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- EMDB-22175: Human mitochondrial Hsp90 (TRAP1) NTD-Middle domain dimer with AD... -

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Basic information

Entry
Database: EMDB / ID: EMD-22175
TitleHuman mitochondrial Hsp90 (TRAP1) NTD-Middle domain dimer with ADP-BeF3
Map dataHsp90 (TRAP1) NTD-Middle domain dimer with ADP-BeF3
Sample
  • Complex: Trap1 NTD-Middle domain dimer with ADP-BeF3
    • Protein or peptide: Mitochondrial Hsp90 (TRAP1)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLiu YX / Wang F / Agard DA
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
American Heart Association 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-
UpdateOct 21, 2020-
Current statusOct 21, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22175.png

Downloads & links

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Map

FileDownload / File: emd_22175.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHsp90 (TRAP1) NTD-Middle domain dimer with ADP-BeF3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 320 pix.
= 260.48 Å		0.81 Å/pix.
x 320 pix.
= 260.48 Å		0.81 Å/pix.
x 320 pix.
= 260.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.814 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.07640258 - 0.17042682
Average (Standard dev.)-0.00003056468 (±0.0038124262)
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/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0760.170-0.000

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Supplemental data

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Sample components

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Entire : Trap1 NTD-Middle domain dimer with ADP-BeF3

EntireName: Trap1 NTD-Middle domain dimer with ADP-BeF3
Components
  • Complex: Trap1 NTD-Middle domain dimer with ADP-BeF3
    • Protein or peptide: Mitochondrial Hsp90 (TRAP1)

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Supramolecule #1: Trap1 NTD-Middle domain dimer with ADP-BeF3

SupramoleculeName: Trap1 NTD-Middle domain dimer with ADP-BeF3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Mitochondrial Hsp90 (TRAP1)

MacromoleculeName: Mitochondrial Hsp90 (TRAP1) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEMEI HLQTNAEKGT ITIQDTGIGM TQEELVSNLG TIARSGSKAF LDALQNQAEA SSKIIGQFGV GFYSAFMVAD RVEVYSRSAA ...String:
GIDPFTSTQT AEDKEEPLHS IISSTESVQG STSKHEFQAE TKKLLDIVAR SLYSEKEVFI RELISNASDA LEKLRHKLVS DGQALPEMEI HLQTNAEKGT ITIQDTGIGM TQEELVSNLG TIARSGSKAF LDALQNQAEA SSKIIGQFGV GFYSAFMVAD RVEVYSRSAA PGSLGYQWLS DGSGVFEIAE ASGVRTGTKI IIHLKSDCKE FSSEARVRDV VTKYSNFVSF PLYLNGRRMN TLQAIWMMDP KDVGEWQHEE FYRYVAQAHD KPRYTLHYKT DAPLNIRSIF YVPDMKPSMF DVSRELGSSV ALYSRKVLIQ TKATDILPKW LRFIRGVVDS EDIPLNLSRE LLQESALIRK LRDVLQQRLI KFFIDQSKKD AEKYAKFFED YGLFMREGIV TATEQEVKED IAKLLRYESS ALPSGQLTSL SEYASRMRAG TRNIYYLCAP NRHLAEHSPY YEAMKKKDTE VLFCFEQFDE LTLLHLREFD KKKLISVETD IVVDHYKEEK FEDRSPAAEC LSEKETEELM AWMRNVLGSR VTNVKVTLRL DTHPAMVTVL EMGAARHFLR MQQLAKTQEE RAQLLQPTLE INPRHALIKK LNQLRASEPG LAQLLVDQIY ENAMIAAGLV DDPRAMVGRL NELLVKALER HGGSGSGSSA MVDTLSGLSS EQGQSGDMTI EEDSATHIKF SKRDEDGKEL AGATMELRDS SGKTISTWIS DGQVKDFYLY PGKYTFVETA APDGYEVATA ITFTVNEQGQ VTVNGKATKG DAHI

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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
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified
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

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85748
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: RIGID BODY FIT

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