[English] 日本語
Yorodumi
- PDB-5zt0: Crystal Structure of Protein Phosphate 1 Complexed with PP1 bindi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zt0
TitleCrystal Structure of Protein Phosphate 1 Complexed with PP1 binding domain of GL
Components
  • Protein phosphatase 1 regulatory subunit 3B
  • Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
KeywordsHYDROLASE / protein phosphorylase 1 holoenzyme
Function / homology
Function and homology information


[phosphorylase] phosphatase activity / glycogen binding / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / regulation of glycogen biosynthetic process / PTW/PP1 phosphatase complex / DARPP-32 events / protein phosphatase type 1 complex / glycogen granule / RNA polymerase II promoter clearance ...[phosphorylase] phosphatase activity / glycogen binding / regulation of glycogen catabolic process / positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled / regulation of glycogen biosynthetic process / PTW/PP1 phosphatase complex / DARPP-32 events / protein phosphatase type 1 complex / 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 / protein phosphatase regulator activity / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of glycogen catabolic process / glycogen metabolic process / entrainment of circadian clock by photoperiod / protein-serine/threonine phosphatase / branching morphogenesis of an epithelial tube / 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 / positive regulation of glycogen biosynthetic process / ribonucleoprotein complex binding / protein dephosphorylation / lung development / adherens junction / circadian regulation of gene expression / positive regulation of transcription elongation by RNA polymerase II / regulation of circadian rhythm / response to lead ion / regulation of translation / presynapse / perikaryon / dendritic spine / chromosome, telomeric region / protein stabilization / iron ion binding / cell division / nucleolus / glutamatergic synapse / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein phosphatase 1 regulatory subunit 3B / Protein phosphatase 1 regulatory subunit 3B/C/D, metazoa / : / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain ...Protein phosphatase 1 regulatory subunit 3B / Protein phosphatase 1 regulatory subunit 3B/C/D, metazoa / : / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / 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
: / PHOSPHATE ION / Serine/threonine-protein phosphatase PP1-alpha catalytic subunit / Protein phosphatase 1 regulatory subunit 3B
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32042678506 Å
AuthorsYu, J. / Xiang, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2011CB910500 China
CitationJournal: FEBS J. / Year: 2018
Title: Structural basis for protein phosphatase 1 recruitment by glycogen-targeting subunits
Authors: Yu, J. / Deng, T. / Xiang, S.
History
DepositionMay 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
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_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.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.value / _struct_conn.pdbx_dist_value / _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

-
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
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
D: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
E: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
F: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
G: Protein phosphatase 1 regulatory subunit 3B
H: Protein phosphatase 1 regulatory subunit 3B
I: Protein phosphatase 1 regulatory subunit 3B
J: Protein phosphatase 1 regulatory subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,48128
Polymers235,25210
Non-polymers1,22918
Water00
1
A: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
G: Protein phosphatase 1 regulatory subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1585
Polymers41,9532
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-30 kcal/mol
Surface area13400 Å2
MethodPISA
2
B: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
I: Protein phosphatase 1 regulatory subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1585
Polymers41,9532
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-29 kcal/mol
Surface area13650 Å2
MethodPISA
3
C: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
H: Protein phosphatase 1 regulatory subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1585
Polymers41,9532
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-30 kcal/mol
Surface area13510 Å2
MethodPISA
4
D: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
J: Protein phosphatase 1 regulatory subunit 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1585
Polymers41,9532
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-31 kcal/mol
Surface area13400 Å2
MethodPISA
5
E: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9244
Polymers33,7201
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-21 kcal/mol
Surface area12680 Å2
MethodPISA
6
F: Serine/threonine-protein phosphatase PP1-alpha catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9244
Polymers33,7201
Non-polymers2053
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-21 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.530, 106.530, 187.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32

-
Components

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


Mass: 33719.645 Da / Num. of mol.: 6 / Fragment: UNP residues 7-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppp1ca, Ppp1a / Production host: Escherichia coli (E. coli)
References: UniProt: P62137, protein-serine/threonine phosphatase
#2: Protein
Protein phosphatase 1 regulatory subunit 3B


Mass: 8233.532 Da / Num. of mol.: 4 / Fragment: UNP residues 31-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R3B / Production host: Escherichia coli (E. coli) / References: UniProt: Q86XI6
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.9 % / Description: rod shaped
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 0.1M Na/K phosphate, 26%MPD

