[English] 日本語
Yorodumi
- EMDB-41817: Cryo-EM structure of the HSP90 dimer (NTD-MD) in the semi-open state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41817
TitleCryo-EM structure of the HSP90 dimer (NTD-MD) in the semi-open state
Map dataSharpened Map
Sample
  • Complex: Heat shock protein 90Hsp90
    • Protein or peptide: Heat shock protein 83Heat shock response
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsHSP / HSP90 / CHAPERONE
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / 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 / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Heat shock protein 83
Similarity search - Component
Biological speciesTrichoplusia ni (cabbage looper)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFinci LI / Simanshu DK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: Commun Biol / Year: 2024
Title: Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements.
Authors: Lorenzo I Finci / Mayukh Chakrabarti / Gulcin Gulten / Joseph Finney / Carissa Grose / Tara Fox / Renbin Yang / Dwight V Nissley / Frank McCormick / Dominic Esposito / Trent E Balius / Dhirendra K Simanshu /
Abstract: RAF kinases are integral to the RAS-MAPK signaling pathway, and proper RAF1 folding relies on its interaction with the chaperone HSP90 and the cochaperone CDC37. Understanding the intricate molecular ...RAF kinases are integral to the RAS-MAPK signaling pathway, and proper RAF1 folding relies on its interaction with the chaperone HSP90 and the cochaperone CDC37. Understanding the intricate molecular interactions governing RAF1 folding is crucial for comprehending this process. Here, we present a cryo-EM structure of the closed-state RAF1-HSP90-CDC37 complex, where the C-lobe of the RAF1 kinase domain binds to one side of the HSP90 dimer, and an unfolded N-lobe segment of the RAF1 kinase domain threads through the center of the HSP90 dimer. CDC37 binds to the kinase C-lobe, mimicking the N-lobe with its HxNI motif. We also describe structures of HSP90 dimers without RAF1 and CDC37, displaying only N-terminal and middle domains, which we term the semi-open state. Employing 1 μs atomistic simulations, energetic decomposition, and comparative structural analysis, we elucidate the dynamics and interactions within these complexes. Our quantitative analysis reveals that CDC37 bridges the HSP90-RAF1 interaction, RAF1 binds HSP90 asymmetrically, and that HSP90 structural elements engage RAF1's unfolded region. Additionally, N- and C-terminal interactions stabilize HSP90 dimers, and molecular interactions in HSP90 dimers rearrange between the closed and semi-open states. Our findings provide valuable insight into the contributions of HSP90 and CDC37 in mediating client folding.
History
DepositionSep 1, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41817.png

Downloads & links

-
Map

FileDownload / File: emd_41817.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 219.648 Å		0.86 Å/pix.
x 256 pix.
= 219.648 Å		0.86 Å/pix.
x 256 pix.
= 219.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.858 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.059835598 - 0.31789973
Average (Standard dev.)0.0016729031 (±0.0126946345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 219.648 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Unsharpened Map

Fileemd_41817_additional_1.map
AnnotationUnsharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered, unsharpened half map 1

Fileemd_41817_half_map_1.map
AnnotationUnfiltered, unsharpened half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Unfiltered, unsharpened half map 2

Fileemd_41817_half_map_2.map
AnnotationUnfiltered, unsharpened half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Heat shock protein 90

EntireName: Heat shock protein 90Hsp90
Components
  • Complex: Heat shock protein 90Hsp90
    • Protein or peptide: Heat shock protein 83Heat shock response
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Heat shock protein 90

SupramoleculeName: Heat shock protein 90 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 166 KDa

-
Macromolecule #1: Heat shock protein 83

MacromoleculeName: Heat shock protein 83 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Trichoplusia ni (cabbage looper)
Molecular weightTheoretical: 83.322133 KDa
SequenceString: MPEEMQTDSG EVETFAFQAE IAQLMSLIIN TFYSNKEIFL RELISNSSDA LDKIRYESLT DPSKLDSGKE LYIKIIPNKS EGTFTIIDT GIGMTKADLV NNLGTIAKSG TKAFMEALQA GADISMIGQF GVGFYSCYLV ADRVTVHSKH NDDEQYMWES S AGGSFTVR ...String:
MPEEMQTDSG EVETFAFQAE IAQLMSLIIN TFYSNKEIFL RELISNSSDA LDKIRYESLT DPSKLDSGKE LYIKIIPNKS EGTFTIIDT GIGMTKADLV NNLGTIAKSG TKAFMEALQA GADISMIGQF GVGFYSCYLV ADRVTVHSKH NDDEQYMWES S AGGSFTVR TDHGEPLGRG TKIVLHIKED LAEYLEVNKI KEIVKKHSQF IGYPIKLTVE KEREKELAYD EEEEKKEGEE DK KEDEKED EKPKIEDVGE DDEEDKDKKK KKTIKEKYTE DEELNKTKPI WTRNADDITQ EEYGDFYKSL TNDWEDHLAV KHF SVEGQL EFRALLFVPR RAPFDLFENK KRKNNIKLYV RRVFIMDNCE DLIPEYLNFI KGVVDSEDLP LNISREMLQQ NKIL KVIRK NLVKKCLELF EELAEDKENY KKYYEQFSKN LKLGIHEDAQ NRTKLADLLR YHTSASGDEA CSLKEYVSRM KENQK HIYY ITGENRDQVA NSSFVERVKK RGYEVVYMTE PIDEYVVQQM REYDGKTLVS VTKEGLELPE DEEEKKKREE DKVKFE GLC KVMKNILDNK VEKVVVSNRL VESPCCIVTA QYGWSANMER IMKAQALRDT STMGYMAAKK HLEINPDHSI VETLRQK AE ADKNDKAVKD LVILLYETAL LSSGFTLDEP QVHASRIYRM IKLGLGIDED EPIQVEESSV GDVPPLEGDA DDASRMEE V D

UniProtKB: Heat shock protein 83

-
Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

-
Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chlorideSodium Chloride
1.0 mMC9H15O6PTCEP
5.0 w/vC3H8O3Glycerol
10.0 mMMgCl2Magnesium Chloride
20.0 mMNa2MoO4Sodium Molybdate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details: Grids were blotted for 4.5 seconds before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1877778
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model / Details: Ab initio model generated in Relion
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 325732
FSC plot (resolution estimation)

+
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