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- EMDB-14883: CryoEM structure of HSP90-CDC37-BRAF(V600E)-PP5(closed) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14883
TitleCryoEM structure of HSP90-CDC37-BRAF(V600E)-PP5(closed) complex
Map data
Sample
  • Complex: HSP90-CDC37-BRAF(V600E)-PP5 (closed) complex
    • Complex: Heat shock protein HSP 90-beta, Hsp90 co-chaperone Cdc37 and Serine/threonine-protein kinase B-raf
      • Protein or peptide: Heat shock protein HSP 90-beta
      • Protein or peptide: Hsp90 co-chaperone Cdc37
      • Protein or peptide: Serine/threonine-protein kinase B-raf
    • Complex: Serine/threonine-protein phosphatase 5
      • Protein or peptide: Serine/threonine-protein phosphatase 5
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsComplex / PROTEIN BINDING
Function / homology
Function and homology information


regulation of type II interferon-mediated signaling pathway / response to arachidonate / HSP90-CDC37 chaperone complex / peptidyl-threonine dephosphorylation / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / peptidyl-serine dephosphorylation / aryl hydrocarbon receptor complex / CD4-positive, alpha-beta T cell differentiation / dynein axonemal particle ...regulation of type II interferon-mediated signaling pathway / response to arachidonate / HSP90-CDC37 chaperone complex / peptidyl-threonine dephosphorylation / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / peptidyl-serine dephosphorylation / aryl hydrocarbon receptor complex / CD4-positive, alpha-beta T cell differentiation / dynein axonemal particle / histone methyltransferase binding / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / receptor ligand inhibitor activity / Signalling to p38 via RIT and RIN / myeloid progenitor cell differentiation / positive regulation of type 2 mitophagy / head morphogenesis / ARMS-mediated activation / ATP-dependent protein binding / endothelial cell apoptotic process / positive regulation of protein localization to cell surface / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / negative regulation of fibroblast migration / positive regulation of D-glucose transmembrane transport / establishment of protein localization to membrane / positive regulation of axonogenesis / protein kinase regulator activity / protein folding chaperone complex / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of T cell differentiation / response to morphine / mitogen-activated protein kinase kinase binding / Negative feedback regulation of MAPK pathway / post-transcriptional regulation of gene expression / protein serine/threonine phosphatase activity / Frs2-mediated activation / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / protein-serine/threonine phosphatase / positive regulation of axon regeneration / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / stress fiber assembly / positive regulation of transforming growth factor beta receptor signaling pathway / 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 / regulation of type I interferon-mediated signaling pathway / TPR domain binding / face development / phosphatase activity / MAP kinase kinase activity / Assembly and release of respiratory syncytial virus (RSV) virions / synaptic vesicle exocytosis / dendritic growth cone / thyroid gland development / phosphoprotein phosphatase activity / The NLRP3 inflammasome / protein phosphatase activator activity / somatic stem cell population maintenance / Sema3A PAK dependent Axon repulsion / MAP kinase kinase kinase activity / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / HSF1 activation / telomere maintenance via telomerase / postsynaptic modulation of chemical synaptic transmission / Attenuation phase / chaperone-mediated protein complex assembly / negative regulation of endothelial cell apoptotic process / protein targeting / axonal growth cone / RHOBTB2 GTPase cycle / Purinergic signaling in leishmaniasis infection / response to cAMP / protein dephosphorylation / supramolecular fiber organization / positive regulation of peptidyl-serine phosphorylation / positive regulation of stress fiber assembly / : / DNA polymerase binding / heat shock protein binding
Similarity search - Function
PP5, C-terminal metallophosphatase domain / PPP domain / PPP5 TPR repeat region / Cdc37, C-terminal / Cdc37, Hsp90 binding / Cdc37, Hsp90-binding domain superfamily / : / Cdc37 C terminal domain / Cdc37 Hsp90 binding domain / Cdc37 C terminal domain ...PP5, C-terminal metallophosphatase domain / PPP domain / PPP5 TPR repeat region / 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 / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / Tetratricopeptide repeat / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / 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 / Metallo-dependent phosphatase-like / C1-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 / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Tetratricopeptide-like helical domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Ribosomal protein S5 domain 2-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 HSP 90-beta / Serine/threonine-protein kinase B-raf / Serine/threonine-protein phosphatase 5 / Hsp90 co-chaperone Cdc37
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsOberoi J / Pearl LH
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: HSP90-CDC37-PP5 forms a structural platform for kinase dephosphorylation.
Authors: Jasmeen Oberoi / Xavi Aran Guiu / Emily A Outwin / Pascale Schellenberger / Theodoros I Roumeliotis / Jyoti S Choudhary / Laurence H Pearl /
Abstract: Activation of client protein kinases by the HSP90 molecular chaperone system is affected by phosphorylation at multiple sites on HSP90, the kinase-specific co-chaperone CDC37, and the kinase client ...Activation of client protein kinases by the HSP90 molecular chaperone system is affected by phosphorylation at multiple sites on HSP90, the kinase-specific co-chaperone CDC37, and the kinase client itself. Removal of regulatory phosphorylation from client kinases and their release from the HSP90-CDC37 system depends on the Ser/Thr phosphatase PP5, which associates with HSP90 via its N-terminal TPR domain. Here, we present the cryoEM structure of the oncogenic protein kinase client BRAF bound to HSP90-CDC37, showing how the V600E mutation favours BRAF association with HSP90-CDC37. Structures of HSP90-CDC37-BRAF complexes with PP5 in autoinhibited and activated conformations, together with proteomic analysis of its phosphatase activity on BRAF and CRAF, reveal how PP5 is activated by recruitment to HSP90 complexes. PP5 comprehensively dephosphorylates client proteins, removing interaction sites for regulatory partners such as 14-3-3 proteins and thus performing a 'factory reset' of the kinase prior to release.
History
DepositionMay 3, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14883.png

