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- PDB-7kcm: Full-length human mitochondrial Hsp90 (TRAP1) in complex with Sdh... -

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Basic information

Entry
Database: PDB / ID: 7kcm
TitleFull-length human mitochondrial Hsp90 (TRAP1) in complex with SdhB in the presence of AMP-PNP
Components
  • Heat shock protein 75 kDa, mitochondrial
  • Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
KeywordsCHAPERONE / Hsp90 / TRAP1 / SdhB / mitochondria
Function / homology
Function and homology information


translational attenuation / negative regulation of cellular respiration / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle ...translational attenuation / negative regulation of cellular respiration / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / Citric acid cycle (TCA cycle) / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / Maturation of TCA enzymes and regulation of TCA cycle / Respiratory electron transport / tumor necrosis factor receptor binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / 3 iron, 4 sulfur cluster binding / ubiquinone binding / proton motive force-driven mitochondrial ATP synthesis / negative regulation of reactive oxygen species biosynthetic process / chaperone-mediated protein folding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / cell periphery / ATP-dependent protein folding chaperone / mitochondrial membrane / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / unfolded protein binding / protein folding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / mitochondrial matrix / protein kinase binding / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
: / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal ...: / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Alpha-helical ferredoxin / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region 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 / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 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 / FE2/S2 (INORGANIC) CLUSTER / : / Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsLiu, Y.X. / 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: To Be Published
Title: Cryo-EM reveals the dynamic interplay between mitochondrial Hsp90 and SdhB folding intermediates
Authors: Liu, Y.X. / Agard, D.A. / Elnatan, D. / Sun, M. / Myasnikov, A.G.
History
DepositionOct 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

Deposited unit
A: Heat shock protein 75 kDa, mitochondrial
B: Heat shock protein 75 kDa, mitochondrial
C: Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,76810
Polymers163,4533
Non-polymers1,3157
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area17400 Å2
ΔGint-148 kcal/mol
Surface area55790 Å2

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Components

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Protein , 2 types, 3 molecules ABC

#1: Protein Heat shock protein 75 kDa, mitochondrial / HSP 75 / TNFR-associated protein 1 / Tumor necrosis factor type 1 receptor-associated protein / TRAP-1


Mass: 74177.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRAP1, HSP75 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12931
#2: Protein Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Iron-sulfur subunit of complex II / Ip


Mass: 15097.539 Da / Num. of mol.: 1 / Fragment: UNP residues 29-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SDHB, SDH, SDH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P21912

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Non-polymers , 4 types, 7 molecules

#3: 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
#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
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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Details

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: human Trap1 in complex with SdhB in the presence of AMP-PNP
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.162 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
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 material: COPPER / Grid mesh size: 300 divisions/in. / Grid 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: 72 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: CTFFIND / Category: CTF correction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57787 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
16XG6

6xg6

6XG61
21ZOY

1zoy

B1ZOY2
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 72.79 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00211034
ELECTRON MICROSCOPYf_angle_d0.514891
ELECTRON MICROSCOPYf_dihedral_angle_d16.3581496
ELECTRON MICROSCOPYf_chiral_restr0.041679
ELECTRON MICROSCOPYf_plane_restr0.0031890

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