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- EMDB-22239: Full-length Hsc82 bound to AMPPNP -

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Basic information

Entry
Database: EMDB / ID: EMD-22239
TitleFull-length Hsc82 bound to AMPPNP
Map dataHsc82 bound to AMPPNP
Sample
  • Complex: Hsc82 bound to AMPPNP
    • Protein or peptide: ATP-dependent molecular chaperone HSC82
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsHsp90 / CHAPERONE
Function / homology
Function and homology information


Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / box C/D snoRNP assembly / proteasome assembly ...Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / Extra-nuclear estrogen signaling / HSF1-dependent transactivation / VEGFR2 mediated vascular permeability / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / HSF1 activation / response to oxygen levels / box C/D snoRNP assembly / proteasome assembly / Neutrophil degranulation / telomere maintenance / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / protein-containing complex / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family 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 / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ATP-dependent molecular chaperone HSC82
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsLiu YX / Sun M
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute United States
American Heart Association United States
CitationJournal: To Be Published
Title: Full-length Hsc82 bound to AMPPNP
Authors: Liu YX / Sun M / Myasnikov AG / Elnatan D / Agard DA
History
DepositionJun 28, 2020-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
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: 0.0375
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0375
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xlc
  • Surface level: 0.0375
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22239.png

Downloads & links

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Map

FileDownload / File: emd_22239.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHsc82 bound to AMPPNP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å		1.06 Å/pix.
x 256 pix.
= 271.104 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0375 / Movie #1: 0.0375
Minimum - Maximum-0.07324751 - 0.16444632
Average (Standard dev.)-0.00006352543 (±0.0052092886)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.104 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z271.104271.104271.104
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0730.164-0.000

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Supplemental data

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Sample components

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Entire : Hsc82 bound to AMPPNP

EntireName: Hsc82 bound to AMPPNP
Components
  • Complex: Hsc82 bound to AMPPNP
    • Protein or peptide: ATP-dependent molecular chaperone HSC82
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Hsc82 bound to AMPPNP

SupramoleculeName: Hsc82 bound to AMPPNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Macromolecule #1: ATP-dependent molecular chaperone HSC82

MacromoleculeName: ATP-dependent molecular chaperone HSC82 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 81.003594 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGETFEFQA EITQLMSLII NTVYSNKEIF LRELISNASD ALDKIRYQAL SDPKQLETEP DLFIRITPKP EEKVLEIRDS GIGMTKAEL INNLGTIAKS GTKAFMEALS AGADVSMIGQ FGVGFYSLFL VADRVQVISK NNEDEQYIWE SNAGGSFTVT L DEVNERIG ...String:
MAGETFEFQA EITQLMSLII NTVYSNKEIF LRELISNASD ALDKIRYQAL SDPKQLETEP DLFIRITPKP EEKVLEIRDS GIGMTKAEL INNLGTIAKS GTKAFMEALS AGADVSMIGQ FGVGFYSLFL VADRVQVISK NNEDEQYIWE SNAGGSFTVT L DEVNERIG RGTVLRLFLK DDQLEYLEEK RIKEVIKRHS EFVAYPIQLL VTKEVEKEVP IPEEEKKDEE KKDEDDKKPK LE EVDEEEE EKKPKTKKVK EEVQELEELN KTKPLWTRNP SDITQEEYNA FYKSISNDWE DPLYVKHFSV EGQLEFRAIL FIP KRAPFD LFESKKKKNN IKLYVRRVFI TDEAEDLIPE WLSFVKGVVD SEDLPLNLSR EMLQQNKIMK VIRKNIVKKL IEAF NEIAE DSEQFDKFYS AFAKNIKLGV HEDTQNRAAL AKLLRYNSTK SVDELTSLTD YVTRMPEHQK NIYYITGESL KAVEK SPFL DALKAKNFEV LFLTDPIDEY AFTQLKEFEG KTLVDITKDF ELEETDEEKA EREKEIKEYE PLTKALKDIL GDQVEK VVV SYKLLDAPAA IRTGQFGWSA NMERIMKAQA LRDSSMSSYM SSKKTFEISP KSPIIKELKK RVDEGGAQDK TVKDLTN LL FETALLTSGF SLEEPTSFAS RINRLISLGL NIDEDEETET APEASTEAPV EEVPADTEME EVD

UniProtKB: ATP-dependent molecular chaperone HSC82

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Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / 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 #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 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
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: 72.0 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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48464
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-6xlc:
Full-length Hsc82 bound to AMPPNP

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