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- PDB-7plk: Crystal structure bovine Hsc70(aa1-554)E213A/D214A in complex wit... -

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Basic information

Entry
Database: PDB / ID: 7plk
TitleCrystal structure bovine Hsc70(aa1-554)E213A/D214A in complex with nicotinic-acid-derivative
ComponentsHeat shock cognate 71 kDa protein
KeywordsCHAPERONE
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
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, nucleotide binding domain
Similarity search - Domain/homology
5-pyrrol-1-ylpyridine-3-carboxylic acid / : / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4878136608 Å
AuthorsZehe, M. / Grimm, C. / Sotriffer, C.
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Combined In-Solution Fragment Screening and Crystallographic Binding-Mode Analysis with a Two-Domain Hsp70 Construct.
Authors: Zehe, M. / Kehrein, J. / Schollmayer, C. / Plank, C. / Kovacs, H. / Merino Asumendi, E. / Holzgrabe, U. / Grimm, C. / Sotriffer, C.
History
DepositionAug 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)61,5375
Polymers60,9791
Non-polymers5584
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint4 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.078, 48.799, 86.476
Angle α, β, γ (deg.)90.000, 99.548, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 60978.867 Da / Num. of mol.: 1 / 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

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Non-polymers , 5 types, 90 molecules

#2: Chemical ChemComp-7UE / 5-pyrrol-1-ylpyridine-3-carboxylic acid


Mass: 188.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 47.45 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: PEG 8000, TMAO, potassium chloride, HEPES-NaOH, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.4878→50 Å / Num. obs: 19088 / % possible obs: 98.19 % / Redundancy: 6.6 % / Biso Wilson estimate: 40.05 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.1852 / Rpim(I) all: 0.07733 / Rrim(I) all: 0.2011 / Net I/av σ(I): 7.83 / Net I/σ(I): 4.8
Reflection shellResolution: 2.488→2.577 Å / Rmerge(I) obs: 1.643 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 1741 / CC1/2: 0.578 / CC star: 0.856 / Rpim(I) all: 0.6779

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FL9

4fl9


Resolution: 2.4878136608→50 Å / SU ML: 0.381428449647 / Cross valid method: FREE R-VALUE / σ(F): 1.33753367553 / Phase error: 31.2617600946
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.286205729041 1907 9.99947564365 %
Rwork0.223482853175 17164 -
obs0.229670514692 19071 98.1776061776 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.8195741819 Å2
Refinement stepCycle: LAST / Resolution: 2.4878136608→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4139 0 36 86 4261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01069931119444246
X-RAY DIFFRACTIONf_angle_d1.238217503555732
X-RAY DIFFRACTIONf_chiral_restr0.0828617609692654
X-RAY DIFFRACTIONf_plane_restr0.00651823244147748
X-RAY DIFFRACTIONf_dihedral_angle_d24.81786587461600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48782-2.550.3598415500651190.317942106471071X-RAY DIFFRACTION85.5499640546
2.55-2.6190.3549085385231350.3111408671831211X-RAY DIFFRACTION99.8516320475
2.619-2.6960.3498884332251380.2859395996821245X-RAY DIFFRACTION99.3534482759
2.696-2.7830.3682974148271350.2979071626781221X-RAY DIFFRACTION99.6326230713
2.783-2.88250.3277548775921390.2855639878361240X-RAY DIFFRACTION99.4949494949
2.8825-2.99780.3210347923291370.2768263782871227X-RAY DIFFRACTION99.416909621
2.9978-3.13420.3426745405681350.2382339370651215X-RAY DIFFRACTION99.2647058824
3.1342-3.29940.2960977580811360.2446059184971234X-RAY DIFFRACTION98.6321094312
3.2994-3.50610.3370763591361340.2336148897161211X-RAY DIFFRACTION97.4637681159
3.5061-3.77660.2807790009881400.2132503039011248X-RAY DIFFRACTION99.7126436782
3.7766-4.15640.2585962701841380.190516610831245X-RAY DIFFRACTION99.4964028777
4.1564-4.75710.2327685229241390.1765779227081252X-RAY DIFFRACTION99.4992846924
4.7571-5.99080.2675013330271380.2071146251041247X-RAY DIFFRACTION98.787446505
5.9908-42.6390.23429614911440.1862500779731297X-RAY DIFFRACTION98.4962406015
Refinement TLS params.Method: refined / Origin x: -20.3946875272 Å / Origin y: -10.3743821943 Å / Origin z: -22.1637177435 Å
111213212223313233
T0.326330972777 Å2-0.0762271059433 Å20.0120883535265 Å2-0.201014950892 Å20.0052617488599 Å2--0.262129403635 Å2
L1.91166592877 °2-0.312658728046 °20.605771528619 °2-0.12392367999 °2-0.181911622888 °2--0.854958868427 °2
S0.062736331116 Å °-0.0834593306797 Å °0.0416013519079 Å °0.0176244454455 Å °-0.0502609589888 Å °-0.00270590952902 Å °0.0742513567998 Å °-0.000603587325755 Å °-0.0218067925417 Å °
Refinement TLS groupSelection details: all

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