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- PDB-6xlc: Full-length Hsc82 bound to AMPPNP -

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Basic information

Entry
Database: PDB / ID: 6xlc
TitleFull-length Hsc82 bound to AMPPNP
ComponentsATP-dependent molecular chaperone HSC82
KeywordsCHAPERONE / Hsp90
Function / homology
Function and homology information


Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / box C/D snoRNP assembly / proteasome assembly ...Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / box C/D snoRNP assembly / proteasome assembly / Neutrophil degranulation / telomere maintenance / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / ATP-dependent molecular chaperone HSC82
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsLiu, Y.X. / Sun, M. / Myasnikov, A.G. / Elnatan, D. / Agard, D.A.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute United States
American Heart Association United States
CitationJournal: To Be Published
Title: Full-length Hsc82 bound to AMPPNP
Authors: Liu, Y.X. / Sun, M. / Myasnikov, A.G. / Elnatan, D. / Agard, D.A.
History
DepositionJun 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: ATP-dependent molecular chaperone HSC82
B: ATP-dependent molecular chaperone HSC82
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,0686
Polymers162,0072
Non-polymers1,0614
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area10440 Å2
ΔGint-81 kcal/mol
Surface area53050 Å2

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Components

#1: Protein ATP-dependent molecular chaperone HSC82 / 82 kDa heat shock cognate protein / Heat shock protein Hsp90 constitutive isoform


Mass: 81003.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HSC82, YMR186W, YM8010.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P15108
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / 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
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hsc82 bound to AMPPNP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 72 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17_3644refinement
PHENIX1.17_3644refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48464 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 43.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001210028
ELECTRON MICROSCOPYf_angle_d0.345113538
ELECTRON MICROSCOPYf_chiral_restr0.03751538
ELECTRON MICROSCOPYf_plane_restr0.00221730
ELECTRON MICROSCOPYf_dihedral_angle_d18.29381320

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