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- PDB-6b1m: Disrupted hydrogen bond network impairs ATPase activity in an Hsc... -

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Basic information

Entry
Database: PDB / ID: 6b1m
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 / chaperone-mediated autophagy translocation complex disassembly / protein carrier chaperone / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Respiratory syncytial virus genome transcription / Lipophagy / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy ...lumenal side of lysosomal membrane / regulation of protein import / negative regulation of supramolecular fiber organization / chaperone-mediated autophagy translocation complex disassembly / protein carrier chaperone / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / Respiratory syncytial virus genome transcription / Lipophagy / GABA synthesis, release, reuptake and degradation / protein targeting to lysosome involved in chaperone-mediated autophagy / clathrin coat disassembly / C3HC4-type RING finger domain binding / negative regulation of NLRP3 inflammasome complex assembly / CHL1 interactions / regulation of protein complex stability / ATP-dependent protein disaggregase activity / membrane organization / protein folding chaperone complex / Lysosome Vesicle Biogenesis / cellular response to steroid hormone stimulus / Golgi Associated Vesicle Biogenesis / chaperone-mediated autophagy / non-chaperonin molecular chaperone ATPase / : / Prp19 complex / Regulation of HSF1-mediated heat shock response / HSF1-dependent transactivation / response to unfolded protein / regulation of protein-containing complex assembly / Attenuation phase / ATP metabolic process / Protein methylation / heat shock protein binding / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / mRNA Splicing - Major Pathway / lysosomal lumen / cellular response to starvation / AUF1 (hnRNP D0) binds and destabilizes mRNA / spliceosomal complex / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / Late endosomal microautophagy / regulation of protein stability / PKR-mediated signaling / mRNA splicing, via spliceosome / Chaperone Mediated Autophagy / MHC class II protein complex binding / unfolded protein binding / melanosome / protein folding / Clathrin-mediated endocytosis / protein-folding chaperone binding / protein refolding / protein-macromolecule adaptor activity / secretory granule lumen / Interleukin-4 and Interleukin-13 signaling / blood microparticle / ficolin-1-rich granule lumen / positive regulation of cell migration / cadherin binding / receptor ligand activity / ribonucleoprotein complex / lysosomal membrane / focal adhesion / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation / nucleolus / enzyme binding / ATP hydrolysis activity / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Heat shock cognate 71 kDa protein
Similarity search - Component
Biological speciesHomo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,5158
Polymers88,2702
Non-polymers1,2456
Water15,385854
1
B: Heat shock protein family A (Hsp70) member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6653
Polymers44,1351
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Heat shock protein family A (Hsp70) member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8495
Polymers44,1351
Non-polymers7154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.809, 78.253, 75.855
Angle α, β, γ (deg.)90.00, 101.42, 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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: NaCl, Tris, PEG 3350, MgCl2, AppNHp

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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: 1.8→47.4 Å / Num. obs: 74694 / % possible obs: 95.9 % / Redundancy: 4.1 % / Net I/σ(I): 9.5

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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: 1.9→40.526 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.67
RfactorNum. reflection% reflection
Rfree0.2296 1781 2.68 %
Rwork0.1794 --
obs0.1807 66355 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→40.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5808 0 76 854 6738
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056096
X-RAY DIFFRACTIONf_angle_d0.7428289
X-RAY DIFFRACTIONf_dihedral_angle_d13.6242249
X-RAY DIFFRACTIONf_chiral_restr0.045951
X-RAY DIFFRACTIONf_plane_restr0.0041081
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.34381450.28544678X-RAY DIFFRACTION94
1.9514-2.00880.33931310.25634934X-RAY DIFFRACTION100
2.0088-2.07360.27721280.2184935X-RAY DIFFRACTION100
2.0736-2.14770.23011430.19414975X-RAY DIFFRACTION100
2.1477-2.23370.25791330.18395012X-RAY DIFFRACTION100
2.2337-2.33540.24051360.17864919X-RAY DIFFRACTION100
2.3354-2.45850.22111360.18085016X-RAY DIFFRACTION100
2.4585-2.61250.23891400.18494998X-RAY DIFFRACTION100
2.6125-2.81420.241380.18174960X-RAY DIFFRACTION100
2.8142-3.09730.20671320.18155029X-RAY DIFFRACTION100
3.0973-3.54520.24011410.16254992X-RAY DIFFRACTION100
3.5452-4.46570.19231380.14375031X-RAY DIFFRACTION100
4.4657-40.53480.17741400.15595095X-RAY DIFFRACTION100
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)
12.4838-0.1637-0.80651.41170.35792.57830.06470.161-0.0707-0.0591-0.1257-0.24480.01640.15920.03380.09880.0079-0.01120.10940.03960.1494100.461622.462110.5148
21.09980.1260.22531.3754-0.1720.98740.071-0.0982-0.08380.113-0.03330.01880.1191-0.0711-0.02930.1079-0.005-0.00230.08020.0140.082186.238217.6738119.3936
30.64860.0429-0.17361.0697-0.68071.33010.04960.0626-0.0137-0.10060.02830.00650.0811-0.0168-0.0630.09580.0065-0.01480.0645-0.00750.085981.366328.6807100.9106
42.57860.429-0.66451.4239-0.06811.74520.03770.15180.0081-0.2052-0.0295-0.1575-0.05020.1110.01550.14630.01180.01970.09970.00390.097562.196213.177262.4745
50.5573-0.00720.60761.36120.18661.1962-0.0778-0.07620.1259-0.0174-0.03290.1375-0.1301-0.20410.08040.09330.02020.00370.1094-0.00450.098950.357918.278675.1924
61.6649-0.9157-0.35651.24490.0320.5969-0.0785-0.0601-0.02990.00630.0396-0.07290.03090.07860.03550.1124-0.0096-0.00010.07320.01040.070267.30667.000783.7744
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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