[English] 日本語
Yorodumi
- PDB-5aqi: Fragment-based screening of HSP70 sheds light on the functional r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aqi
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 / protein transmembrane import into intracellular organelle / positive regulation of lysosomal membrane permeability / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity ...lumenal side of lysosomal membrane / regulation of protein import / protein transmembrane import into intracellular organelle / positive regulation of lysosomal membrane permeability / negative regulation of supramolecular fiber organization / positive regulation of protein refolding / prostaglandin binding / chaperone-mediated autophagy translocation complex disassembly / slow axonal transport / clathrin-uncoating ATPase activity / lysosomal matrix / A1 adenosine receptor binding / late endosomal microautophagy / protein carrier chaperone / response to nickel cation / Respiratory syncytial virus genome transcription / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Lipophagy / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / adenyl-nucleotide exchange factor activity / response to odorant / C3HC4-type RING finger domain binding / synaptic vesicle uncoating / positive regulation by host of viral genome replication / positive regulation of smooth muscle cell apoptotic process / clathrin coat disassembly / CHL1 interactions / ATP-dependent protein disaggregase activity / negative regulation of NLRP3 inflammasome complex assembly / regulation of protein complex stability / photoreceptor ribbon synapse / maintenance of postsynaptic specialization structure / membrane organization / glycinergic synapse / Prp19 complex / presynaptic cytosol / protein folding chaperone complex / positive regulation of mRNA splicing, via spliceosome / postsynaptic specialization membrane / intermediate filament / regulation of postsynapse organization / Lysosome Vesicle Biogenesis / negative regulation of cardiac muscle cell apoptotic process / chaperone-mediated autophagy / cellular response to steroid hormone stimulus / postsynaptic cytosol / Golgi Associated Vesicle Biogenesis / non-chaperonin molecular chaperone ATPase / phosphatidylserine binding / positive regulation of proteolysis / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / regulation of protein-containing complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / estrous cycle / Protein methylation / ATP metabolic process / positive regulation of phagocytosis / forebrain development / skeletal muscle tissue development / heat shock protein binding / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to cadmium ion / cellular response to starvation / autophagosome / photoreceptor inner segment / lysosomal lumen / mRNA Splicing - Major Pathway / cerebellum development / kidney development / dendritic shaft / response to activity / response to progesterone / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / spliceosomal complex / peptide binding / ADP binding / Late endosomal microautophagy / regulation of protein stability / PKR-mediated signaling / terminal bouton / mRNA splicing, via spliceosome / cellular response to hydrogen peroxide / Chaperone Mediated Autophagy / positive regulation of T cell mediated cytotoxicity / protein import into nucleus / G1/S transition of mitotic cell cycle / unfolded protein binding / late endosome / melanosome / protein folding / synaptic vesicle / MHC class II protein complex binding / response to estradiol
Similarity search - Function
BAG domain / Molecular chaperone regulator BAG / BAG domain superfamily / 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 / Molecular chaperone regulator BAG / BAG domain superfamily / 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 / Nucleotidyltransferase; domain 5 / Ubiquitin homologues / 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
ADENINE / 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: 1.98 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: 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.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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)113,35520
Polymers111,8374
Non-polymers1,51816
Water4,594255
1
A: HEAT SHOCK COGNATE 71 KDA PROTEIN
B: BAG FAMILY MOLECULAR CHAPERONE REGULATOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,85512
Polymers55,9192
Non-polymers93610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)56,5008
Polymers55,9192
Non-polymers5826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)229.200, 41.120, 115.970
Angle α, β, γ (deg.)90.00, 90.58, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#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.: 2 / 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.: 2 / 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

-
Non-polymers , 4 types, 271 molecules

#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H5N5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.65 % / Description: COMPLETENESS IN INNER SHELL 97.8
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9775
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9775 Å / Relative weight: 1
ReflectionResolution: 1.98→40.96 Å / Num. obs: 34725 / % possible obs: 45.7 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 20.88 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.4
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 0.5 / % possible all: 13

