
2.6259-2.71070.2851420.19152710X-RAY DIFFRACTION96
2.7107-2.80750.25051570.17982721X-RAY DIFFRACTION95
2.8075-2.91990.24311540.18252704X-RAY DIFFRACTION96
2.9199-3.05270.23931430.17832744X-RAY DIFFRACTION96
3.0527-3.21360.2081330.1872799X-RAY DIFFRACTION96
3.2136-3.41480.20441440.1872701X-RAY DIFFRACTION96
3.4148-3.67830.19881810.1842750X-RAY DIFFRACTION97
3.6783-4.04810.18681440.16032770X-RAY DIFFRACTION97
4.0481-4.63310.16471540.13632762X-RAY DIFFRACTION97
4.6331-5.8340.19521520.16632800X-RAY DIFFRACTION98
5.834-38.85830.18571250.18192813X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4081-0.49440.14052.3318-0.76932.14240.0912-0.1493-0.0766-0.0904-0.03040.05310.20490.0053-0.03610.1056-0.0217-0.01380.0916-0.00980.1209-14.7401-19.5365-6.4427
21.96460.153-0.35960.613-0.11380.86030.04310.08580.0727-0.1032-0.06040.0447-0.04640.07850.01360.1859-0.0289-0.00930.1280.00140.0996-5.7404-9.5156-22.1582
33.1213-0.69183.0637-0.0318-0.04862.2523-0.07990.13120.1461-0.0867-0.0544-0.0358-0.20140.20490.12410.2083-0.07770.02870.24810.05340.1809-43.9-3.4096-36.2231
42.779-0.39962.14111.5297-1.2152.7188-0.0828-0.0973-0.10990.1980.0594-0.1088-0.0501-0.06970.04850.20330.00410.08060.1762-0.00620.1621-45.9684-4.7046-35.8235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:151)
2X-RAY DIFFRACTION2chain 'A' and (resseq 152:367)
3X-RAY DIFFRACTION3chain 'A' and (resseq 368:473)
4X-RAY DIFFRACTION4chain 'A' and (resseq 474:553)

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