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- PDB-5aqg: Fragment-based screening of HSP70 sheds light on the functional r... -

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Basic information

Entry
Database: PDB / ID: 5aqg
TitleFragment-based screening of HSP70 sheds light on the functional role of ATP-binding site residues
Components
  • BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
  • HEAT SHOCK COGNATE 71 KDA PROTEIN
KeywordsCHAPERONE / HEAT SHOCK PROTEIN / HSP70 / HSP72 / HSC70 / ATPASE / BAG1 / FRAGMENT
Function / homology
Function and homology information


lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / protein carrier chaperone / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Lipophagy / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / GABA synthesis, release, reuptake and degradation ...lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / protein carrier chaperone / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Lipophagy / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / adenyl-nucleotide exchange factor activity / late endosomal microautophagy / C3HC4-type RING finger domain binding / clathrin coat disassembly / negative regulation of NLRP3 inflammasome complex assembly / CHL1 interactions / ATP-dependent protein disaggregase activity / regulation of protein complex stability / membrane organization / Prp19 complex / presynaptic cytosol / protein folding chaperone complex / postsynaptic cytosol / Lysosome Vesicle Biogenesis / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / Golgi Associated Vesicle Biogenesis / non-chaperonin molecular chaperone ATPase / chaperone cofactor-dependent protein refolding / regulation of protein-containing complex assembly / HSF1-dependent transactivation / response to unfolded protein / autophagosome / Regulation of HSF1-mediated heat shock response / Attenuation phase / Protein methylation / protein folding chaperone / ATP metabolic process / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to starvation / mRNA Splicing - Major Pathway / lysosomal lumen / G protein-coupled receptor binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / ATP-dependent protein folding chaperone / spliceosomal complex / Late endosomal microautophagy / regulation of protein stability / PKR-mediated signaling / terminal bouton / mRNA splicing, via spliceosome / Chaperone Mediated Autophagy / melanosome / unfolded protein binding / protein-macromolecule adaptor activity / protein folding / Clathrin-mediated endocytosis / MHC class II protein complex binding / protein-folding chaperone binding / protein refolding / blood microparticle / Interleukin-4 and Interleukin-13 signaling / secretory granule lumen / ficolin-1-rich granule lumen / lysosome / protein stabilization / cell surface receptor signaling pathway / cadherin binding / ribonucleoprotein complex / lysosomal membrane / focal adhesion / negative regulation of DNA-templated transcription / dendrite / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / nucleolus / negative regulation of apoptotic process / enzyme binding / ATP hydrolysis activity / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Defensin A-like - #30 / Defensin A-like / Heat shock hsp70 proteins family signature 2. ...BAG domain / BAG domain superfamily / Molecular chaperone regulator BAG / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / ATPase, nucleotide binding domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Nucleotidyltransferase; domain 5 / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-ZJB / Heat shock cognate 71 kDa protein / BAG family molecular chaperone regulator 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 / 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 / _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: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
C: HEAT SHOCK COGNATE 71 KDA PROTEIN
D: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
E: HEAT SHOCK COGNATE 71 KDA PROTEIN
F: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,13725
Polymers167,7566
Non-polymers2,38119
Water8,377465
1
A: HEAT SHOCK COGNATE 71 KDA PROTEIN
B: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5817
Polymers55,9192
Non-polymers6625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-5.4 kcal/mol
Surface area22060 Å2
MethodPISA
2
C: HEAT SHOCK COGNATE 71 KDA PROTEIN
D: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,94911
Polymers55,9192
Non-polymers1,0309
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-5.7 kcal/mol
Surface area22380 Å2
MethodPISA
3
E: HEAT SHOCK COGNATE 71 KDA PROTEIN
F: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6077
Polymers55,9192
Non-polymers6895
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-0.8 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.864, 40.772, 205.792
Angle α, β, γ (deg.)90.00, 122.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein HEAT SHOCK COGNATE 71 KDA PROTEIN / HEAT SHOCK 70 KDA PROTEIN 8 / LIPOPOLYSACCHARIDE-ASSOCIATED PROTEIN 1 / LAP-1 / LPS-ASSOCIATED PROTEIN 1


Mass: 42406.980 Da / Num. of mol.: 3 / Fragment: NUCLEOTIDE BINDING DOMAIN, RESIDUES 1-381
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: P11142, EC: 3.6.3.51
#2: Protein BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1 / BAG-1 / BCL-2-ASSOCIATED ATHANOGENE 1


Mass: 13511.571 Da / Num. of mol.: 3 / Fragment: RESIDUES 222-334
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: Q99933

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Non-polymers , 5 types, 484 molecules

#3: Chemical ChemComp-ZJB / (2R,3R,4S,5R)-2-(3-AMINO-5-METHYL-1,4,5,6,8-PENTAAZAACENAPHTHYLEN-1(5H)-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL / Triciribine


Mass: 320.304 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H16N6O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 465 / 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: 2.46 Å3/Da / Density % sol: 49.92 % / Description: NONE
Crystal growpH: 8.5
Details: 16-26% (W/V) PEG3350, 0.1 M K-NA TARTRATE, 0.1 M TRIS.HCL PH 8.5 AND 25% (V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.24→47.59 Å / Num. obs: 78546 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 34.87 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.1
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 0.4 / % possible all: 84.3

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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 1HX1

