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Basic information

Entry
Database: PDB / ID: 5aqy
TitleFragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues
ComponentsHEAT SHOCK 70 KDA PROTEIN 1A
KeywordsCHAPERONE / HEAT SHOCK PROTEIN / HSP70 / HSP72 / HSC70 / ATPASE / BAG1 / FRAGMENT
Function / homology
Function and homology information


positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / death receptor agonist activity / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation ...positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / death receptor agonist activity / C3HC4-type RING finger domain binding / ATP-dependent protein disaggregase activity / positive regulation of microtubule nucleation / misfolded protein binding / regulation of mitotic spindle assembly / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / chaperone cofactor-dependent protein refolding / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Regulation of HSF1-mediated heat shock response / chaperone-mediated protein complex assembly / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / inclusion body / ATP metabolic process / protein folding chaperone / negative regulation of protein ubiquitination / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / G protein-coupled receptor binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / positive regulation of interleukin-8 production / ATP-dependent protein folding chaperone / negative regulation of transforming growth factor beta receptor signaling pathway / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / virus receptor activity / cellular response to heat / cellular response to oxidative stress / positive regulation of NF-kappaB transcription factor activity / protein refolding / blood microparticle / vesicle / ficolin-1-rich granule lumen / receptor ligand activity / protein stabilization / nuclear speck / cadherin binding / ribonucleoprotein complex / negative regulation of cell population proliferation / signaling receptor binding / focal adhesion / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / 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
ADENOSINE / Heat shock 70 kDa protein 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsJones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. ...Jones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. / Liu, M. / Richards, M. / McAndrew, C. / Yahya, N. / Dobson, S.E. / Jones, K. / Workman, P. / Collins, I. / van Montfort, R.L.M.
CitationJournal: Sci Rep / Year: 2016
Title: A fragment-based approach applied to a highly flexible target: Insights and challenges towards the inhibition of HSP70 isoforms.
Authors: Jones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. / Liu, M. / Richards, M. / McAndrew, C. / ...Authors: Jones, A.M. / Westwood, I.M. / Osborne, J.D. / Matthews, T.P. / Cheeseman, M.D. / Rowlands, M.G. / Jeganathan, F. / Burke, R. / Lee, D. / Kadi, N. / Liu, M. / Richards, M. / McAndrew, C. / Yahya, N. / Dobson, S.E. / Jones, K. / Workman, P. / Collins, I. / van Montfort, R.L.
History
DepositionSep 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_detector
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _diffrn_detector.type
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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 70 KDA PROTEIN 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,86925
Polymers43,1961
Non-polymers1,67324
Water5,783321
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.521, 89.046, 95.944
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein HEAT SHOCK 70 KDA PROTEIN 1A / HEAT SHOCK 70 KDA PROTEIN 1 / HSP70-1 / HSP70.1


Mass: 43195.902 Da / Num. of mol.: 1 / Fragment: NUCLEOTIDE BINDING DOMAIN, UNP RESIDUES 1-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: P0DMV8, EC: 3.6.3.51

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Non-polymers , 5 types, 345 molecules

#2: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES 382 ONWARDS ARE A CLONING ARTEFACT DERIVED FROM THE EXPRESSION VECTOR PGEX-6P-1

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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: 2.4 Å3/Da / Density % sol: 48.8 % / Description: NONE
Crystal growpH: 7.5
Details: 17-28% (W/V) PEG3350, 0.1M HEPES PH 7.5, 2MM MGCL2, 2MM NAH2PO4 AND 5MM ADENOSINE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9728
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9728 Å / Relative weight: 1
ReflectionResolution: 1.56→47.97 Å / Num. obs: 58145 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.2
Reflection shellResolution: 1.56→1.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 1 / % possible all: 97

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S3X

1s3x


Resolution: 1.56→47.97 Å / Cor.coef. Fo:Fc: 0.9582 / Cor.coef. Fo:Fc free: 0.9477 / SU R Cruickshank DPI: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.079 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 2866 4.94 %RANDOM
Rwork0.174 ---
obs0.1754 58071 98.82 %-
Displacement parametersBiso mean: 28.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.3595 Å20 Å20 Å2
2---5.1664 Å20 Å2
3---2.807 Å2
Refine analyzeLuzzati coordinate error obs: 0.205 Å
Refinement stepCycle: LAST / Resolution: 1.56→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 108 321 3391
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013130HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.974201HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1098SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes80HARMONIC2
X-RAY DIFFRACTIONt_gen_planes467HARMONIC5
X-RAY DIFFRACTIONt_it3130HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion14.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion420SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3875SEMIHARMONIC4
LS refinement shellResolution: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2427 217 5.18 %
Rwork0.2444 3973 -
all0.2443 4190 -
obs--97.48 %
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)
12.7494-1.28350.09683.7887-0.24151.43960.0184-0.096-0.15450.14240.0039-0.1809-0.02640.2882-0.0223-0.03690.0044-0.0210.0195-0.0086-0.040916.9263-8.08959.8163
21.81380.1046-0.52780.2319-0.06310.32440.02980.139-0.02450.00040.0387-0.04590.0728-0.0676-0.0685-0.0128-0.0032-0.0092-0.0063-0.03540.0083-1.0277-10.9776-1.4796
31.3948-0.38950.33141.8540.33980.56570.10440.04520.1075-0.0713-0.04220.15990.0207-0.0837-0.0622-0.06210.00290.0051-0.0117-0.0281-0.0044-11.4744-7.04320.7913
41.23630.2005-0.04710.03030.14460.75350.0387-0.0002-0.08040.0811-0.00790.13670.0972-0.0135-0.0308-0.01480.0025-0.0145-0.0268-0.0183-0.01394.3041-7.79629.7838
51.4770.65130.03370.67020.0190.63430.0994-0.1420.16490.0763-0.08290.0953-0.10070.0137-0.0166-0.0001-0.00090.0046-0.0069-0.0244-0.00447.90961.99459.8949
61.6280.29780.88331.1151.00683.2152-0.06270.00810.2782-0.00610.0686-0.0946-0.28910.0149-0.0059-0.0291-0.0209-0.0078-0.021-0.0055-0.026418.57918.1231-1.8037
70.45560.8209-0.67853.38840.44470.03450.0005-0.0673-0.1103-0.16150.0842-0.02890.5442-0.1974-0.08470.162-0.1331-0.07770.00490.0471-0.11816.5362-13.9849-25.5663
83.18791.82550.69092.6141.73711.6607-0.1470.0089-0.23210.22990.0956-0.19150.5442-0.23440.05140.2308-0.1037-0.0242-0.09170.0158-0.1857.4504-20.9226-20.9631
91.42210.94821.32452.40412.91045.6230.07390.1963-0.1339-0.08840.1026-0.18610.19160.0391-0.1765-0.069-0.01070.0008-0.02360.0318-0.118215.0813-1.3981-20.6005
101.1383-0.4749-0.07791.63331.0374.8080.06340.2390.1825-0.10390.1383-0.2565-0.12310.4779-0.2017-0.11250.0103-0.00150.0627-0.0039-0.054523.87393.3593-10.2298
111.92220.23270.75421.2004-0.95612.5960.074-0.30460.03170.2235-0.0666-0.2736-0.13490.1955-0.0074-0.0254-0.0282-0.04170.0352-0.0246-0.031321.21410.64117.3517

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