[English] 日本語
Yorodumi
- PDB-6alz: Crystal structure of Protein Phosphatase 1 bound to the natural i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6alz
TitleCrystal structure of Protein Phosphatase 1 bound to the natural inhibitor Tautomycetin
ComponentsSerine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity ...regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity / protein serine/threonine phosphatase activity / branching morphogenesis of an epithelial tube / glycogen metabolic process / protein-serine/threonine phosphatase / entrainment of circadian clock by photoperiod / Triglyceride catabolism / phosphatase activity / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / dephosphorylation / Downregulation of TGF-beta receptor signaling / protein dephosphorylation / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / dendritic spine / cell cycle / cell division / glutamatergic synapse / nucleolus / extracellular exosome / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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
Chem-BKM / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.208 Å
AuthorsChoy, M.S. / Peti, W. / Page, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)GM098482 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)NS091336 United States
American Diabetes Association1-14-A-CN-31 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: PP1:Tautomycetin Complex Reveals a Path toward the Development of PP1-Specific Inhibitors.
Authors: Choy, M.S. / Swingle, M. / D'Arcy, B. / Abney, K. / Rusin, S.F. / Kettenbach, A.N. / Page, R. / Honkanen, R.E. / Peti, W.
History
DepositionAug 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Dec 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,01413
Polymers68,3242
Non-polymers1,68911
Water5,188288
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0818
Polymers34,1621
Non-polymers9197
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9325
Polymers34,1621
Non-polymers7704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-75 kcal/mol
Surface area22790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.199, 78.855, 133.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsMonomer as determined by gel filtration

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / PP-1A


Mass: 34162.148 Da / Num. of mol.: 2 / Fragment: residues 7-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli)
References: UniProt: P62136, protein-serine/threonine phosphatase

-
Non-polymers , 5 types, 299 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-BKM / (2Z)-2-[(1R)-3-{[(2R,3S,4R,7S,8S,11S,13R,16E)-17-ethyl-4,8-dihydroxy-3,7,11,13-tetramethyl-6,15-dioxononadeca-16,18-dien-2-yl]oxy}-1-hydroxy-3-oxopropyl]-3-methylbut-2-enedioic acid / Tautomycetin diacid form


Mass: 624.759 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H52O11
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 6000, 1 M lithium chloride, 0.1 M Tris pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→38.8222 Å / Num. obs: 35351 / % possible obs: 97.5 % / Redundancy: 7 % / Biso Wilson estimate: 36.82 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.047 / Rrim(I) all: 0.127 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.814 / Num. unique obs: 2260 / CC1/2: 0.503 / Rpim(I) all: 0.427 / Rrim(I) all: 0.927 / % possible all: 72.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
Aimless0.5.17data scaling
PHASER1.11.1phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MOV

4mov


Resolution: 2.208→38.816 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 1795 5.11 %
Rwork0.1842 --
obs0.1858 35156 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.208→38.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 100 288 5052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024922
X-RAY DIFFRACTIONf_angle_d0.5626669
X-RAY DIFFRACTIONf_dihedral_angle_d7.5184015
X-RAY DIFFRACTIONf_chiral_restr0.038725
X-RAY DIFFRACTIONf_plane_restr0.003871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2075-2.26720.28761010.29871891X-RAY DIFFRACTION74
2.2672-2.33390.28641470.23542559X-RAY DIFFRACTION100
2.3339-2.40920.30091460.22592594X-RAY DIFFRACTION100
2.4092-2.49530.29891550.22172547X-RAY DIFFRACTION100
2.4953-2.59520.24531220.232600X-RAY DIFFRACTION100
2.5952-2.71330.27991360.22062616X-RAY DIFFRACTION100
2.7133-2.85630.25771410.21092603X-RAY DIFFRACTION100
2.8563-3.03520.23751460.20112602X-RAY DIFFRACTION100
3.0352-3.26940.23961400.19792589X-RAY DIFFRACTION100
3.2694-3.59820.21011540.17512608X-RAY DIFFRACTION100
3.5982-4.11840.21811180.15882685X-RAY DIFFRACTION100
4.1184-5.18680.13211390.13632672X-RAY DIFFRACTION100
5.1868-38.82220.18451500.17822795X-RAY DIFFRACTION100

+
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