Downloads & links

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Map

FileDownload / File: emd_14883.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 328 pix.
= 282.08 Å		0.86 Å/pix.
x 328 pix.
= 282.08 Å		0.86 Å/pix.
x 328 pix.
= 282.08 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0017264087 - 1.7961782
Average (Standard dev.)0.0015282275 (±0.027419921)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 282.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_14883_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_14883_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : HSP90-CDC37-BRAF(V600E)-PP5 (closed) complex

EntireName: HSP90-CDC37-BRAF(V600E)-PP5 (closed) complex
Components
  • Complex: HSP90-CDC37-BRAF(V600E)-PP5 (closed) complex
    • Complex: Heat shock protein HSP 90-beta, Hsp90 co-chaperone Cdc37 and Serine/threonine-protein kinase B-raf
      • Protein or peptide: Heat shock protein HSP 90-beta
      • Protein or peptide: Hsp90 co-chaperone Cdc37
      • Protein or peptide: Serine/threonine-protein kinase B-raf
    • Complex: Serine/threonine-protein phosphatase 5
      • Protein or peptide: Serine/threonine-protein phosphatase 5
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: HSP90-CDC37-BRAF(V600E)-PP5 (closed) complex

SupramoleculeName: HSP90-CDC37-BRAF(V600E)-PP5 (closed) complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Heat shock protein HSP 90-beta, Hsp90 co-chaperone Cdc37 and Seri...

SupramoleculeName: Heat shock protein HSP 90-beta, Hsp90 co-chaperone Cdc37 and Serine/threonine-protein kinase B-raf
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Serine/threonine-protein phosphatase 5

SupramoleculeName: Serine/threonine-protein phosphatase 5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.223469 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MRGSHHHHHH HHGMALEVLF QGPSAMPEEV HHGEEEVETF AFQAEIAQLM SLIINTFYSN KEIFLRELIS NASDALDKIR YESLTDPSK LDSGKELKID IIPNPQERTL TLVDTGIGMT KADLINNLGT IAKSGTKAFM EALQAGADIS MIGQFGVGFY S AYLVAEKV ...String:
MRGSHHHHHH HHGMALEVLF QGPSAMPEEV HHGEEEVETF AFQAEIAQLM SLIINTFYSN KEIFLRELIS NASDALDKIR YESLTDPSK LDSGKELKID IIPNPQERTL TLVDTGIGMT KADLINNLGT IAKSGTKAFM EALQAGADIS MIGQFGVGFY S AYLVAEKV VVITKHNDDE QYAWESSAGG SFTVRADHGE PIGRGTKVIL HLKEDQTEYL EERRVKEVVK KHSQFIGYPI TL YLEKERE KEISDDEAEE EKGEKEEEDK DDEEKPKIED VGSDEEDDSG KDKKKKTKKI KEKYIDQEEL NKTKPIWTRN PDD ITQEEY GEFYKSLTND WEDHLAVKHF SVEGQLEFRA LLFIPRRAPF DLFENKKKKN NIKLYVRRVF IMDSCDELIP EYLN FIRGV VDSEDLPLNI SREMLQQSKI LKVIRKNIVK KCLELFSELA EDKENYKKFY EAFSKNLKLG IHEDSTNRRR LSELL RYHT SQSGDEMTSL SEYVSRMKET QKSIYYITGE SKEQVANSAF VERVRKRGFE VVYMTEPIDE YCVQQLKEFD GKSLVS VTK EGLELPEDEE EKKKMEESKA KFENLCKLMK EILDKKVEKV TISNRLVSSP CCIVTSTYGW TANMERIMKA QALRDNS TM GYMMAKKHLE INPDHPIVET LRQKAEADKN DKAVKDLVVL LFETALLSSG FSLEDPQTHS NRIYRMIKLG LGIDEDEV A AEEPNAAVPD EIPPLEGDED ASRMEEVD

