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- EMDB-29895: Hsp90 provides platform for CRaf dephosphorylation by PP5 -

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Basic information

Entry
Database: EMDB / ID: EMD-29895
TitleHsp90 provides platform for CRaf dephosphorylation by PP5
Map dataComposite map, used to dock and improve model alignment.
Sample
  • Complex: Hsp90:Cdc37:CRaf:PP5 complex
    • Complex: Protein Phosphatase 5 (H304A)
      • Protein or peptide: Serine/threonine-protein phosphatase 5
    • Protein or peptide: Heat shock protein HSP 90-beta
    • Protein or peptide: Hsp90 co-chaperone Cdc37
    • Protein or peptide: RAF proto-oncogene serine/threonine-protein kinase
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MANGANESE (II) ION
Keywordschaperone / kinase / phosphatase / complex
Function / homology
Function and homology information


regulation of type II interferon-mediated signaling pathway / response to arachidonate / HSP90-CDC37 chaperone complex / death-inducing signaling complex assembly / peptidyl-threonine dephosphorylation / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / peptidyl-serine dephosphorylation / aryl hydrocarbon receptor complex / intermediate filament cytoskeleton organization ...regulation of type II interferon-mediated signaling pathway / response to arachidonate / HSP90-CDC37 chaperone complex / death-inducing signaling complex assembly / peptidyl-threonine dephosphorylation / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / peptidyl-serine dephosphorylation / aryl hydrocarbon receptor complex / intermediate filament cytoskeleton organization / dynein axonemal particle / histone methyltransferase binding / type B pancreatic cell proliferation / receptor ligand inhibitor activity / regulation of Rho protein signal transduction / positive regulation of type 2 mitophagy / ATP-dependent protein binding / positive regulation of protein localization to cell surface / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / protein kinase regulator activity / insulin secretion involved in cellular response to glucose stimulus / protein folding chaperone complex / regulation of cyclin-dependent protein serine/threonine kinase activity / response to morphine / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / post-transcriptional regulation of gene expression / protein serine/threonine phosphatase activity / GP1b-IX-V activation signalling / 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 / ERBB2-ERBB3 signaling pathway / Respiratory syncytial virus genome replication / telomerase holoenzyme complex 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 / pseudopodium / Assembly and release of respiratory syncytial virus (RSV) virions / neurotrophin TRK receptor signaling pathway / regulation of cell differentiation / dendritic growth cone / thyroid gland development / phosphoprotein phosphatase activity / The NLRP3 inflammasome / protein phosphatase activator activity / somatic stem cell population maintenance / extrinsic apoptotic signaling pathway via death domain receptors / Sema3A PAK dependent Axon repulsion / MAP kinase kinase kinase activity / regulation of protein ubiquitination / type II interferon-mediated signaling pathway / HSF1-dependent transactivation / response to unfolded protein / HSF1 activation / telomere maintenance via telomerase / negative regulation of protein-containing complex assembly / Attenuation phase / chaperone-mediated protein complex assembly / protein targeting / Schwann cell development / axonal growth cone / RHOBTB2 GTPase cycle / Purinergic signaling in leishmaniasis infection / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein dephosphorylation / supramolecular fiber organization / activation of adenylate cyclase activity / positive regulation of peptidyl-serine phosphorylation / : / DNA polymerase binding / heat shock protein binding / response to muscle stretch / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Signaling by ERBB2 / myelination / nitric-oxide synthase regulator activity
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 / 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 / Serine/threonine-protein phosphatase 5 / Hsp90 co-chaperone Cdc37
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJaime-Garza M / Nowotny CA / Coutandin D / Wang F / Tabios M / Agard DA
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118099 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10OD026881 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10OD020054 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1S10OD021741 United States
CitationJournal: Nat Commun / Year: 2023
Title: Hsp90 provides a platform for kinase dephosphorylation by PP5.
Authors: Maru Jaime-Garza / Carlos A Nowotny / Daniel Coutandin / Feng Wang / Mariano Tabios / David A Agard /
Abstract: The Hsp90 molecular chaperone collaborates with the phosphorylated Cdc37 cochaperone for the folding and activation of its many client kinases. As with many kinases, the Hsp90 client kinase CRaf is ...The Hsp90 molecular chaperone collaborates with the phosphorylated Cdc37 cochaperone for the folding and activation of its many client kinases. As with many kinases, the Hsp90 client kinase CRaf is activated by phosphorylation at specific regulatory sites. The cochaperone phosphatase PP5 dephosphorylates CRaf and Cdc37 in an Hsp90-dependent manner. Although dephosphorylating Cdc37 has been proposed as a mechanism for releasing Hsp90-bound kinases, here we show that Hsp90 bound kinases sterically inhibit Cdc37 dephosphorylation indicating kinase release must occur before Cdc37 dephosphorylation. Our cryo-EM structure of PP5 in complex with Hsp90:Cdc37:CRaf reveals how Hsp90 both activates PP5 and scaffolds its association with the bound CRaf to dephosphorylate phosphorylation sites neighboring the kinase domain. Thus, we directly show how Hsp90's role in maintaining protein homeostasis goes beyond folding and activation to include post translationally modifying its client kinases.
History
DepositionFeb 22, 2023-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29895.png

Downloads & links

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Map

FileDownload / File: emd_29895.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map, used to dock and improve model alignment.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 267.2 Å		0.84 Å/pix.
x 320 pix.
= 267.2 Å		0.84 Å/pix.
x 320 pix.
= 267.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00615
Minimum - Maximum-0.00045233668 - 0.03099295
Average (Standard dev.)0.00024724336 (±0.0013204123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 267.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened composite map, used for detailed model fitting.

