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- EMDB-14472: Structure of the RAF1-HSP90-CDC37 complex (RHC-II) -

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Entry
Database: EMDB / ID: EMD-14472
TitleStructure of the RAF1-HSP90-CDC37 complex (RHC-II)
Map dataRHC-II map, local resolution filtered
Sample
  • Complex: RAF1-HSP90-CDC37 complex, RHC-II
    • Protein or peptide: Heat shock protein HSP 90-betaHeat shock response
    • Protein or peptide: RAF proto-oncogene serine/threonine-protein kinase
    • Protein or peptide: Hsp90 co-chaperone Cdc37
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information


regulation of type II interferon-mediated signaling pathway / : / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / death-inducing signaling complex assembly / positive regulation of mitophagy in response to mitochondrial depolarization / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex ...regulation of type II interferon-mediated signaling pathway / : / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / death-inducing signaling complex assembly / positive regulation of mitophagy in response to mitochondrial depolarization / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex / intermediate filament cytoskeleton organization / histone methyltransferase binding / type B pancreatic cell proliferation / protein kinase regulator activity / positive regulation of protein localization to cell surface / regulation of Rho protein signal transduction / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / ATP-dependent protein binding / regulation of cell motility / protein folding chaperone complex / negative regulation of protein metabolic process / insulin secretion involved in cellular response to glucose stimulus / Negative feedback regulation of MAPK pathway / positive regulation of tau-protein kinase activity / post-transcriptional regulation of gene expression / telomerase holoenzyme complex assembly / GP1b-IX-V activation signalling / IFNG signaling activates MAPKs / Uptake and function of diphtheria toxin / 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 / TPR domain binding / regulation of cell differentiation / face development / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / pseudopodium / dendritic growth cone / somatic stem cell population maintenance / neurotrophin TRK receptor signaling pathway / thyroid gland development / regulation of type I interferon-mediated signaling pathway / positive regulation of phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / telomere maintenance via telomerase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / extrinsic apoptotic signaling pathway via death domain receptors / response to unfolded protein / MAP kinase kinase kinase activity / protein targeting / HSF1 activation / chaperone-mediated protein complex assembly / Attenuation phase / negative regulation of protein-containing complex assembly / RHOBTB2 GTPase cycle / DNA polymerase binding / Purinergic signaling in leishmaniasis infection / supramolecular fiber organization / Schwann cell development / axonal growth cone / type II interferon-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Signaling by ERBB2 / positive regulation of telomerase activity / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to muscle stretch / activation of adenylate cyclase activity / myelination / cellular response to interleukin-4 / nitric-oxide synthase regulator activity / CD209 (DC-SIGN) signaling / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / insulin-like growth factor receptor signaling pathway / thymus development / placenta development / positive regulation of cell differentiation / peptide binding / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / Hsp90 protein binding / RAF activation / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by high-kinase activity BRAF mutants
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
RAF proto-oncogene serine/threonine-protein kinase / Heat shock protein HSP 90-beta / Hsp90 co-chaperone Cdc37
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsMesa P / Garcia-Alonso S / Barbacid M / Montoya G
Funding support Denmark, 4 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
Novo Nordisk FoundationNNF0024386 Denmark
Novo Nordisk FoundationNNF17SA0030214 Denmark
Novo Nordisk FoundationNNF18OC0055061 Denmark
CitationJournal: Mol Cell / Year: 2022
Title: Structure of the RAF1-HSP90-CDC37 complex reveals the basis of RAF1 regulation.
Authors: Sara García-Alonso / Pablo Mesa / Laura de la Puente Ovejero / Gonzalo Aizpurua / Carmen G Lechuga / Eduardo Zarzuela / Clara M Santiveri / Manuel Sanclemente / Javier Muñoz / Mónica ...Authors: Sara García-Alonso / Pablo Mesa / Laura de la Puente Ovejero / Gonzalo Aizpurua / Carmen G Lechuga / Eduardo Zarzuela / Clara M Santiveri / Manuel Sanclemente / Javier Muñoz / Mónica Musteanu / Ramón Campos-Olivas / Jorge Martínez-Torrecuadrada / Mariano Barbacid / Guillermo Montoya /
Abstract: RAF kinases are RAS-activated enzymes that initiate signaling through the MAPK cascade to control cellular proliferation, differentiation, and survival. Here, we describe the structure of the full- ...RAF kinases are RAS-activated enzymes that initiate signaling through the MAPK cascade to control cellular proliferation, differentiation, and survival. Here, we describe the structure of the full-length RAF1 protein in complex with HSP90 and CDC37 obtained by cryoelectron microscopy. The reconstruction reveals a RAF1 kinase with an unfolded N-lobe separated from its C-lobe. The hydrophobic core of the N-lobe is trapped in the HSP90 dimer, while CDC37 wraps around the chaperone and interacts with the N- and C-lobes of the kinase. The structure indicates how CDC37 can discriminate between the different members of the RAF family. Our structural analysis also reveals that the folded RAF1 assembles with 14-3-3 dimers, suggesting that after folding RAF1 follows a similar activation as B-RAF. Finally, disruption of the interaction between CDC37 and the DFG segment of RAF1 unveils potential vulnerabilities in attempting the pharmacological degradation of RAF1 for therapeutic purposes.
History
DepositionMar 1, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateSep 28, 2022-
Current statusSep 28, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14472.png