UniProtKB: Heat shock protein HSP 90-beta

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Macromolecule #2: Hsp90 co-chaperone Cdc37

MacromoleculeName: Hsp90 co-chaperone Cdc37 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.853816 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
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 SVLEVLFQGP LEHHHHHHHH

UniProtKB: Hsp90 co-chaperone Cdc37

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Macromolecule #3: Serine/threonine-protein kinase B-raf

MacromoleculeName: Serine/threonine-protein kinase B-raf / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.934508 KDa
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: MGGSHHHHHH HHGGSWSHPQ FEKGGGSGGG SGGGSWSHPQ FEKGAETAVP NSLEVLFQGP SAMAALSGGG GGGAEPGQAL FNGDMEPEA GAGAGAAASS AADPAIPEEV WNIKQMIKLT QEHIEALLDK FGGEHNPPSI YLEAYEEYTS KLDALQQREQ Q LLESLGNG ...String:
MGGSHHHHHH HHGGSWSHPQ FEKGGGSGGG SGGGSWSHPQ FEKGAETAVP NSLEVLFQGP SAMAALSGGG GGGAEPGQAL FNGDMEPEA GAGAGAAASS AADPAIPEEV WNIKQMIKLT QEHIEALLDK FGGEHNPPSI YLEAYEEYTS KLDALQQREQ Q LLESLGNG TDFSVSSSAS MDTVTSSSSS SLSVLPSSLS VFQNPTDVAR SNPKSPQKPI VRVFLPNKQR TVVPARCGVT VR DSLKKAL MMRGLIPECC AVYRIQDGEK KPIGWDTDIS WLTGEELHVE VLENVPLTTH NFVRKTFFTL AFCDFCRKLL FQG FRCQTC GYKFHQRCST EVPLMCVNYD QLDLLFVSKF FEHHPIPQEE ASLAETALTS GSSPSAPASD SIGPQILTSP SPSK SIPIP QPFRPADEDH RNQFGQRDRS SSAPNVHINT IEPVNIDDLI RDQGFRGDGG STTGLSATPP ASLPGSLTNV KALQK SPGP QRERKSSSSS EDRNRMKTLG RRDSSDDWEI PDGQITVGQR IGSGSFGTVY KGKWHGDVAV KMLNVTAPTP QQLQAF KNE VGVLRKTRHV NILLFMGYST KPQLAIVTQW CEGSSLYHHL HIIETKFEMI KLIDIARQTA QGMDYLHAKS IIHRDLK SN NIFLHEDLTV KIGDFGLATE KSRWSGSHQF EQLSGSILWM APEVIRMQDK NPYSFQSDVY AFGIVLYELM TGQLPYSN I NNRDQIIFMV GRGYLSPDLS KVRSNCPKAM KRLMAECLKK KRDERPLFPQ ILASIELLAR SLPKIHRSAS EPSLNRAGF QTEDFSLYAC ASPKTPIQAG GYGAFPVH

UniProtKB: Serine/threonine-protein kinase B-raf

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Macromolecule #4: Serine/threonine-protein phosphatase 5

MacromoleculeName: Serine/threonine-protein phosphatase 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.020387 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DEPPADGALK RAEELKTQAN DYFKAKDYEN AIKFYSQAIE LNPSNAIYYG NRSLAYLRTE CYGYALGDAT RAIELDKKYI KGYYRRAAS NMALGKFRAA LRDYETVVKV KPHDKDAKMK YQECNKIVKQ KAFERAIAGD EHKRSVVDSL DIESMTIEDE Y SGPKLEDG ...String:
DEPPADGALK RAEELKTQAN DYFKAKDYEN AIKFYSQAIE LNPSNAIYYG NRSLAYLRTE CYGYALGDAT RAIELDKKYI KGYYRRAAS NMALGKFRAA LRDYETVVKV KPHDKDAKMK YQECNKIVKQ KAFERAIAGD EHKRSVVDSL DIESMTIEDE Y SGPKLEDG KVTISFMKEL MQWYKDQKKL HRKCAYQILV QVKEVLSKLS TLVETTLKET EKITVCGDTH GQFYDLLNIF EL NGLPSET NPYIFNGDFV DRGSFSVEVI LTLFGFKLLY PDHFHLLRGN HETDNMNQIY GFEGEVKAKY TAQMYELFSE VFE WLPLAQ CINGKVLIMH GGLFSEDGVT LDDIRKIERN RQPPDSGPMC DLLWSDPQPQ NGRSISKRGV SCQFGPDVTK AFLE ENNLD YIIRSHEVKA EGYEVAHGGR CVTVFSAPNY CDQMGNKASY IHLQGSDLRP QFHQFTAVPH PNVKPMAYAN TLLQL GMMH HHHHH

UniProtKB: Serine/threonine-protein phosphatase 5

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

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

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

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 105063
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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