[English] 日本語
Yorodumi
- PDB-4iyp: structure of the nPP2Ac-alpha4 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4iyp
Titlestructure of the nPP2Ac-alpha4 complex
Components
  • Immunoglobulin-binding protein 1
  • Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
KeywordsSIGNALING PROTEIN / alpha4 / PP2A / latency / helix motif
Function / homology
Function and homology information


regulation of dephosphorylation / Integration of energy metabolism / regulation of microtubule-based movement / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation ...regulation of dephosphorylation / Integration of energy metabolism / regulation of microtubule-based movement / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / positive regulation of microtubule binding / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / GABA receptor binding / protein phosphatase regulator activity / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / ERKs are inactivated / 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 / regulation of growth / negative regulation of stress-activated MAPK cascade / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of epithelial to mesenchymal transition / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / CTLA4 inhibitory signaling / Platelet sensitization by LDL / protein serine/threonine phosphatase activity / myosin phosphatase activity / regulation of cell differentiation / protein-serine/threonine phosphatase / ERK/MAPK targets / T cell homeostasis / regulation of G1/S transition of mitotic cell cycle / B cell activation / mesoderm development / phosphoprotein phosphatase activity / chromosome, centromeric region / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / DARPP-32 events / negative regulation of hippo signaling / response to tumor necrosis factor / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / protein dephosphorylation / response to interleukin-1 / : / protein tyrosine phosphatase activity / protein phosphatase 2A binding / meiotic cell cycle / RHO GTPases Activate Formins / response to lead ion / RAF activation / Spry regulation of FGF signaling / regulation of protein phosphorylation / tau protein binding / positive regulation of protein serine/threonine kinase activity / Degradation of beta-catenin by the destruction complex / PKR-mediated signaling / spindle pole / Negative regulation of MAPK pathway / Separation of Sister Chromatids / Cyclin D associated events in G1 / microtubule cytoskeleton / Regulation of TP53 Degradation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / intracellular signal transduction / protein heterodimerization activity / membrane raft / synapse / negative regulation of transcription by RNA polymerase II / signal transduction / mitochondrion / extracellular exosome / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
TAP42-like family / TAP46-like protein / TAP42/TAP46-like superfamily / TAP42-like family / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase ...TAP42-like family / TAP46-like protein / TAP42/TAP46-like superfamily / TAP42-like family / : / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Immunoglobulin-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.797 Å
AuthorsJiang, L. / Stanevich, V. / Satyshur, K.A. / Xing, Y.
CitationJournal: Nat Commun / Year: 2013
Title: Structural basis of protein phosphatase 2A stable latency.
Authors: Jiang, L. / Stanevich, V. / Satyshur, K.A. / Kong, M. / Watkins, G.R. / Wadzinski, B.E. / Sengupta, R. / Xing, Y.
History
DepositionJan 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoglobulin-binding protein 1
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform


Theoretical massNumber of molelcules
Total (without water)43,8232
Polymers43,8232
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.127, 116.127, 81.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Immunoglobulin-binding protein 1 / B-cell signal transduction molecule alpha 4 / Protein alpha-4 / CD79a-binding protein 1 / Protein ...B-cell signal transduction molecule alpha 4 / Protein alpha-4 / CD79a-binding protein 1 / Protein phosphatase 2/4/6 regulatory subunit / Renal carcinoma antigen NY-REN-16


Mass: 25926.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: alpha4, IBP1, IGBP1 / Plasmid: pQlink / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P78318
#2: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 17896.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PP2Ac, ppp2c, PPP2CA / Plasmid: pQlink / Production host: Escherichia coli (E. coli) / Strain (production host): PP2A
References: UniProt: P67775, protein-serine/threonine phosphatase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 12-15% PEG3350 (v/v), 0.3 M Na/K tartrate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.797→50 Å / Num. all: 15948 / Num. obs: 15948 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.1 % / Rsym value: 0.07 / Net I/σ(I): 28.7
Reflection shellResolution: 2.797→2.85 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 3.22 / Num. unique all: 777 / Rsym value: 0.545 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CRANKphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.797→34.428 Å / SU ML: 0.33 / σ(F): 0.61 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2224 796 5.01 %random
Rwork0.1787 ---
obs0.1807 15885 99.54 %-
all-15948 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.797→34.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 0 0 34 2708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092715
X-RAY DIFFRACTIONf_angle_d1.2073648
X-RAY DIFFRACTIONf_dihedral_angle_d18.2661035
X-RAY DIFFRACTIONf_chiral_restr0.079403
X-RAY DIFFRACTIONf_plane_restr0.005467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7967-2.97180.32251410.24492451X-RAY DIFFRACTION99
2.9718-3.20110.28721440.21782464X-RAY DIFFRACTION100
3.2011-3.5230.24741430.19442494X-RAY DIFFRACTION100
3.523-4.03210.20641240.16612516X-RAY DIFFRACTION100
4.0321-5.07740.21961170.14922542X-RAY DIFFRACTION100
5.0774-34.4310.18561270.18412622X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.4692-0.8326-0.89914.8414-0.53855.47640.4764-0.737-0.57380.9037-0.6941-1.56460.22130.4425-0.14030.6265-0.0321-0.10580.7445-0.06520.640372.1813-6.4288-19.3837
27.8738-0.4268-0.93397.0905-0.59255.1890.67170.12450.9635-0.0078-0.3357-0.5172-1.1327-0.2429-0.27110.4168-0.097-0.12040.4092-0.02910.46164.958-11.4909-24.7391
38.2236-1.5319-1.36523.97421.59635.80020.37640.06210.2543-0.3219-0.4080.2734-0.3037-0.4131-0.01680.4451-0.04110.00580.36470.00370.404555.2101-16.2999-29.7107
45.24522.11154.4858.14592.28674.10880.39980.39290.3219-0.3794-0.50190.75260.385-0.02510.12930.5637-0.0322-0.03760.54940.04240.550258.6864-32.8752-21.0238
53.6365-0.75342.53825.6731-1.59064.4630.2747-0.6837-0.3845-0.0651-0.15380.37490.3051-0.3517-0.05580.5104-0.01770.04520.3891-0.04880.325357.5126-23.083-25.5446
65.43141.21830.05457.01850.02215.88250.3258-1.5977-0.11951.2324-0.5034-0.6658-0.31730.91980.19570.6187-0.22140.09261.15130.13710.552139.3649-29.3743-5.4084
75.94765.3145-1.50084.7243-0.96132.34740.0956-0.9672-0.26860.3537-0.1581-0.13770.1762-0.11390.14520.4803-0.19460.16970.97090.17710.636228.1864-32.675-11.2736
88.6805-0.2288-1.89495.23653.65454.32110.6632-0.64210.7349-0.2257-0.6851.1362-0.8952-0.60690.06130.5341-0.03770.18250.8212-0.06270.672339.1582-18.5754-15.9322
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:28)
2X-RAY DIFFRACTION2chain 'A' and (resseq 29:72)
3X-RAY DIFFRACTION3chain 'A' and (resseq 73:154)
4X-RAY DIFFRACTION4chain 'A' and (resseq 155:180)
5X-RAY DIFFRACTION5chain 'A' and (resseq 181:221)
6X-RAY DIFFRACTION6chain 'C' and (resseq 6:64)
7X-RAY DIFFRACTION7chain 'C' and (resseq 65:126)
8X-RAY DIFFRACTION8chain 'C' and (resseq 127:153)

+
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