[English] 日本語
Yorodumi
- EMDB-42428: Protein Phosphatase 2A B55 subunit in complex with IER5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42428
TitleProtein Phosphatase 2A B55 subunit in complex with IER5
Map dataProtein Phosphatase 2A B55 subunit in complex with IER5
Sample
  • Complex: PP2A complex with B55 regulatory subunit bound by IER5
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
    • Protein or peptide: Immediate early response gene 5 protein
  • Ligand: FE (III) ION
  • Ligand: ZINC ION
KeywordsPhosphatase / complex / SIGNALING PROTEIN
Function / homology
Function and homology information


positive regulation of cellular response to heat / regulation of chromosome segregation / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity ...positive regulation of cellular response to heat / regulation of chromosome segregation / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / peptidyl-threonine dephosphorylation / meiotic sister chromatid cohesion, centromeric / INTAC complex / FAR/SIN/STRIPAK complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein phosphatase regulator activity / GABA receptor binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / protein antigen binding / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / RNA polymerase II transcription initiation surveillance / Co-stimulation by CD28 / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of epithelial to mesenchymal transition / response to morphine / Co-inhibition by CTLA4 / Platelet sensitization by LDL / protein-serine/threonine phosphatase / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / ERK/MAPK targets / protein serine/threonine phosphatase activity / mesoderm development / vascular endothelial cell response to oscillatory fluid shear stress / T cell homeostasis / regulation of G1/S transition of mitotic cell cycle / regulation of cell differentiation / regulation of microtubule polymerization / phosphoprotein phosphatase activity / lateral plasma membrane / chromosome, centromeric region / DARPP-32 events / enzyme-substrate adaptor activity / negative regulation of hippo signaling / Cyclin A/B1/B2 associated events during G2/M transition / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein dephosphorylation / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein tyrosine phosphatase activity / Resolution of Sister Chromatid Cohesion / protein phosphatase 2A binding / AURKA Activation by TPX2 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Spry regulation of FGF signaling / meiotic cell cycle / chromosome segregation / Degradation of beta-catenin by the destruction complex / RAF activation / RHO GTPases Activate Formins / negative regulation of canonical Wnt signaling pathway / PKR-mediated signaling / tau protein binding / response to lead ion / Negative regulation of MAPK pathway / Cyclin D associated events in G1 / Separation of Sister Chromatids / Regulation of TP53 Degradation / spindle pole / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / regulation of cell population proliferation / cellular response to heat / microtubule cytoskeleton / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly
Similarity search - Function
Immediate early response / Immediate early response protein (IER) / Protein phosphatase 2A regulatory subunit PR55 / Protein phosphatase 2A regulatory subunit PR55, conserved site / Protein phosphatase 2A regulatory subunit PR55 signature 1. / Protein phosphatase 2A regulatory subunit PR55 signature 2. / : / : / HEAT repeat / HEAT repeat ...Immediate early response / Immediate early response protein (IER) / Protein phosphatase 2A regulatory subunit PR55 / Protein phosphatase 2A regulatory subunit PR55, conserved site / Protein phosphatase 2A regulatory subunit PR55 signature 1. / Protein phosphatase 2A regulatory subunit PR55 signature 2. / : / : / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Armadillo-like helical / Armadillo-type fold / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Immediate early response gene 5 protein
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsJones DTD / Cao R / Rawson SD / Blacklow SC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA220340 United States
CitationJournal: To Be Published
Title: Protein Phosphatase 2A B55 subunit in complex with IER5
Authors: Jones DTD / Cao R / Rawson SD / Blacklow SC
History
DepositionOct 19, 2023-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42428.png

Downloads & links

-
Map

FileDownload / File: emd_42428.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationProtein Phosphatase 2A B55 subunit in complex with IER5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å		0.83 Å/pix.
x 360 pix.
= 297. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.89121747 - 1.2246362
Average (Standard dev.)-0.0006465101 (±0.025100712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #2

Fileemd_42428_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: #1

Fileemd_42428_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_42428_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_42428_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PP2A complex with B55 regulatory subunit bound by IER5

EntireName: PP2A complex with B55 regulatory subunit bound by IER5
Components
  • Complex: PP2A complex with B55 regulatory subunit bound by IER5
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
    • Protein or peptide: Immediate early response gene 5 protein
  • Ligand: FE (III) ION
  • Ligand: ZINC ION

-
Supramolecule #1: PP2A complex with B55 regulatory subunit bound by IER5

SupramoleculeName: PP2A complex with B55 regulatory subunit bound by IER5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)

