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

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Basic information

Entry
Database: PDB / ID: 5aqm
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
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: 1.63 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,99814
Polymers111,9574
Non-polymers1,04110
Water18,3211017
1
A: HEAT SHOCK COGNATE 71 KDA PROTEIN
B: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5918
Polymers55,9792
Non-polymers6136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-0.4 kcal/mol
Surface area27100 Å2
MethodPQS
2
C: HEAT SHOCK COGNATE 71 KDA PROTEIN
D: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4076
Polymers55,9792
Non-polymers4284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint0.7 kcal/mol
Surface area26540 Å2
MethodPQS
Unit cell
Length a, b, c (Å)230.826, 40.851, 115.779
Angle α, β, γ (deg.)90.00, 90.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-2014-

HOH

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Components

#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: 42467.074 Da / Num. of mol.: 2 / Fragment: NUCLEOTIDE BINDING DOMAIN, RESIDUES 1-381 / Mutation: YES
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.: 2 / Fragment: RESIDUES 222-334
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
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 1017 / 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: 2.44 Å3/Da / Density % sol: 49.54 % / 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: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.63→57.89 Å / Num. obs: 124835 / % possible obs: 92.2 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 23.36 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 0.9 / % possible all: 58.1

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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: 1.63→57.89 Å / Cor.coef. Fo:Fc: 0.9539 / Cor.coef. Fo:Fc free: 0.9428 / SU R Cruickshank DPI: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.093 / SU Rfree Blow DPI: 0.09 / SU Rfree Cruickshank DPI: 0.087
RfactorNum. reflection% reflectionSelection details
Rfree0.1952 6185 4.95 %RANDOM
Rwork0.168 ---
obs0.1693 124833 91.85 %-
Displacement parametersBiso mean: 28.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.7191 Å20 Å26.1611 Å2
2--1.4953 Å20 Å2
3----2.2144 Å2
Refine analyzeLuzzati coordinate error obs: 0.208 Å
Refinement stepCycle: LAST / Resolution: 1.63→57.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7597 0 68 1017 8682
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017844HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9710603HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2819SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes227HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1135HARMONIC5
X-RAY DIFFRACTIONt_it7844HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion15.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1063SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10475SEMIHARMONIC4
LS refinement shellResolution: 1.63→1.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2282 264 4.59 %
Rwork0.2171 5484 -
all0.2176 5748 -
obs--57.96 %
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)
10.82530.10340.23420.8270.29390.85060.0391-0.08420.02580.0509-0.03010.05860.0281-0.0328-0.009-0.0511-0.0165-0.0166-0.0527-0.0210.0058-37.91971.101346.4162
20.88870.13160.64471.1556-0.03090.73040.0378-0.0412-0.0541-0.0357-0.03890.1370.1127-0.23050.0011-0.0566-0.0121-0.0434-0.0168-0.03070.0612-48.3283-2.296337.3448
31.68760.4419-0.12071.0564-0.00010.36470.03050.4055-0.0587-0.13160.0250.2798-0.0851-0.117-0.0555-0.03080.0368-0.08910.0417-0.0690.0213-41.0868-1.639519.52
42.4249-0.5570.67240.0159-1.10471.05040.03230.1023-0.2322-0.1660.0170.3061-0.0837-0.1113-0.0493-0.04090.0168-0.1074-0.022-0.06910.1131-40.0618-8.607425.1811
53.0718-0.78540.69370.66380.23021.2018-0.0449-0.1941-0.0838-0.08220.01970.1427-0.081-0.09830.02520.0087-0.02370.00180.0022-0.0152-0.0488-8.7747-3.066835.1617
61.39690.26990.37660.94530.49220.9621-0.08760.1541-0.0084-0.01320.02390.0377-0.06480.06740.0638-0.022-0.01960.00090.0095-0.0073-0.0629-9.24144.255738.8563
74.26550.68961.46270.41170.28661.14590.02710.5186-0.3987-0.12870.03860.0344-0.0040.1766-0.0657-0.0340.01-0.04070.0052-0.0958-0.0442-24.7112-5.545122.2203
83.5809-1.203-1.12851.09980.83471.83430.06510.42110.1841-0.1711-0.02940.0525-0.0851-0.0446-0.0357-0.0084-0.0112-0.0458-0.00970.0017-0.0355-35.4122.575421.8267
91.11331.3436-2.31721.7917-2.88926.01940.1813-0.10920.3159-0.03110.0520.236-0.0610.1863-0.2333-0.04920.0080.0156-0.0137-0.05920.0091-10.029920.676853.3106
100.93850.173-0.45950.69310.151.7518-0.0116-0.15110.1732-0.06160.04810.08640.2324-0.0657-0.0365-0.03640.00330.00510.0637-0.03460.0156-13.899110.271857.5717
111.36951.0056-1.59092.2915-2.51854.63650.0647-0.15790.2212-0.13130.01090.06640.05650.2551-0.0756-0.0977-0.0115-0.0003-0.0153-0.0341-0.0673-5.82811.671754.1721
121.11780.35960.48132.57330.40321.29070.0943-0.10320.01120.3047-0.16620.01410.0955-0.06520.0719-0.0552-0.0317-0.0036-0.0901-0.0295-0.0464-38.712518.169-5.6404
131.34590.21040.20070.44550.20170.36240.00150.177-0.0657-0.0619-0.03590.1224-0.0084-0.03410.0344-0.03550.0029-0.0239-0.0424-0.0389-0.0189-31.76115.7166-24.6941
140.87581.0141-0.53192.5711-2.61673.86430.1982-0.12440.12440.2986-0.01650.1275-0.1408-0.007-0.18170.0327-0.00240.045-0.0629-0.0647-0.0331-11.088137.8538-3.0593
151.24890.5892-0.17932.5644-0.62091.65220.0993-0.25540.00490.2069-0.06720.05790.1351-0.0612-0.0321-0.0475-0.0032-0.0033-0.0085-0.0357-0.0118-13.797427.18592.3503
162.03480.7664-1.4861.7516-1.99233.66690.0913-0.26840.0107-0.1386-0.093-0.08170.17450.36190.0017-0.0608-0.01860.0018-0.0563-0.0441-0.058-6.026128.5333-2.5273

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