Downloads & links

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Map

FileDownload / File: emd_14472.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRHC-II map, local resolution filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.05413721 - 0.10846931
Average (Standard dev.)4.8792394e-06 (±0.0018055115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14472_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: RHC-II map, half map 2 unfiltered

Fileemd_14472_half_map_1.map
AnnotationRHC-II map, half map 2 unfiltered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: RHC-II map, half map 1 unfiltered

Fileemd_14472_half_map_2.map
AnnotationRHC-II map, half map 1 unfiltered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RAF1-HSP90-CDC37 complex, RHC-II

EntireName: RAF1-HSP90-CDC37 complex, RHC-II
Components
  • Complex: RAF1-HSP90-CDC37 complex, RHC-II
    • Protein or peptide: Heat shock protein HSP 90-betaHeat shock response
    • Protein or peptide: RAF proto-oncogene serine/threonine-protein kinase
    • Protein or peptide: Hsp90 co-chaperone Cdc37
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: RAF1-HSP90-CDC37 complex, RHC-II

SupramoleculeName: RAF1-HSP90-CDC37 complex, RHC-II / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Expi293F cells
Molecular weightTheoretical: 289.1338 KDa

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Macromolecule #1: Heat shock protein HSP 90-beta

MacromoleculeName: Heat shock protein HSP 90-beta / type: protein_or_peptide / ID: 1 / Details: N-terminal HA-tag + HSP90-beta / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.371281 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYPYDVPDYA EEVHHGEEEV ETFAFQAEIA QLMSLIINTF YSNKEIFLRE LISNASDALD KIRYESLTDP SKLDSGKELK IDIIPNPQE RTLTLVDTGI GMTKADLINN LGTIAKSGTK AFMEALQAGA DISMIGQFGV GFYSAYLVAE KVVVITKHND D EQYAWESS ...String:
MYPYDVPDYA EEVHHGEEEV ETFAFQAEIA QLMSLIINTF YSNKEIFLRE LISNASDALD KIRYESLTDP SKLDSGKELK IDIIPNPQE RTLTLVDTGI GMTKADLINN LGTIAKSGTK AFMEALQAGA DISMIGQFGV GFYSAYLVAE KVVVITKHND D EQYAWESS AGGSFTVRAD HGEPIGRGTK VILHLKEDQT EYLEERRVKE VVKKHSQFIG YPITLYLEKE REKEISDDEA EE EKGEKEE EDKDDEEKPK IEDVGSDEED DSGKDKKKKT KKIKEKYIDQ EELNKTKPIW TRNPDDITQE EYGEFYKSLT NDW EDHLAV KHFSVEGQLE FRALLFIPRR APFDLFENKK KKNNIKLYVR RVFIMDSCDE LIPEYLNFIR GVVDSEDLPL NISR EMLQQ SKILKVIRKN IVKKCLELFS ELAEDKENYK KFYEAFSKNL KLGIHEDSTN RRRLSELLRY HTSQSGDEMT SLSEY VSRM KETQKSIYYI TGESKEQVAN SAFVERVRKR GFEVVYMTEP IDEYCVQQLK EFDGKSLVSV TKEGLELPED EEEKKK MEE SKAKFENLCK LMKEILDKKV EKVTISNRLV SSPCCIVTST YGWTANMERI MKAQALRDNS TMGYMMAKKH LEINPDH PI VETLRQKAEA DKNDKAVKDL VVLLFETALL SSGFSLEDPQ THSNRIYRMI KLGLGIDEDE VAAEEPNAAV PDEIPPLE G DEDASRMEEV D

