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- EMDB-41816: Cryo-EM structure of the RAF1-HSP90-CDC37 complex in the closed state -

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Entry
Database: EMDB / ID: EMD-41816
TitleCryo-EM structure of the RAF1-HSP90-CDC37 complex in the closed state
Map dataSharpened Map
Sample
  • Complex: Complex of RAF1-HSP90-CDC37
    • Complex: Heat shock protein 90Hsp90
      • Protein or peptide: Heat shock protein 83Heat shock response
    • Complex: RAF1 & HSP90 co-chaperone CDC37
      • Protein or peptide: RAF proto-oncogene serine/threonine-protein kinase
      • Protein or peptide: Hsp90 co-chaperone Cdc37, N-terminally processed
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsCRAF / RAF1 / HSP90 / CDC37 / SIGNALING PROTEIN-CHAPERONE complex
Function / homology
Function and homology information


regulation of type II interferon-mediated signaling pathway / HSP90-CDC37 chaperone complex / death-inducing signaling complex assembly / positive regulation of mitophagy in response to mitochondrial depolarization / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / protein kinase regulator activity / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling ...regulation of type II interferon-mediated signaling pathway / HSP90-CDC37 chaperone complex / death-inducing signaling complex assembly / positive regulation of mitophagy in response to mitochondrial depolarization / intermediate filament cytoskeleton organization / type B pancreatic cell proliferation / protein kinase regulator activity / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / regulation of cell motility / protein folding chaperone complex / insulin secretion involved in cellular response to glucose stimulus / Negative feedback regulation of MAPK pathway / post-transcriptional regulation of gene expression / GP1b-IX-V activation signalling / IFNG signaling activates MAPKs / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / ERBB2-ERBB3 signaling pathway / regulation of cell differentiation / face development / regulation of cyclin-dependent protein serine/threonine kinase activity / pseudopodium / somatic stem cell population maintenance / neurotrophin TRK receptor signaling pathway / thyroid gland development / regulation of type I interferon-mediated signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / MAP kinase kinase kinase activity / protein targeting / negative regulation of protein-containing complex assembly / RHOBTB2 GTPase cycle / Schwann cell development / type II interferon-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Signaling by ERBB2 / heat shock protein binding / response to muscle stretch / activation of adenylate cyclase activity / myelination / CD209 (DC-SIGN) signaling / Constitutive Signaling by Overexpressed ERBB2 / insulin-like growth factor receptor signaling pathway / thymus development / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / Hsp90 protein binding / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / wound healing / MAP2K and MAPK activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Regulation of necroptotic cell death / Stimuli-sensing channels / Downregulation of ERBB2 signaling / kinase binding / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / unfolded protein binding / Signaling by BRAF and RAF1 fusions / protein folding / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / insulin receptor signaling pathway / positive regulation of peptidyl-serine phosphorylation / protein-folding chaperone binding / scaffold protein binding / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of MAPK cascade / protein stabilization / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of cell population proliferation / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / negative regulation of apoptotic process / protein kinase binding / Golgi apparatus / enzyme binding / signal transduction / ATP hydrolysis activity
Similarity search - Function
Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding / Cdc37 / Cdc37, N-terminal domain ...Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 N terminal kinase binding / Cdc37 / Cdc37, N-terminal domain / Cdc37 N terminal kinase binding / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / C1-like domain superfamily / 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 / Ubiquitin-like domain superfamily / Ribosomal protein S5 domain 2-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Heat shock protein 83 / RAF proto-oncogene serine/threonine-protein kinase / Hsp90 co-chaperone Cdc37
Similarity search - Component
Biological speciesTrichoplusia ni (cabbage looper) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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

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Structure visualization

Supplemental images

emd_41816.png

Downloads & links

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Map

FileDownload / File: emd_41816.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Map
Voxel sizeX=Y=Z: 0.858 Å
Density
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.11872228 - 0.33644938
Average (Standard dev.)0.0026283802 (±0.016217608)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Additional map: Unsharpened Map

Fileemd_41816_additional_1.map
AnnotationUnsharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered, unsharpened, Halfmap 1

Fileemd_41816_half_map_1.map
AnnotationUnfiltered, unsharpened, Halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered, unsharpened, Halfmap 2

Fileemd_41816_half_map_2.map
AnnotationUnfiltered, unsharpened, Halfmap 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Sample components

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Entire : Complex of RAF1-HSP90-CDC37

