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

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Basic information

Entry
Database: PDB / ID: 5aqo
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 / positive regulation of protein refolding / prostaglandin binding / positive regulation of lysosomal membrane permeability / lysosomal matrix / A1 adenosine receptor binding / protein carrier chaperone / response to nickel cation ...lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / positive regulation of lysosomal membrane permeability / lysosomal matrix / A1 adenosine receptor binding / protein carrier chaperone / response to nickel cation / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Respiratory syncytial virus genome transcription / protein transmembrane import into intracellular organelle / 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 / response to odorant / positive regulation by host of viral genome replication / synaptic vesicle uncoating / C3HC4-type RING finger domain binding / positive regulation of smooth muscle cell apoptotic process / negative regulation of NLRP3 inflammasome complex assembly / clathrin coat disassembly / ATP-dependent protein disaggregase activity / CHL1 interactions / regulation of protein complex stability / photoreceptor ribbon synapse / maintenance of postsynaptic specialization structure / membrane organization / Prp19 complex / glycinergic synapse / presynaptic cytosol / postsynaptic specialization membrane / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic cytosol / regulation of postsynapse organization / negative regulation of cardiac muscle cell apoptotic process / Lysosome Vesicle Biogenesis / intermediate filament / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / Golgi Associated Vesicle Biogenesis / phosphatidylserine binding / non-chaperonin molecular chaperone ATPase / positive regulation of proteolysis / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / estrous cycle / Regulation of HSF1-mediated heat shock response / regulation of protein-containing complex assembly / autophagosome / Attenuation phase / Protein methylation / ATP metabolic process / protein folding chaperone / skeletal muscle tissue development / positive regulation of phagocytosis / forebrain development / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to cadmium ion / cellular response to starvation / photoreceptor inner segment / lysosomal lumen / mRNA Splicing - Major Pathway / cerebellum development / dendritic shaft / response to activity / kidney development / AUF1 (hnRNP D0) binds and destabilizes mRNA / response to progesterone / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / peptide binding / spliceosomal complex / Late endosomal microautophagy / regulation of protein stability / PKR-mediated signaling / terminal bouton / ADP binding / mRNA splicing, via spliceosome / Chaperone Mediated Autophagy / cellular response to hydrogen peroxide / G1/S transition of mitotic cell cycle / positive regulation of T cell mediated cytotoxicity / protein import into nucleus / unfolded protein binding / melanosome / synaptic vesicle / late endosome / protein folding / response to estradiol / MHC class II protein complex binding
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 / Nucleotidyltransferase; domain 5 / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
6-METHYLQUINAZOLIN-4-AMINE / 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: 2.12 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)170,87439
Polymers167,7566
Non-polymers3,11933
Water12,088671
1
A: HEAT SHOCK COGNATE 71 KDA PROTEIN
B: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,86612
Polymers55,9192
Non-polymers94710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-1.2 kcal/mol
Surface area21650 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)57,23416
Polymers55,9192
Non-polymers1,31614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint1.9 kcal/mol
Surface area22160 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)56,77411
Polymers55,9192
Non-polymers8559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint2.4 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.611, 40.680, 205.580
Angle α, β, γ (deg.)90.00, 122.72, 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) / Plasmid: PGEX-6P-1 / 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 TO 334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): AI / References: UniProt: Q99933

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Non-polymers , 6 types, 704 molecules

#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CWS / 6-METHYLQUINAZOLIN-4-AMINE


Mass: 159.188 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H9N3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.45 Å3/Da / Density % sol: 49.79 % / 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: May 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.12→98.27 Å / Num. obs: 93349 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 40.04 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.2 / % possible all: 97.5

