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- PDB-6b1n: Disrupted hydrogen bond network impairs ATPase activity in an Hsc... -

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Basic information

Entry
Database: PDB / ID: 6b1n
TitleDisrupted hydrogen bond network impairs ATPase activity in an Hsc70 cysteine mutant
ComponentsHeat shock protein family A (Hsp70) member 8
KeywordsCHAPERONE / Hsp70 family member / ATPase
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 / late endosomal microautophagy / response to odorant / positive regulation by host of viral genome replication / synaptic vesicle uncoating / C3HC4-type RING finger domain binding / 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 / Clathrin-mediated endocytosis / protein-macromolecule adaptor activity
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-5'-DIPHOSPHATE / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesHomo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsO'Donnell, J.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105958 United States
CitationJournal: Biochemistry / Year: 2018
Title: Disrupted Hydrogen-Bond Network and Impaired ATPase Activity in an Hsc70 Cysteine Mutant.
Authors: O'Donnell, J.P. / Marsh, H.M. / Sondermann, H. / Sevier, C.S.
History
DepositionSep 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock protein family A (Hsp70) member 8
B: Heat shock protein family A (Hsp70) member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,81713
Polymers88,2702
Non-polymers1,54811
Water14,520806
1
A: Heat shock protein family A (Hsp70) member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7705
Polymers44,1351
Non-polymers6364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heat shock protein family A (Hsp70) member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0478
Polymers44,1351
Non-polymers9127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.388, 77.598, 75.523
Angle α, β, γ (deg.)90.00, 101.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heat shock protein family A (Hsp70) member 8


Mass: 44134.797 Da / Num. of mol.: 2 / Mutation: C17W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo Sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P11142
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: NaCl, Tris, PEG 3350, MgCl2, ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.7→47.3 Å / Num. obs: 87978 / % possible obs: 96.3 % / Redundancy: 4.3 % / CC1/2: 0.993 / Net I/σ(I): 7.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B1I

6b1i


Resolution: 1.8→37.048 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.18
RfactorNum. reflection% reflection
Rfree0.2257 1748 2.29 %
Rwork0.1844 --
obs0.1854 76460 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→37.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5809 0 98 806 6713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126052
X-RAY DIFFRACTIONf_angle_d1.1938201
X-RAY DIFFRACTIONf_dihedral_angle_d14.4872226
X-RAY DIFFRACTIONf_chiral_restr0.064934
X-RAY DIFFRACTIONf_plane_restr0.0071064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8530.32881510.28046122X-RAY DIFFRACTION98
1.853-1.91280.30291420.24386159X-RAY DIFFRACTION99
1.9128-1.98110.2841520.22876206X-RAY DIFFRACTION99
1.9811-2.06040.27411360.21776136X-RAY DIFFRACTION99
2.0604-2.15420.24181430.19116229X-RAY DIFFRACTION99
2.1542-2.26780.2261470.17526214X-RAY DIFFRACTION99
2.2678-2.40980.22511460.18056210X-RAY DIFFRACTION99
2.4098-2.59580.23491420.18486259X-RAY DIFFRACTION100
2.5958-2.8570.22111460.17736260X-RAY DIFFRACTION100
2.857-3.27020.22381450.17686286X-RAY DIFFRACTION100
3.2702-4.11920.17111460.15436307X-RAY DIFFRACTION100
4.1192-37.05550.19341520.1656324X-RAY DIFFRACTION99
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)
12.49230.7203-0.63231.5675-0.27411.79690.05090.13160.0226-0.1776-0.0674-0.09960.00950.10210.02230.14310.0285-0.01350.09590.01340.054862.359115.240562.4402
20.7562-0.02550.84011.28140.14831.4214-0.0715-0.05660.09-0.0075-0.02320.092-0.0971-0.14390.09120.12060.0168-0.03350.1032-0.00340.091950.765619.986973.9226
30.9867-0.6596-0.16131.23130.09960.5854-0.0638-0.04280.05370.07610.0388-0.11020.03050.02810.01060.1383-0.008-0.04490.07690.00650.072267.42719.116183.3995
42.2257-0.6203-0.4891.78020.47612.48390.02530.09490.0258-0.0191-0.1348-0.3018-0.00330.2160.06480.1127-0.0081-0.04550.10520.04880.1586100.427424.5739110.6647
50.9152-0.13720.46451.1569-0.17450.69460.0117-0.0961-0.0440.1182-0.0163-0.00880.0607-0.0525-0.0340.1522-0.0173-0.04940.09790.01910.099385.185819.1402119.1252
60.62880.2555-0.11741.153-0.6361.1350.01690.0597-0.0054-0.07820.03920.02780.0705-0.0327-0.0470.12990.011-0.05450.0785-0.00140.090281.070830.3804100.7442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 0:119 )A0 - 119
2X-RAY DIFFRACTION2( CHAIN A AND RESID 120:231 )A120 - 231
3X-RAY DIFFRACTION3( CHAIN A AND RESID 232:381 )A232 - 381
4X-RAY DIFFRACTION4( CHAIN B AND RESID 0:126 )B0 - 126
5X-RAY DIFFRACTION5( CHAIN B AND RESID 127:231 )B127 - 231
6X-RAY DIFFRACTION6( CHAIN B AND RESID 232:381 )B232 - 381

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