EntireName: Complex of RAF1-HSP90-CDC37
Components
  • Complex: Complex of RAF1-HSP90-CDC37
    • Complex: Heat shock protein 90Hsp90
      • Protein or peptide: Heat shock protein 83Heat shock response
    • Complex: RAF1 & HSP90 co-chaperone CDC37
      • Protein or peptide: RAF proto-oncogene serine/threonine-protein kinase
      • Protein or peptide: Hsp90 co-chaperone Cdc37, N-terminally processed
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of RAF1-HSP90-CDC37

SupramoleculeName: Complex of RAF1-HSP90-CDC37 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Heat shock protein 90

SupramoleculeName: Heat shock protein 90 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Trichoplusia ni (cabbage looper)

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Supramolecule #3: RAF1 & HSP90 co-chaperone CDC37

SupramoleculeName: RAF1 & HSP90 co-chaperone CDC37 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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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

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Macromolecule #2: RAF proto-oncogene serine/threonine-protein kinase

MacromoleculeName: RAF proto-oncogene serine/threonine-protein kinase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.021445 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GGEHIQGAWK TISNGFGFKD AVFDGSSCIS PTIVQQFGYQ RRASDDGKLT DPSKTSNTIR VFLPNKQRTV VNVRNGMSLH DCLMKALKV RGLQPECCAV FRLLHEHKGK KARLDWNTDA ASLIGEELQV DFLDHVPLTT HNFARKTFLK LAFCDICQKF L LNGFRCQT ...String:
GGEHIQGAWK TISNGFGFKD AVFDGSSCIS PTIVQQFGYQ RRASDDGKLT DPSKTSNTIR VFLPNKQRTV VNVRNGMSLH DCLMKALKV RGLQPECCAV FRLLHEHKGK KARLDWNTDA ASLIGEELQV DFLDHVPLTT HNFARKTFLK LAFCDICQKF L LNGFRCQT CGYKFHEHCS TKVPTMCVDW SNIRQLLLFP NSTIGDSGVP ALPSLTMRRM RESVSRMPVS SQHRYSTPHA FT FNTSSPS SEGSLSQRQR STSTPNVHMV STTLPVDSRM IEDAIRSHSE SASPSALSSS PNNLSPTGWS QPKTPVPAQR ERA PVSGTQ EKNKIRPRGQ RDSSYYWEIE ASEVMLSTRI GSGSFGTVYK GKWHGDVAVK ILKVVDPTPE QFQAFRNEVA VLRK TRHVN ILLFMGYMTK DNLAIVTQWC EGSSLYKHLH VQETKFQMFQ LIDIARQTAQ GMDYLHAKNI IHRDMKSNNI FLHEG LTVK IGDFGLATVK SRWSGSQQVE QPTGSVLWMA PEVIRMQDNN PFSFQSDVYS YGIVLYELMT GELPYSHINN RDQIIF MVG RGYASPDLSK LYKNCPKAMK RLVADCVKKV KEERPLFPQI LSSIELLQHS LPKINRSASE PSLHRAAHTE DINACTL TT SPRLPVFGHH HHHH

UniProtKB: RAF proto-oncogene serine/threonine-protein kinase

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Macromolecule #3: Hsp90 co-chaperone Cdc37, N-terminally processed

MacromoleculeName: Hsp90 co-chaperone Cdc37, N-terminally processed / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.622363 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MVDYSVWDHI EV(SEP)DDEDETH PNIDTASLFR WRHQARVERM EQFQKEKEEL DRGCRECKRK VAECQRKLKE LEVAEG GKA ELERLQAEAQ QLRKEERSWE QKLEEMRKKE KSMPWNVDTL SKDGFSKSMV NTKPEKTEED SEEVREQKHK TFVEKYE KQ IKHFGMLRRW ...String:
MVDYSVWDHI EV(SEP)DDEDETH PNIDTASLFR WRHQARVERM EQFQKEKEEL DRGCRECKRK VAECQRKLKE LEVAEG GKA ELERLQAEAQ QLRKEERSWE QKLEEMRKKE KSMPWNVDTL SKDGFSKSMV NTKPEKTEED SEEVREQKHK TFVEKYE KQ IKHFGMLRRW DDSQKYLSDN VHLVCEETAN YLVIWCIDLE VEEKCALMEQ VAHQTIVMQF ILELAKSLKV DPRACFRQ F FTKIKTADRQ YMEGFNDELE AFKERVRGRA KLRIEKAMKE YEEEERKKRL GPGGLDPVEV YESLPEELQK CFDVKDVQM LQDAISKMDP TDAKYHMQRC IDSGLWVPNS KASEAKEGEE AGPGDPLLEA VPKTGDEKDV SV

UniProtKB: Hsp90 co-chaperone Cdc37

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / 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

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / 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

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.

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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

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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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 97569
FSC plot (resolution estimation)

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