[English] 日本語
Yorodumi
- EMDB-22243: Full-length Hsc82 in complex with two Aha1 CTD in the presence of... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-22243
TitleFull-length Hsc82 in complex with two Aha1 CTD in the presence of ATPgammaS
Map dataHsc82 in complex with two Aha1 CTD in the presence of ATPgammaS
Sample
  • Complex: Full-length Hsc82 in complex with Aha1-CTD in the presence of ATPgammaS
    • Protein or peptide: ATP-dependent molecular chaperone HSC82
    • Protein or peptide: Hsp90 co-chaperone AHA1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
KeywordsCo-chaperone / activator / 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 / ATPase activator activity ...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 / ATPase activator activity / proteasome assembly / Neutrophil degranulation / telomere maintenance / ATP-dependent protein folding chaperone / protein import into nucleus / unfolded protein binding / protein folding / protein-folding chaperone binding / cellular response to heat / protein stabilization / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, Aha1 / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START-like domain superfamily / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain ...Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, Aha1 / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase, N-terminal / Activator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START-like domain superfamily / 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 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ATP-dependent molecular chaperone HSC82 / Hsp90 co-chaperone AHA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.71 Å
AuthorsLiu YX / Sun M
Funding support United States, 5 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
American Heart Association United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U54CA209891 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD020054 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD021741 United States
CitationJournal: To Be Published
Title: Cryo-EM structures reveal a multistep mechanism of Hsp90 activation by co-chaperone Aha1
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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6xlg
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22243.png

Downloads & links

-
Map

FileDownload / File: emd_22243.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHsc82 in complex with two Aha1 CTD in the presence of ATPgammaS
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 320 pix.
= 263.04 Å		0.82 Å/pix.
x 320 pix.
= 263.04 Å		0.82 Å/pix.
x 320 pix.
= 263.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.822 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.08411852 - 0.1766419
Average (Standard dev.)-0.00008350685 (±0.004237423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 263.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z263.040263.040263.040
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0840.177-0.000

-
Supplemental data

-
Sample components

-
Entire : Full-length Hsc82 in complex with Aha1-CTD in the presence of ATP...

EntireName: Full-length Hsc82 in complex with Aha1-CTD in the presence of ATPgammaS
Components
  • Complex: Full-length Hsc82 in complex with Aha1-CTD in the presence of ATPgammaS
    • Protein or peptide: ATP-dependent molecular chaperone HSC82
    • Protein or peptide: Hsp90 co-chaperone AHA1
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION

-
Supramolecule #1: Full-length Hsc82 in complex with Aha1-CTD in the presence of ATP...

SupramoleculeName: Full-length Hsc82 in complex with Aha1-CTD in the presence of ATPgammaS
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

-
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

-
Macromolecule #2: Hsp90 co-chaperone AHA1

MacromoleculeName: Hsp90 co-chaperone AHA1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 39.486422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVVNNPNNWH WVDKNCIGWA KEYFKQKLVG VEAGSVKDKK YAKIKSVSSI EGDCEVNQRK GKVISLFDLK ITVLIEGHVD SKDGSALPF EGSINVPEVA FDSEASSYQF DISIFKETSE LSEAKPLIRS ELLPKLRQIF QQFGKDLLAT HGNDIQVPES Q VKSNYTRG ...String:
MVVNNPNNWH WVDKNCIGWA KEYFKQKLVG VEAGSVKDKK YAKIKSVSSI EGDCEVNQRK GKVISLFDLK ITVLIEGHVD SKDGSALPF EGSINVPEVA FDSEASSYQF DISIFKETSE LSEAKPLIRS ELLPKLRQIF QQFGKDLLAT HGNDIQVPES Q VKSNYTRG NQKSSFTEIK DSASKPKKNA LPSSTSTSAP VSSTNKVPQN GSGNSTSIYL EPTFNVPSSE LYETFLDKQR IL AWTRSAQ FFNSGPKLET KEKFELFGGN VISELVSCEK DKKLVFHWKL KDWSAPFNST IEMTFHESQE FHETKLQVKW TGI PVGEED RVRANFEEYY VRSIKLTFGF GAVL

UniProtKB: Hsp90 co-chaperone AHA1

-
Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126867
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6xlg:
Full-length Hsc82 in complex with two Aha1 CTD in the presence of ATPgammaS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more