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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: 2.12→98.27 Å / Cor.coef. Fo:Fc: 0.9471 / Cor.coef. Fo:Fc free: 0.9349 / SU R Cruickshank DPI: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.202 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 4624 4.95 %RANDOM
Rwork0.1797 ---
obs0.1812 93343 99.47 %-
Displacement parametersBiso mean: 51.16 Å2
Baniso -1Baniso -2Baniso -3
1--4.8247 Å20 Å2-7.5902 Å2
2--6.2719 Å20 Å2
3----1.4473 Å2
Refine analyzeLuzzati coordinate error obs: 0.281 Å
Refinement stepCycle: LAST / Resolution: 2.12→98.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11197 0 201 671 12069
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111568HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0415629HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4050SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes313HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1723HARMONIC5
X-RAY DIFFRACTIONt_it11568HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.9
X-RAY DIFFRACTIONt_other_torsion16.32
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1578SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14016SEMIHARMONIC4
LS refinement shellResolution: 2.12→2.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2444 326 4.86 %
Rwork0.2143 6376 -
all0.2157 6702 -
obs--98.31 %
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)
12.08120.4033-0.6353.3687-0.45681.3340.1878-0.11350.1385-0.1494-0.2842-0.7072-0.09820.10720.0964-0.13450.0430.0915-0.19560.20830.0945216.2536-1.929618.6354
24.31880.2512-1.08361.0538-0.42520.94490.15880.64970.478-0.4094-0.1986-0.36960.0093-0.00430.03980.03970.05430.1601-0.08180.1966-0.1527202.78560.2840.148
30.33640.93270.79942.56091.89482.0378-0.0105-0.0250.0189-0.11670.1150.06080.12290.0846-0.10450.03430.07410.00090.01780.0153-0.0956186.3514-21.34624.7337
40.48780.40490.21982.3959-0.36360.498-0.05770.02870.0534-0.14010.0712-0.11650.01680.071-0.0135-0.04960.04270.00930.03260.0145-0.0089189.9005-10.892728.3118
51.6841-1.1426-1.8653.96031.92951.7370.0305-0.25320.2229-0.11280.13310.1029-0.0212-0.0452-0.1636-0.02990.00940.0121-0.05540.0186-0.0729182.0836-12.32125.2676
63.15190.2958-1.48743.43630.10652.49710.02030.0275-0.275-0.3121-0.1024-0.0160.1037-0.03010.0821-0.0526-0.02530.068-0.10830.02490.0419219.7016-27.814172.0236
70.5730.3036-0.50026.04690.30821.0169-0.0389-0.1059-0.01040.1269-0.06810.531-0.1473-0.12970.1069-0.018-0.03960.0817-0.0560.01240.0906210.6989-12.400683.4459
8-0.5769-1.63811.53972.5931.04533.8004-0.0245-0.23770.06920.1855-0.0650.1270.00820.00660.08960.0102-0.02070.1086-0.11650.00710.0277213.3739-7.923689.7312
90.99750.2258-0.06512.50320.18471.2670.021-0.1235-0.05140.2169-0.187-0.0802-0.09730.15270.166-0.0492-0.05120.0732-0.08020.0580.0262222.5668-20.256680.207
101.59010.2911-1.16272.1031-0.4244-0.23280.0741-0.11890.1248-0.1164-0.0642-0.3282-0.20580.1684-0.0099-0.0325-0.07740.0669-0.05710.06330.0818228.2782-15.115172.8456
112.94510.90950.60931.9791.00311.4898-0.09340.06140.1302-0.3320.0788-0.2672-0.06460.12990.01460.0723-0.07110.0995-0.06780.0888-0.002222.9014-11.798557.1418
121.46670.1662-1.902200.42992.36820.0543-0.1056-0.025-0.08030.06270.12690.0903-0.0772-0.1170.04530.0013-0.0958-0.15190.03360.0557189.2694-13.23565.1216
131.9458-0.3631-1.37292.2997-0.39143.6643-0.06010.03720.1349-0.09860.1080.0409-0.04740.0825-0.0479-0.0268-0.0518-0.073-0.09160.01830.0272191.77-18.687870.3576
143.20241.3914-1.18841.4811-0.67951.4394-0.12690.4090.3343-0.3530.10740.1401-0.0884-0.07120.01950.0611-0.0315-0.0422-0.11540.0619-0.0323202.0454-13.967357.4815
152.7942-0.36480.69671.8428-0.17920.8784-0.14410.3492-0.0182-0.550.0626-0.1375-0.05160.02530.08150.1113-0.07710.0927-0.07370.0298-0.0672217.5666-19.345355.8529
160.55830.59151.28710.88892.50444.06160.1191-0.118-0.23510.02160.077-0.03380.1437-0.0038-0.19610.03010.0016-0.0372-0.09140.07390.0852188.5205-37.234482.695
170.4542-0.0774-0.14641.3003-0.44442.95110.0527-0.1285-0.13580.09030.00270.0405-0.07710.0891-0.0554-0.1014-0.0053-0.0195-0.0140.03870.033191.9354-26.695888.4061
181.684-0.1934-0.1380.2826-0.50232.4138-0.0059-0.2345-0.0996-0.0272-0.02190.148-0.0387-0.13890.0278-0.0574-0.0051-0.0169-0.05930.04110.0473183.8352-28.050183.3867
191.1-0.1181-0.31982.06020.21511.18190.06220.16090.0146-0.3099-0.0128-0.0310.0272-0.0696-0.04950.03-0.11280.1528-0.1325-0.0937-0.0281136.647-0.216341.0018
204.86110.4986-0.02154.15450.4177-0.17910.03210.01020.0971-0.0459-0.05530.28710.1648-0.17390.02320.0104-0.1120.1727-0.066-0.1068-0.0409135.61265.821563.4097
211.4317-0.0435-0.64830.54870.17610.4303-0.0209-0.1680.02740.07810.05030.00090.11460.104-0.02940.0819-0.07450.115-0.0552-0.0845-0.0475155.63780.518857.4052
221.5975-1.04491.73420.2523-1.15283.74780.06060.369-0.3555-0.1782-0.08320.0670.1643-0.06910.02270.0441-0.06670.0866-0.0504-0.1774-0.0391165.596-21.073533.3288
23-0.3263-0.39680.72111.29430.11712.11360.0412-0.0016-0.2468-0.2528-0.12740.0986-0.0503-0.06110.08620.0522-0.06790.12880.0098-0.165-0.0428162.3828-10.126328.4325
241.08451.47250.46580.77630.35232.0246-0.19220.3807-0.0921-0.2610.1403-0.12870.1160.16560.05190.0605-0.09510.1917-0.011-0.1332-0.0904170.5977-11.735532.106

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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