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- PDB-6obr: PP1 Y134A in complex with Microcystin LR -

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Basic information

Entry
Database: PDB / ID: 6obr
TitlePP1 Y134A in complex with Microcystin LR
Components
  • Microcystin LR
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE/TOXIN / phosphatase / HYDROLASE-TOXIN complex
Function / homology
Function and homology information


regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / regulation of translational initiation in response to stress ...regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / PTW/PP1 phosphatase complex / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / 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 / glycogen metabolic process / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / protein serine/threonine phosphatase activity / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / negative regulation of transcription elongation by RNA polymerase II / transition metal ion binding / DARPP-32 events / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / 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 / : / presynapse / perikaryon / dendritic spine / protein stabilization / iron ion binding / cell division / nucleolus / glutamatergic synapse / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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 ...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 / : / : / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Microcystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChoy, M.S. / Moon, T.M. / Bray, J.A. / Archuleta, T.L. / Shi, W. / Peti, W. / Page, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: SDS22 selectively recognizes and traps metal-deficient inactive PP1.
Authors: Choy, M.S. / Moon, T.M. / Ravindran, R. / Bray, J.A. / Robinson, L.C. / Archuleta, T.L. / Shi, W. / Peti, W. / Tatchell, K. / Page, R.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jul 9, 2025Group: Database references / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_ref
Item: _struct_ref.db_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,45910
Polymers70,1694
Non-polymers2916
Water6,287349
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2305
Polymers35,0842
Non-polymers1453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-28 kcal/mol
Surface area11870 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
E: Microcystin LR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2305
Polymers35,0842
Non-polymers1453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-29 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.932, 76.550, 131.213
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34070.055 Da / Num. of mol.: 2 / Fragment: UNP residues 7-300 / Mutation: Y134A
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
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 20% PEG6000, 1 M lithium chloride, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 5, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.5→38.28 Å / Num. obs: 105369 / % possible obs: 99.8 % / Redundancy: 7.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.6
Reflection shellResolution: 1.5→1.52 Å / Rmerge(I) obs: 1.127 / Num. unique obs: 5069 / CC1/2: 0.691

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MOV

4mov


Resolution: 1.5→38.275 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22
RfactorNum. reflection% reflection
Rfree0.2101 5395 5.13 %
Rwork0.1878 --
obs0.1889 105245 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→38.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4621 0 148 349 5118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155017
X-RAY DIFFRACTIONf_angle_d0.9176792
X-RAY DIFFRACTIONf_dihedral_angle_d20.5921835
X-RAY DIFFRACTIONf_chiral_restr0.085741
X-RAY DIFFRACTIONf_plane_restr0.005893
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4988-1.51590.33791710.313159X-RAY DIFFRACTION96
1.5159-1.53370.31711550.28093280X-RAY DIFFRACTION100
1.5337-1.55240.30541870.2763310X-RAY DIFFRACTION100
1.5524-1.57210.2811540.26463325X-RAY DIFFRACTION100
1.5721-1.59280.27151490.25393353X-RAY DIFFRACTION100
1.5928-1.61460.25631790.24063249X-RAY DIFFRACTION100
1.6146-1.63760.23771780.23823315X-RAY DIFFRACTION100
1.6376-1.66210.28091680.24063329X-RAY DIFFRACTION100
1.6621-1.68810.27671900.24393243X-RAY DIFFRACTION100
1.6881-1.71570.26331690.2383305X-RAY DIFFRACTION100
1.7157-1.74530.26661840.23183319X-RAY DIFFRACTION100
1.7453-1.7770.27571830.22613312X-RAY DIFFRACTION100
1.777-1.81120.24531770.22393296X-RAY DIFFRACTION100
1.8112-1.84820.2621990.22273299X-RAY DIFFRACTION100
1.8482-1.88840.2541700.22733308X-RAY DIFFRACTION100
1.8884-1.93230.26431960.22043301X-RAY DIFFRACTION100
1.9323-1.98060.23591810.21233333X-RAY DIFFRACTION100
1.9806-2.03420.22061640.20253328X-RAY DIFFRACTION100
2.0342-2.0940.21872020.19743309X-RAY DIFFRACTION100
2.094-2.16160.22011770.19643325X-RAY DIFFRACTION100
2.1616-2.23890.21361850.19413324X-RAY DIFFRACTION100
2.2389-2.32850.23251830.19113348X-RAY DIFFRACTION100
2.3285-2.43450.21941910.18953318X-RAY DIFFRACTION100
2.4345-2.56280.20871780.18463348X-RAY DIFFRACTION100
2.5628-2.72330.20091940.1893350X-RAY DIFFRACTION100
2.7233-2.93350.18871950.18473348X-RAY DIFFRACTION100
2.9335-3.22860.2221590.17623408X-RAY DIFFRACTION100
3.2286-3.69540.16951850.16473396X-RAY DIFFRACTION100
3.6954-4.65460.16171990.14553414X-RAY DIFFRACTION100
4.6546-38.28750.19581930.16663598X-RAY DIFFRACTION100

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