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HX1

1hx1


Resolution: 1.98→40.96 Å / Cor.coef. Fo:Fc: 0.9333 / Cor.coef. Fo:Fc free: 0.8758 / SU R Cruickshank DPI: 0.691 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.706 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.297
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1776 5.12 %RANDOM
Rwork0.1717 ---
obs0.1753 34721 45.45 %-
Displacement parametersBiso mean: 30.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.6605 Å20 Å22.1285 Å2
2--1.4376 Å20 Å2
3----4.0981 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 1.98→40.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7517 0 98 255 7870
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017716HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1510418HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2729SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes220HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1137HARMONIC5
X-RAY DIFFRACTIONt_it7716HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion18.7
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1050SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9114SEMIHARMONIC4
LS refinement shellResolution: 1.98→2.04 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.3073 52 6.07 %
Rwork0.2417 805 -
all0.2456 857 -
obs--13.03 %
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)
11.78370.73661.65962.13430.94934.0642-0.08360.07760.2023-0.0407-0.07390.0721-0.4489-0.13210.15750.13060.048-0.1068-0.0866-0.0063-0.1753-39.9812-9.325537.8021
21.12151.11160.81341.68750.66083.64980.059-0.14650.00220.27280.0551-0.01430.1116-0.0042-0.11410.04530.0137-0.0907-0.04080.0188-0.1072-33.1575-26.400652.1176
30.0244-0.09770.28971.7553-0.67641.6833-0.0763-0.2156-0.03170.2128-0.02060.1791-0.1749-0.43770.0969-0.04680.0229-0.06820.062-0.0274-0.1107-45.3297-19.377241.6546
42.5933-2.0018-1.44183.03090.82020.21150.03710.05440.0441-0.0996-0.02340.0402-0.1671-0.2963-0.01370.14790.0204-0.04990.0617-0.047-0.2777-41.6038-21.887118.1626
54.27570.82860.31350.09120.06390.40270.0004-0.3854-0.062-0.0996-0.06210.0934-0.0427-0.2090.06170.11280.0006-0.0728-0.0251-0.0104-0.092-25.0772-26.650429.7898
65.0951-1.9511.50563.71530.97712.7452-0.10760.0231-0.1026-0.0350.10050.15290.2308-0.10210.00710.092-0.104-0.0397-0.0751-0.0366-0.2406-11.1284-18.435940.1442
70.4273-0.11160.444700.45471.0301-0.0570.2821-0.0887-0.14780.0331-0.0338-0.11220.26140.02390.0907-0.0516-0.08250.0171-0.0412-0.1319-19.9091-23.022425.6126
83.3604-0.3241-1.20090.63460.57521.40030.00540.15350.2757-0.13080.0339-0.1157-0.1333-0.0351-0.03930.11680.0459-0.06740.0117-0.0124-0.1904-35.0996-17.99221.677
91.14010.3246-1.15870.93-0.11852.53720.0627-0.0980.1405-0.0155-0.05560.1781-0.1309-0.2484-0.0071-0.04780.0216-0.1047-0.0582-0.0685-0.0458-10.2633-0.133454.1245
101.21610.5-0.20441.36062.62612.01540.0138-0.0731-0.10820.284-0.0915-0.04150.1688-0.02420.07770.00590.0187-0.09260.0072-0.0157-0.1104-16.235-12.465962.8157
111.5899-0.54220.35841.36980.60090.0305-0.01340.0210.1091-0.10530.1617-0.22-0.15570.0013-0.14830.027-0.0172-0.0861-0.0284-0.0693-0.1497-5.1967-7.526850.453
121.18781.08880.36493.43720.64372.47640.1604-0.1192-0.13010.4302-0.2311-0.28590.1395-0.01580.0707-0.0031-0.0259-0.0563-0.0692-0.0129-0.1531-36.4883-3.2144-4.4276
131.47270.21020.26770.49370.25560.73430.02870.1671-0.0805-0.0024-0.07220.02590.0143-0.05350.04350.0638-0.0035-0.0604-0.0898-0.0441-0.1668-33.4159-3.8162-22.4092
141.16530.5514-0.86773.19270.06461.44860.0813-0.1771-0.04530.4691-0.0337-0.03730.02610.0081-0.04760.0246-0.0583-0.0863-0.041-0.0654-0.1376-10.771615.82190.34
151.12680.6635-0.14973.1355-0.14961.45520.0185-0.1255-0.01010.1057-0.0174-0.06490.01920.1094-0.0011-0.00510.033-0.0839-0.0723-0.0693-0.1413-10.11117.506-1.8185
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - 41 }
2X-RAY DIFFRACTION2{ A|42 - 110 }
3X-RAY DIFFRACTION3{ A|111 - 182 }
4X-RAY DIFFRACTION4{ A|183 - 201 }
5X-RAY DIFFRACTION5{ A|202 - 249 }
6X-RAY DIFFRACTION6{ A|250 - 275 }
7X-RAY DIFFRACTION7{ A|276 - 343 }
8X-RAY DIFFRACTION8{ A|344 - 381 }
9X-RAY DIFFRACTION9{ B|150 - 188 }
10X-RAY DIFFRACTION10{ B|189 - 223 }
11X-RAY DIFFRACTION11{ B|224 - 261 }
12X-RAY DIFFRACTION12{ C|1 - 115 }
13X-RAY DIFFRACTION13{ C|116 - 381 }
14X-RAY DIFFRACTION14{ D|150 - 192 }
15X-RAY DIFFRACTION15{ D|193 - 260 }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more