Fileemd_29895_additional_1.map
AnnotationSharpened composite map, used for detailed model fitting.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Composite half map. Used to obtain composite resolution.

Fileemd_29895_half_map_1.map
AnnotationComposite half map. Used to obtain composite resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Composite half map. Used to obtain composite resolution.

Fileemd_29895_half_map_2.map
AnnotationComposite half map. Used to obtain composite resolution.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hsp90:Cdc37:CRaf:PP5 complex

EntireName: Hsp90:Cdc37:CRaf:PP5 complex
Components
  • Complex: Hsp90:Cdc37:CRaf:PP5 complex
    • Complex: Protein Phosphatase 5 (H304A)
      • Protein or peptide: Serine/threonine-protein phosphatase 5
    • Protein or peptide: Heat shock protein HSP 90-beta
    • Protein or peptide: Hsp90 co-chaperone Cdc37
    • Protein or peptide: RAF proto-oncogene serine/threonine-protein kinase
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: Hsp90:Cdc37:CRaf:PP5 complex

SupramoleculeName: Hsp90:Cdc37:CRaf:PP5 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Yeast purified Hsp90:Cdc37:CRaf complex incubated with e. Coli purified PP5 (mutant H304A). Sample then cross-linked with 0.05% glutaraldehyde for 15m at room temperature, and ran over S200 sizing column.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57 KDa

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Supramolecule #2: Protein Phosphatase 5 (H304A)

SupramoleculeName: Protein Phosphatase 5 (H304A) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4
Details: E coli purified Protein Phosphatase 5, with inactivating H304A mutation.
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
Details: Sequence starts with HRV 3C cleavage site, followed by human Hsp90B sequence.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.595484 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: GPGMPEEVHH GEEEVETFAF QAEIAQLMSL IINTFYSNKE IFLRELISNA SDALDKIRYE SLTDPSKLDS GKELKIDIIP NPQERTLTL VDTGIGMTKA DLINNLGTIA KSGTKAFMEA LQAGADISMI GQFGVGFYSA YLVAEKVVVI TKHNDDEQYA W ESSAGGSF ...String:
GPGMPEEVHH GEEEVETFAF QAEIAQLMSL IINTFYSNKE IFLRELISNA SDALDKIRYE SLTDPSKLDS GKELKIDIIP NPQERTLTL VDTGIGMTKA DLINNLGTIA KSGTKAFMEA LQAGADISMI GQFGVGFYSA YLVAEKVVVI TKHNDDEQYA W ESSAGGSF TVRADHGEPI GRGTKVILHL KEDQTEYLEE RRVKEVVKKH SQFIGYPITL YLEKEREKEI SDDEAEEEKG EK EEEDKDD EEKPKIEDVG SDEEDDSGKD KKKKTKKIKE KYIDQEELNK TKPIWTRNPD DITQEEYGEF YKSLTNDWED HLA VKHFSV EGQLEFRALL FIPRRAPFDL FENKKKKNNI KLYVRRVFIM DSCDELIPEY LNFIRGVVDS EDLPLNISRE MLQQ SKILK VIRKNIVKKC LELFSELAED KENYKKFYEA FSKNLKLGIH EDSTNRRRLS ELLRYHTSQS GDEMTSLSEY VSRMK ETQK SIYYITGESK EQVANSAFVE RVRKRGFEVV YMTEPIDEYC VQQLKEFDGK SLVSVTKEGL ELPEDEEEKK KMEESK AKF ENLCKLMKEI LDKKVEKVTI SNRLVSSPCC IVTSTYGWTA NMERIMKAQA LRDNSTMGYM MAKKHLEINP DHPIVET LR QKAEADKNDK AVKDLVVLLF ETALLSSGFS LEDPQTHSNR IYRMIKLGLG IDEDEVAAEE PNAAVPDEIP PLEGDEDA S RMEEVD

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: 45.352223 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
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 SVLEVLFQ

UniProtKB: Hsp90 co-chaperone Cdc37

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Macromolecule #3: RAF proto-oncogene serine/threonine-protein kinase

