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- EMDB-22174: Full-length human mitochondrial Hsp90 (TRAP1) with ADP-BeF3 -

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Basic information

Entry
Database: EMDB / ID: EMD-22174
TitleFull-length human mitochondrial Hsp90 (TRAP1) with ADP-BeF3
Map dataHsp90 (TRAP1) with ADP-BeF3
Sample
  • Complex: Trap1 dimer with ADP-BeF3
    • Protein or peptide: Heat shock protein 75 kDa, mitochondrial, Fibronectin binding protein fusion
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
KeywordsHsp90 / CHAPERONE
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-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
Heat shock protein 75 kDa, mitochondrial / Fibronectin binding protein
Similarity search - Component
Biological speciesHomo sapiens (human) / Streptococcus pyogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLiu YX / Wang F
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: 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, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xg6
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22174.png

Downloads & links

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Map

FileDownload / File: emd_22174.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHsp90 (TRAP1) with ADP-BeF3
Voxel sizeX=Y=Z: 0.814 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.058464434 - 0.13549043
Average (Standard dev.)-0.000010584753 (±0.0040955665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 260.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8140.8140.814
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z260.480260.480260.480
α/β/γ90.00090.00090.000
start NX/NY/NZ212211153
NX/NY/NZ80102186
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0580.135-0.000

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Supplemental data

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Mask #1

Fileemd_22174_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Hsp90 (TRAP1) with ADP-BeF3

Fileemd_22174_half_map_1.map
AnnotationHsp90 (TRAP1) with ADP-BeF3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Hsp90 (TRAP1) with ADP-BeF3

Fileemd_22174_half_map_2.map
AnnotationHsp90 (TRAP1) with ADP-BeF3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trap1 dimer with ADP-BeF3

EntireName: Trap1 dimer with ADP-BeF3
Components
  • Complex: Trap1 dimer with ADP-BeF3
    • Protein or peptide: Heat shock protein 75 kDa, mitochondrial, Fibronectin binding protein fusion
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: Trap1 dimer with ADP-BeF3

SupramoleculeName: Trap1 dimer with ADP-BeF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 147 KDa

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Macromolecule #1: Heat shock protein 75 kDa, mitochondrial, Fibronectin binding pro...

MacromoleculeName: Heat shock protein 75 kDa, mitochondrial, Fibronectin binding protein fusion
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus pyogenes (bacteria)
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, Fibronectin binding protein

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / 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: 2 / 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 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 69.0 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
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70998
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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