[English] 日本語
Yorodumi
- PDB-1fjm: Protein serine/threonine phosphatase-1 (alpha isoform, type 1) co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fjm
TitleProtein serine/threonine phosphatase-1 (alpha isoform, type 1) complexed with microcystin-LR toxin
Components
  • PROTEIN SERINE/THREONINE PHOSPHATASE-1 (ALPHA ISOFORM, TYPE 1)
  • microcystin LR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / TOXIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of translational initiation by eIF2 alpha dephosphorylation / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / fatty acid derivative binding / beta-catenin destruction complex disassembly / cell cycle / regulation of glycogen catabolic process / peptidyl-serine dephosphorylation / regulation of glycogen biosynthetic process / PTW/PP1 phosphatase complex ...regulation of translational initiation by eIF2 alpha dephosphorylation / protein serine/threonine phosphatase activity => GO:0004722 / protein serine/threonine phosphatase activity => GO:0004722 / fatty acid derivative binding / beta-catenin destruction complex disassembly / cell cycle / regulation of glycogen catabolic process / peptidyl-serine dephosphorylation / regulation of glycogen biosynthetic process / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / peptidyl-threonine dephosphorylation / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / cadherin binding involved in cell-cell adhesion / protein phosphatase 1 binding / regulation of translational initiation in response to stress / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / dephosphorylation / regulation of canonical Wnt signaling pathway / regulation of translational initiation / glycogen metabolic process / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / Triglyceride catabolism / entrainment of circadian clock by photoperiod / protein serine/threonine phosphatase activity / phosphatase activity / phosphoprotein phosphatase activity / negative regulation of transcription elongation by RNA polymerase II / protein phosphatase activator activity / transition metal ion binding / DARPP-32 events / viral process / ribonucleoprotein complex binding / protein dephosphorylation / negative regulation of protein binding / lung development / Downregulation of TGF-beta receptor signaling / adherens junction / circadian regulation of gene expression / positive regulation of transcription elongation by RNA polymerase II / regulation of circadian rhythm / response to lead ion / : / positive regulation of canonical Wnt signaling pathway / presynapse / perikaryon / dendritic spine / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type ...Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Microcystin LR / BETA-MERCAPTOETHANOL / : / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Microcystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsGoldberg, J. / Nairn, A.C. / Kuriyan, J.
CitationJournal: Nature / Year: 1995
Title: Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1.
Authors: Goldberg, J. / Huang, H.B. / Kwon, Y.G. / Greengard, P. / Nairn, A.C. / Kuriyan, J.
History
DepositionDec 17, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN SERINE/THREONINE PHOSPHATASE-1 (ALPHA ISOFORM, TYPE 1)
B: PROTEIN SERINE/THREONINE PHOSPHATASE-1 (ALPHA ISOFORM, TYPE 1)
M: microcystin LR
N: microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,52110
Polymers77,1444
Non-polymers3766
Water4,990277
1
A: PROTEIN SERINE/THREONINE PHOSPHATASE-1 (ALPHA ISOFORM, TYPE 1)
M: microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7605
Polymers38,5722
Non-polymers1883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN SERINE/THREONINE PHOSPHATASE-1 (ALPHA ISOFORM, TYPE 1)
N: microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7605
Polymers38,5722
Non-polymers1883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.740, 77.110, 130.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.251034, -0.966528, 0.052974), (0.966022, 0.253628, 0.049734), (-0.061505, 0.038689, 0.997357)
Vector: 102.07645, -60.61361, -23.67177)

-
Components

#1: Protein PROTEIN SERINE/THREONINE PHOSPHATASE-1 (ALPHA ISOFORM, TYPE 1)


Mass: 37558.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: P08129, UniProt: P62139*PLUS, protein-serine/threonine phosphatase
#2: Protein/peptide microcystin LR


Type: Oligopeptide / Class: Toxin / Mass: 1014.195 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Microcystis aeruginosa (bacteria) / References: NOR: NOR00109, Microcystin LR
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Compound detailsELECTRON DENSITY MAPS SHOW THAT RESIDUE CYSTEINE 127 IS OXIDIZED, WITH A TERMINAL SULPHINYL OR ...ELECTRON DENSITY MAPS SHOW THAT RESIDUE CYSTEINE 127 IS OXIDIZED, WITH A TERMINAL SULPHINYL OR SULPHONYL GROUP. HOWEVER, THE TERMINAL OXYGEN ATOMS OF THE SIDE CHAIN HAVE NOT BEEN MODELLED.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
18 mg/mlprotein1drop
20.5 M1dropNaCl
450 mMTris-HCl1drop
510 mMbeta-mercaptoethanol1drop
60.9 mM1dropMnCl2
70.1 mMEGTA1drop
865 mMTris-HCl1reservoir
9200 mM1reservoirMgCl2
3microcystin-LR1drop4-fold molar excess
1032 %PEG40001reservoir
111.0 M1,7-diaminoheptane1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. obs: 38768 / % possible obs: 99.5 % / Num. measured all: 180676 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 97.2 % / Rmerge(I) obs: 0.136

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→6 Å / Rfactor Rwork: 0.178 / Rfactor obs: 0.178 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4715 0 12 277 5004
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Num. reflection all: 36974 / Rfactor all: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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