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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 / Details: RAF1 + linker Gly-Ser-Ala + C-terminal StrepTagII / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.409953 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVR GLQPECCAVF RLLHEHKGKK ARLDWNTDAA SLIGEELQVD FLDHVPLTTH NFARKTFLKL AFCDICQKFL L NGFRCQTC ...String:
MEHIQGAWKT ISNGFGFKDA VFDGSSCISP TIVQQFGYQR RASDDGKLTD PSKTSNTIRV FLPNKQRTVV NVRNGMSLHD CLMKALKVR GLQPECCAVF RLLHEHKGKK ARLDWNTDAA SLIGEELQVD FLDHVPLTTH NFARKTFLKL AFCDICQKFL L NGFRCQTC GYKFHEHCST KVPTMCVDWS NIRQLLLFPN STIGDSGVPA LPSLTMRRMR ESVSRMPVSS QHRYSTPHAF TF NTSSPSS EGSLSQRQRS TSTPNVHMVS TTLPVDSRMI EDAIRSHSES ASPSALSSSP NNLSPTGWSQ PKTPVPAQRE RAP VSGTQE KNKIRPRGQR DSSYYWEIEA SEVMLSTRIG SGSFGTVYKG KWHGDVAVKI LKVVDPTPEQ FQAFRNEVAV LRKT RHVNI LLFMGYMTKD NLAVITQWCE GSSLYKHLHV QETKFQMFQL IDIARQTAQG MDYLHAKNII HRDMKSNNIF LHEGL TVKI GDFGLATVKS RWSGSQQVEQ PTGSVLWMAP EVIRMQDNNP FSFQSDVYSY GIVLYELMTG ELPYSHINNR DQIIFM VGR GYASPDLSKL YKNCPKAMKR LVADCVKKVK EERPLFPQIL SSIELLQHSL PKINRSASEP SLHRAAHTED INACTLT TS PRLPVFGSAW SHPQFEK

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Macromolecule #3: Hsp90 co-chaperone Cdc37

MacromoleculeName: Hsp90 co-chaperone Cdc37 / type: protein_or_peptide / ID: 3 / Details: CDC37 + C-terminal Myc-DDK tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.535516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 SVTRTRPLEQ KLISEEDL

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMTris-HClTristris buffer
150.0 mMNaClSodium chloridesodium chloride
10.0 mMMgCl2magnesium chloride
10.0 mMKClpotassium chloride
20.0 mMNa2MoO4sodium molybdate
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 8138 / Average electron dose: 30.0 e/Å2
Details: 8138 images (4430 non-tilted and 3708 30 degrees tilted)
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3760000
Details: 3760k in total: 1353k RAF1:HSP90:CDC37 complex, 1127k 14-3-3 dimer, RAF1:14-3-3 complex 1245k
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Software - details: patch CTF protocol
Startup modelType of model: INSILICO MODEL
Details: ab-initio reconstruction: SGD method (cryoSPARC and Relion)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 46000
FSC plot (resolution estimation)

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