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- PDB-6xg6: Full-length human mitochondrial Hsp90 (TRAP1) with ADP-BeF3 -

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Basic information

Entry
Database: PDB / ID: 6xg6
TitleFull-length human mitochondrial Hsp90 (TRAP1) with ADP-BeF3
ComponentsHeat shock protein 75 kDa, mitochondrial, Fibronectin binding protein fusion
KeywordsCHAPERONE / Hsp90
Function / homology
Function and homology information


translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space ...translational attenuation / negative regulation of cellular respiration / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / chaperone-mediated protein folding / negative regulation of reactive oxygen species biosynthetic process / cell periphery / ATP-dependent protein folding chaperone / mitochondrial intermembrane space / unfolded protein binding / protein folding / mitochondrial inner membrane / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane
Similarity search - Function
Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / HSP90, C-terminal domain ...Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / 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-, 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / : / Heat shock protein 75 kDa, mitochondrial / Fibronectin binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pyogenes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu, Y.X. / Wang, F. / Agard, D.A.
Funding support United States, 6items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
American Heart Association18POST33990362 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118099 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U54CA209891 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)U01MH115747 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19AI135990 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: General and robust covalently linked graphene oxide affinity grids for high-resolution cryo-EM.
Authors: Feng Wang / Yanxin Liu / Zanlin Yu / Sam Li / Shengjie Feng / Yifan Cheng / David A Agard /
Abstract: Affinity grids have great potential to facilitate rapid preparation of even quite impure samples in single-particle cryo-electron microscopy (EM). Yet despite the promising advances of affinity grids ...Affinity grids have great potential to facilitate rapid preparation of even quite impure samples in single-particle cryo-electron microscopy (EM). Yet despite the promising advances of affinity grids over the past decades, no single strategy has demonstrated general utility. Here we chemically functionalize cryo-EM grids coated with mostly one or two layers of graphene oxide to facilitate affinity capture. The protein of interest is tagged using a system that rapidly forms a highly specific covalent bond to its cognate catcher linked to the grid via a polyethylene glycol (PEG) spacer. Importantly, the spacer keeps particles away from both the air-water interface and the graphene oxide surface, protecting them from potential denaturation and rendering them sufficiently flexible to avoid preferential sample orientation concerns. Furthermore, the PEG spacer successfully reduces nonspecific binding, enabling high-resolution reconstructions from a much cruder lysate sample.
History
DepositionJun 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 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: Heat shock protein 75 kDa, mitochondrial, Fibronectin binding protein fusion
B: Heat shock protein 75 kDa, mitochondrial, Fibronectin binding protein fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,30210
Polymers174,1892
Non-polymers1,1138
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area13850 Å2
ΔGint-87 kcal/mol
Surface area50740 Å2

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Components

#1: Protein Heat shock protein 75 kDa, mitochondrial, Fibronectin binding protein fusion / HSP 75 / TNFR-associated protein 1 / Tumor necrosis factor type 1 receptor-associated protein / ...HSP 75 / TNFR-associated protein 1 / Tumor necrosis factor type 1 receptor-associated protein / TRAP-1 / Thioester-forming surface-anchored protein


Mass: 87094.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Streptococcus pyogenes (bacteria)
Gene: TRAP1, HSP75, fba2, E0F66_06355, GQY31_00620 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12931, UniProt: Q8G9G1
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
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: Trap1 dimer with ADP-BeF3 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.147 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Streptococcus pyogenes (bacteria)1314
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
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: 69 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_refinedev_3965refinement
PHENIXdev_3965refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70998 / 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: 58.1 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00189993
ELECTRON MICROSCOPYf_angle_d0.484713480
ELECTRON MICROSCOPYf_chiral_restr0.0381519
ELECTRON MICROSCOPYf_plane_restr0.00431714
ELECTRON MICROSCOPYf_dihedral_angle_d16.21761356

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