MacromoleculeName: RAF proto-oncogene serine/threonine-protein kinase / 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: 23.841605 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: NILLFMGYMT KDNLAIVTQW CEGSSLYKHL HVQETKFQMF QLIDIARQTA QGMDYLHAKN IIHRDMKSNN IFLHEGLTVK IGDFGLATV KSRWSGSQQV EQPTGSVLWM APEVIRMQDN NPFSFQSDVY SYGIVLYELM TGELPYSHIN NRDQIIFMVG R GYASPDLS ...String:
NILLFMGYMT KDNLAIVTQW CEGSSLYKHL HVQETKFQMF QLIDIARQTA QGMDYLHAKN IIHRDMKSNN IFLHEGLTVK IGDFGLATV KSRWSGSQQV EQPTGSVLWM APEVIRMQDN NPFSFQSDVY SYGIVLYELM TGELPYSHIN NRDQIIFMVG R GYASPDLS KLYKNCPKAM KRLVADCVKK VKEERPLFPQ ILSSIELLQ

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

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Macromolecule #4: Serine/threonine-protein phosphatase 5

MacromoleculeName: Serine/threonine-protein phosphatase 5 / type: protein_or_peptide / ID: 4
Details: Sequence starts with HRV 3C cleavage site, continued by human PP5 sequence.
Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.18473 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: GPGSMAMAEG ERTECAEPPR DEPPADGALK RAEELKTQAN DYFKAKDYEN AIKFYSQAIE LNPSNAIYYG NRSLAYLRTE CYGYALGDA TRAIELDKKY IKGYYRRAAS NMALGKFRAA LRDYETVVKV KPHDKDAKMK YQECNKIVKQ KAFERAIAGD E HKRSVVDS ...String:
GPGSMAMAEG ERTECAEPPR DEPPADGALK RAEELKTQAN DYFKAKDYEN AIKFYSQAIE LNPSNAIYYG NRSLAYLRTE CYGYALGDA TRAIELDKKY IKGYYRRAAS NMALGKFRAA LRDYETVVKV KPHDKDAKMK YQECNKIVKQ KAFERAIAGD E HKRSVVDS LDIESMTIED EYSGPKLEDG KVTISFMKEL MQWYKDQKKL HRKCAYQILV QVKEVLSKLS TLVETTLKET EK ITVCGDT HGQFYDLLNI FELNGLPSET NPYIFNGDFV DRGSFSVEVI LTLFGFKLLY PDHFHLLRGN AETDNMNQIY GFE GEVKAK YTAQMYELFS EVFEWLPLAQ CINGKVLIMH GGLFSEDGVT LDDIRKIERN RQPPDSGPMC DLLWSDPQPQ NGRS ISKRG VSCQFGPDVT KAFLEENNLD YIIRSHEVKA EGYEVAHGGR CVTVFSAPNY CDQMGNKASY IHLQGSDLRP QFHQF TAVP HPNVKPMAYA NTLLQLGMM

UniProtKB: Serine/threonine-protein phosphatase 5

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Macromolecule #5: POTASSIUM ION

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

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #9: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 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

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
50.0 mMKClKCl
10.0 mMMgCl2Magnesium Chloride
0.5 mMC9H15O6PTCEP
1.0 mMC10H16N2O8EDTA
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Support film - Film thickness: 1
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3UL OF SAMPLE 10C 100% HUMIDITY 30S WAIT TIME 3S BLOT TIME -2 BLOT FORCE.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
SoftwareName: SerialEM (ver. 3.8-beta)
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 4160 / Average electron dose: 69.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3730385 / Details: Gaussian blob particle picking in cryoSPARC.
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4.1)
RELION (ver. 3.1.3)CTF refinement

Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5fwl


Details: 5FWL was used to fit the Hsp90 complex. 1WAO and 1S95 were used to fit the PP5 components.
Final reconstructionNumber classes used: 3 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
Software:
Namedetails
RELION (ver. 3.1.3)
UCSF ChimeraX (ver. 1.2.5)vop max was used for the creation of the composite map

Details: Three different maps were used for final composite map: Hsp90:Cdc37: 288k particles, 3.2A PP5 TPR: 215k particles, 3.3A PP5 catalytic domain and CRaf kinase C-lobe: 22k particles, 4.0A ...Details: Three different maps were used for final composite map: Hsp90:Cdc37: 288k particles, 3.2A PP5 TPR: 215k particles, 3.3A PP5 catalytic domain and CRaf kinase C-lobe: 22k particles, 4.0A Composite half maps were used to get the final resolution in Relion PostProcessing. All original maps provided in the "Related entries" tab.
Number images used: 522000
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 3D classificationSoftware - Name: RELION (ver. 3.1.3)
Details: Initial refinement on the Hsp90 component of the complex was followed up with focused classification with subtraction to obtain the separate maps used in this composite entry.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5fwl

source_name: PDB, initial_model_type: experimental model

1wao

source_name: PDB, initial_model_type: experimental model

1s95

source_name: PDB, initial_model_type: experimental model
DetailsThis model was built using rigid body docking in Chimera and ChimeraX for all main chains, and RosettaCM to add remaining fragments not included in previous models. Refinement was done using iterative Phenix and RosettaRelax, and finalized with ISOLDE.
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8gae:
Hsp90 provides platform for CRaf dephosphorylation by PP5

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  • 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

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