1hx1


Resolution: 2.24→43.4 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.266 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.267 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.194
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 3928 5 %RANDOM
Rwork0.1916 ---
obs0.1931 78540 98.26 %-
Displacement parametersBiso mean: 48.14 Å2
Baniso -1Baniso -2Baniso -3
1--2.468 Å20 Å2-5.9356 Å2
2--4.7209 Å20 Å2
3----2.2529 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: LAST / Resolution: 2.24→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11202 0 159 465 11826
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111531HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0615600HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4058SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes313HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1738HARMONIC5
X-RAY DIFFRACTIONt_it11531HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion16.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1577SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13287SEMIHARMONIC4
LS refinement shellResolution: 2.24→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2774 263 5.32 %
Rwork0.2598 4681 -
all0.2608 4944 -
obs--84.55 %
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)
11.6331-0.4159-0.72022.85550.22041.85110.09660.1947-0.0101-0.3804-0.0833-0.12190.00040.0025-0.01340.0217-0.02140.1284-0.1921-0.0845-0.036620.1303-0.104141.5457
25.8515-0.3158-1.96110.80160.21761.33860.01370.08040.13350.1475-0.05580.16990.1519-0.22610.04210.0685-0.02780.0929-0.1289-0.0808-0.061930.29815.151159.9074
31.566-0.079-0.64830.6260.12640.5119-0.0518-0.26610.05840.08680.01870.0940.15770.08990.03310.10340.00230.0917-0.0943-0.053-0.05537.20960.456258.9757
40.7526-1.1561.75410.8216-1.81255.40270.0550.2682-0.2433-0.0852-0.1180.18270.0695-0.09520.0630.17-0.02470.029-0.0984-0.0745-0.071348.7324-19.273930.0053
51.8519-0.29572.01282.27980.2996.3716-0.04740.2709-0.0605-0.2514-0.08660.0701-0.1042-0.15510.1340.0112-0.00350.0739-0.1155-0.0597-0.106749.6599-10.674132.5304
61.603-1.186-0.60794.1080.39241.39910.16590.07190.1223-0.4434-0.1877-0.3169-0.1186-0.05420.0218-0.00270.05260.1092-0.203-0.0283-0.038520.2527-17.389293.5021
72.0479-0.1818-0.21811.03520.03890.4606-0.0322-0.22130.06460.25290.00840.0352-0.06950.0240.02380.09240.02560.0167-0.119-0.0288-0.105432.461-14.7559113.3596
80.4378-0.1317-0.117600.5177-0.3272-0.0043-0.0434-0.0131-0.00480.0034-0.03170.0080.12740.00090.18130.0061-0.0982-0.1481-0.0489-0.052361.4312-48.9636111.889
90.6026-0.78061.13870.4439-1.14122.66180.0680.2467-0.125-0.10290.00930.03180.0453-0.1151-0.07730.1124-0.026-0.0124-0.0841-0.04210.015349.6924-35.825388.4433
100.2538-0.2962-0.12832.38950.26981.9970.03520.1997-0.1044-0.1856-0.07670.0214-0.0605-0.1290.0415-0.11030.0039-0.0079-0.0087-0.0134-0.010447.4806-26.290185.0563
112.2041-0.13771.12070.01291.17981.7299-0.02260.4243-0.0474-0.0425-0.0176-0.2016-0.00710.09470.0401-0.03970.0294-0.0317-0.0546-0.03050.033155.4839-27.646989.8661
122.53880.9356-0.74813.5411-0.00691.97720.1516-0.21860.05210.4489-0.1473-0.2602-0.0120.1044-0.0044-0.1004-0.0256-0.0765-0.14010.1639-0.049799.6841-1.325419.1354
133.8520.3996-0.43440.8886-0.54370.8478-0.00370.53960.4781-0.1118-0.0958-0.22010.09020.16580.0995-0.0073-0.04250.0067-0.06340.1531-0.114385.60771.630.2634
14-0.15130.7079-0.47732.71832.36253.3436-0.0239-0.0457-0.0148-0.20540.1123-0.05510.15180.058-0.08840.06720.0815-0.0242-0.0365-0.0075-0.059669.4337-20.230925.1399
150.8605-0.01421.34191.7605-1.43394.2763-0.0214-0.0001-0.0117-0.10950.0554-0.0841-0.04410.0621-0.0339-0.09080.0173-0.0089-0.0388-0.0020.012773.1988-9.722228.9096
160.5193-0.6538-0.79582.0754-0.01971.6106-0.0247-0.23990.1243-0.18710.14090.22720.1344-0.0672-0.11620.0354-0.00590.0223-0.06220.0286-0.059165.0161-11.442725.1335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|1 - 182}
2X-RAY DIFFRACTION2{A|183 - 249}
3X-RAY DIFFRACTION3{A|250 - 381}
4X-RAY DIFFRACTION4{B|149 - 192}
5X-RAY DIFFRACTION5{B|193 - 261}
6X-RAY DIFFRACTION6{C|1 - 182}
7X-RAY DIFFRACTION7{C|183 - 381}
8X-RAY DIFFRACTION8{D|147 - 152}
9X-RAY DIFFRACTION9{D|153 - 187}
10X-RAY DIFFRACTION10{D|188 - 230}
11X-RAY DIFFRACTION11{D|231 - 260}
12X-RAY DIFFRACTION12{E|1 - 182}
13X-RAY DIFFRACTION13{E|183 - 380}
14X-RAY DIFFRACTION14{F|149 - 188}
15X-RAY DIFFRACTION15{F|189 - 230}
16X-RAY DIFFRACTION16{F|231 - 260}

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