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- EMDB-22918: Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of A... -

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Basic information

Entry
Database: EMDB / ID: EMD-22918
TitleTetrameric human mitochondrial Hsp90 (TRAP1) in the presence of AMP-PNP
Map data
Sample
  • Complex: Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of AMP-PNP
    • Protein or peptide: Heat shock protein 75 kDa, mitochondrial, SpyCatcher
    • Protein or peptide: Heat shock protein 75 kDa, mitochondrial, SpyTag, Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (chimera)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
KeywordsHsp90 / CHAPERONE / TRAP1 / SdhB / mitochondria / SpyTag / SpyCatcher
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
Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial / Heat shock protein 75 kDa, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLiu YX / Agard DA
Funding support United States, 6 items
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 analysis of human mitochondrial Hsp90 in multiple tetrameric states
Authors: Liu YX / Agard DA / Elnatan D / Sun M / Larson AG
History
DepositionNov 1, 2020-
Header (metadata) releaseNov 3, 2021-
Map releaseNov 3, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7klu
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22918.png

Downloads & links

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Map

FileDownload / File: emd_22918.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 271.616 Å		0.85 Å/pix.
x 320 pix.
= 271.616 Å		0.85 Å/pix.
x 320 pix.
= 271.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8488 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.032109138 - 0.0730181
Average (Standard dev.)-0.000027474734 (±0.0025653187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 271.616 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.84880.84880.8488
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z271.616271.616271.616
α/β/γ90.00090.00090.000
start NX/NY/NZ799196
NX/NY/NZ149138117
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0320.073-0.000

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Supplemental data

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Sample components

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Entire : Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of A...

EntireName: Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of AMP-PNP
Components
  • Complex: Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of AMP-PNP
    • Protein or peptide: Heat shock protein 75 kDa, mitochondrial, SpyCatcher
    • Protein or peptide: Heat shock protein 75 kDa, mitochondrial, SpyTag, Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (chimera)
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of A...

SupramoleculeName: Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of AMP-PNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: Heat shock protein 75 kDa, mitochondrial, SpyCatcher

MacromoleculeName: Heat shock protein 75 kDa, mitochondrial, SpyCatcher / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 87.094617 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEME IHLQTNAEKG TITIQDTGIG MTQEELVSNL GTIARSGSKA FLDALQNQAE ASSKIIGQFG VGFYSAFMVA D RVEVYSRS ...String:
GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEME IHLQTNAEKG TITIQDTGIG MTQEELVSNL GTIARSGSKA FLDALQNQAE ASSKIIGQFG VGFYSAFMVA D RVEVYSRS AAPGSLGYQW LSDGSGVFEI AEASGVRTGT KIIIHLKSDC KEFSSEARVR DVVTKYSNFV SFPLYLNGRR MN TLQAIWM MDPKDVGEWQ HEEFYRYVAQ AHDKPRYTLH YKTDAPLNIR SIFYVPDMKP SMFDVSRELG SSVALYSRKV LIQ TKATDI LPKWLRFIRG VVDSEDIPLN LSRELLQESA LIRKLRDVLQ QRLIKFFIDQ SKKDAEKYAK FFEDYGLFMR EGIV TATEQ EVKEDIAKLL RYESSALPSG QLTSLSEYAS RMRAGTRNIY YLCAPNRHLA EHSPYYEAMK KKDTEVLFCF EQFDE LTLL HLREFDKKKL ISVETDIVVD HYKEEKFEDR SPAAECLSEK ETEELMAWMR NVLGSRVTNV KVTLRLDTHP AMVTVL EMG AARHFLRMQQ LAKTQEERAQ LLQPTLEINP RHALIKKLNQ LRASEPGLAQ LLVDQIYENA MIAAGLVDDP RAMVGRL NE LLVKALERHG GSGSGSSAMV DTLSGLSSEQ GQSGDMTIEE DSATHIKFSK RDEDGKELAG ATMELRDSSG KTISTWIS D GQVKDFYLYP GKYTFVETAA PDGYEVATAI TFTVNEQGQV TVNGKATKGD AHI

UniProtKB: Heat shock protein 75 kDa, mitochondrial

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Macromolecule #2: Heat shock protein 75 kDa, mitochondrial, SpyTag, Succinate dehyd...

MacromoleculeName: Heat shock protein 75 kDa, mitochondrial, SpyTag, Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (chimera)
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.121344 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEME IHLQTNAEKG TITIQDTGIG MTQEELVSNL GTIARSGSKA FLDALQNQAE ASSKIIGQFG VGFYSAFMVA D RVEVYSRS ...String:
GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEME IHLQTNAEKG TITIQDTGIG MTQEELVSNL GTIARSGSKA FLDALQNQAE ASSKIIGQFG VGFYSAFMVA D RVEVYSRS AAPGSLGYQW LSDGSGVFEI AEASGVRTGT KIIIHLKSDC KEFSSEARVR DVVTKYSNFV SFPLYLNGRR MN TLQAIWM MDPKDVGEWQ HEEFYRYVAQ AHDKPRYTLH YKTDAPLNIR SIFYVPDMKP SMFDVSRELG SSVALYSRKV LIQ TKATDI LPKWLRFIRG VVDSEDIPLN LSRELLQESA LIRKLRDVLQ QRLIKFFIDQ SKKDAEKYAK FFEDYGLFMR EGIV TATEQ EVKEDIAKLL RYESSALPSG QLTSLSEYAS RMRAGTRNIY YLCAPNRHLA EHSPYYEAMK KKDTEVLFCF EQFDE LTLL HLREFDKKKL ISVETDIVVD HYKEEKFEDR SPAAECLSEK ETEELMAWMR NVLGSRVTNV KVTLRLDTHP AMVTVL EMG AARHFLRMQQ LAKTQEERAQ LLQPTLEINP RHALIKKLNQ LRASEPGLAQ LLVDQIYENA MIAAGLVDDP RAMVGRL NE LLVKALERHG GSGSGSSAHI VMVDAYKPTK GGGGSGGGGS GGGGSLEVLF QGPGSAQTAA ATAPRIKKFA IYRWDPDK A GDKPHMQTYE VDLNKCGPMV LDALIKIKNE VDSTLTFRRS CREGICGSCA MNINGGNTLA CTRRIDTNLN KVSKIYPLP HMYVIKDLVP DLSNFYAQYK SIEPYLKKK

UniProtKB: Heat shock protein 75 kDa, mitochondrial, Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 4 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xg6

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 94355
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6xg6


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7klu:
Tetrameric human mitochondrial Hsp90 (TRAP1) in the presence of AMP-PNP

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