-
Macromolecule #1: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.065211 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSSHHHHHH SAVDENLYFQ GGGRMAAADG DDSLYPIAVL IDELRNEDVQ LRLNSIKKLS TIALALGVER TRSELLPFLT DTIYDEDEV LLALAEQLGT FTTLVGGPEY VHCLLPPLES LATVEETVVR DKAVESLRAI SHEHSPSDLE AHFVPLVKRL A GGDWFTSR ...String:
MGSSHHHHHH SAVDENLYFQ GGGRMAAADG DDSLYPIAVL IDELRNEDVQ LRLNSIKKLS TIALALGVER TRSELLPFLT DTIYDEDEV LLALAEQLGT FTTLVGGPEY VHCLLPPLES LATVEETVVR DKAVESLRAI SHEHSPSDLE AHFVPLVKRL A GGDWFTSR TSACGLFSVC YPRVSSAVKA ELRQYFRNLC SDDTPMVRRA AASKLGEFAK VLELDNVKSE IIPMFSNLAS DE QDSVRLL AVEACVNIAQ LLPQEDLEAL VMPTLRQAAE DKSWRVRYMV ADKFTELQKA VGPEITKTDL VPAFQNLMKD CEA EVRAAA SHKVKEFCEN LSADCRENVI MSQILPCIKE LVSDANQHVK SALASVIMGL SPILGKDNTI EHLLPLFLAQ LKDE CPEVR LNIISNLDCV NEVIGIRQLS QSLLPAIVEL AEDAKWRVRL AIIEYMPLLA GQLGVEFFDE KLNSLCMAWL VDHVY AIRE AATSNLKKLV EKFGKEWAHA TIIPKVLAMS GDPNYLHRMT TLFCINVLSE VCGQDITTKH MLPTVLRMAG DPVANV RFN VAKSLQKIGP ILDNSTLQSE VKPILEKLTQ DQDVDVKYFA QEALTVLSLA

UniProtKB: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform

-
Macromolecule #2: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.762012 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAGAGGGNDI QWCFSQVKGA VDDDVAEADI ISTVEFNHSG ELLATGDKGG RVVIFQQEQE NKIQSHSRGE YNVYSTFQSH EPEFDYLKS LEIEEKINKI RWLPQKNAAQ FLLSTNDKTI KLWKISERDK RPEGYNLKEE DGRYRDPTTV TTLRVPVFRP M DLMVEASP ...String:
MAGAGGGNDI QWCFSQVKGA VDDDVAEADI ISTVEFNHSG ELLATGDKGG RVVIFQQEQE NKIQSHSRGE YNVYSTFQSH EPEFDYLKS LEIEEKINKI RWLPQKNAAQ FLLSTNDKTI KLWKISERDK RPEGYNLKEE DGRYRDPTTV TTLRVPVFRP M DLMVEASP RRIFANAHTY HINSISINSD YETYLSADDL RINLWHLEIT DRSFNIVDIK PANMEELTEV ITAAEFHPNS CN TFVYSSS KGTIRLCDMR ASALCDRHSK LFEEPEDPSN RSFFSEIISS ISDVKFSHSG RYMMTRDYLS VKIWDLNMEN RPV ETYQVH EYLRSKLCSL YENDCIFDKF ECCWNGSDSV VMTGSYNNFF RMFDRNTKRD ITLEASRENN KPRTVLKPRK VCAS GKRKK DEISVDSLDF NKKILHTAWH PKENIIAVAT TNNLYIFQDK VN

UniProtKB: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform

-
Macromolecule #3: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...

MacromoleculeName: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.259879 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYKDDDDKS AVDENLYFQG GGRMDEKVFT KELDQWIEQL NECKQLSESQ VKSLCEKAKE ILTKESNVQE VRCPVTVCGD VHGQFHDLM ELFRIGGKSP DTNYLFMGDY VDRGYYSVET VTLLVALKVR YRERITILRG NHESRQITQV YGFYDECLRK Y GNANVWKY ...String:
MDYKDDDDKS AVDENLYFQG GGRMDEKVFT KELDQWIEQL NECKQLSESQ VKSLCEKAKE ILTKESNVQE VRCPVTVCGD VHGQFHDLM ELFRIGGKSP DTNYLFMGDY VDRGYYSVET VTLLVALKVR YRERITILRG NHESRQITQV YGFYDECLRK Y GNANVWKY FTDLFDYLPL TALVDGQIFC LHGGLSPSID TLDHIRALDR LQEVPHEGPM CDLLWSDPDD RGGWGISPRG AG YTFGQDI SETFNHANGL TLVSRAHQLV MEGYNWCHDR NVVTIFSAPN YCYRCGNQAA IMELDDTLKY SFLQFDPAPR RGE PHVTRR TPDYFL

UniProtKB: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform

-
Macromolecule #4: Immediate early response gene 5 protein

MacromoleculeName: Immediate early response gene 5 protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.532818 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MDWSHPQFEK SAVDENLYFQ GGGRMEFKLE AHRIVSISLG KIYNSRVQRG GIKLHKNLLV SLVLRSARQV YLSD

UniProtKB: Immediate early response gene 5 protein

-
Macromolecule #5: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

-
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66568
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationNumber classes: 4
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