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.41
11K, H, -L20.103
11-h,-k,l30.097
11-K, -H, -L40.39
ReflectionResolution: 3.32→92.258 Å / Num. obs: 35147 / % possible obs: 98.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 97.3634629316 Å2 / Rmerge(I) obs: 0.197 / Net I/av σ(I): 3.4 / Net I/σ(I): 6.8
Reflection shellResolution: 3.32→3.5 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.644 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5089 / CC1/2: 0.507 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PHENIX1.10.1_2155refinement
SCALA3.3.22data scaling
iMOSFLM7.2.1data reduction
MOLREP11.0.05phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MP0

4mp0


Resolution: 3.32042678506→41.7919786749 Å / SU ML: 0.319973062552 / Cross valid method: THROUGHOUT / σ(F): 1.42921288806 / Phase error: 24.5433750059
RfactorNum. reflection% reflection
Rfree0.233151062001 1748 4.98659211502 %
Rwork0.199851525938 --
obs0.20157166675 35054 99.7808203581 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 106.693222412 Å2
Refinement stepCycle: LAST / Resolution: 3.32042678506→41.7919786749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14732 0 42 0 14774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025126818083615080
X-RAY DIFFRACTIONf_angle_d0.6125486054820362
X-RAY DIFFRACTIONf_chiral_restr0.03921647355292190
X-RAY DIFFRACTIONf_plane_restr0.002811681094952648
X-RAY DIFFRACTIONf_dihedral_angle_d12.22374803225630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3204-3.41810.2508656110291600.2141928512622819X-RAY DIFFRACTION99.966442953
3.4181-3.52840.2719145052851300.1980251027162779X-RAY DIFFRACTION100
3.5284-3.65440.2300261582031320.2017710209062773X-RAY DIFFRACTION99.9655884377
3.6544-3.80060.1834750049581500.1797422993732769X-RAY DIFFRACTION99.9657534247
3.8006-3.97350.1996157764721320.1744576302972790X-RAY DIFFRACTION99.9657885734
3.9735-4.18280.1971432846081240.1759990262882814X-RAY DIFFRACTION99.9659748214
4.1828-4.44460.2193376643611520.1719922228562772X-RAY DIFFRACTION99.9658119658
4.4446-4.78730.2180320025891320.1933463415392786X-RAY DIFFRACTION99.8631074606
4.7873-5.26820.2543327403261400.2278583969112791X-RAY DIFFRACTION99.931810433
5.2682-6.02860.2693506361660.2483210299592742X-RAY DIFFRACTION99.8283556471
6.0286-7.5880.2652793946061860.235689888352756X-RAY DIFFRACTION100
7.588-41.79530.214227877511440.1818610307442715X-RAY DIFFRACTION97.9445015416
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)
10.88150.47320.2181.48260.41131.22750.0286-0.0054-0.0269-0.0041-0.03150.0261-0.0159-0.33580.00290.1269-0.1593-0.01010.3154-0.00290.5174-5.3209-31.88790.0107
21.1299-0.27230.11711.3981-0.03881.65610.0027-0.0855-0.0464-0.09670.00530.07630.2925-0.0893-0.0080.4675-0.0277-0.01130.01120.00980.511116.7511-27.614441.4643
31.3942-0.13310.03760.65680.21491.62810.10580.0435-0.02660.0031-0.11180.04520.1615-0.08390.00610.0995-0.1307-0.00380.2349-0.03260.5484-30.339111.7204-5.1302
41.94090.47350.27651.34240.47951.81950.0639-0.06050.1436-0.0047-0.006-0.0472-0.06880.0444-0.05790.1132-0.18050.02180.2925-0.00840.497232.07-0.435215.7966
51.07060.0550.11270.5997-0.05011.2472-0.01010.12660.05590.06830.0242-0.1555-0.28210.1806-0.01420.0775-0.064-0.03220.46160.01030.535424.477-22.1614-25.8682
61.6570.1911-0.29751.6237-0.65671.48970.03630.13390.13760.1655-0.0245-0.0485-0.11140.1372-0.01180.3111-0.1744-0.00470.16730.03180.4909-6.221332.163220.8059
74.18293.1056-0.15625.230.49071.1707-0.38860.183-0.2113-0.48210.27420.4401-0.1847-0.67240.11440.3205-0.01740.08880.5197-0.04910.6883-26.6421-29.927-0.2594
86.474-1.58491.23160.7645-0.55330.4363-0.24830.11250.3377-0.20410.10250.01380.143-0.02480.14580.4065-0.1721-0.00830.453-0.05770.8698-39.4601-8.0479-5.0674
96.3506-3.44385.54891.8816-3.09595.48750.4714-0.026-0.294-0.2510.05880.16710.3798-0.4364-0.53020.545-0.19960.11520.40320.00380.9029-1.1059-40.027441.1798
101.3295-1.62150.94562.79540.48943.9729-0.036-0.01160.22260.17510.1272-0.39810.24550.2126-0.09120.3791-0.2879-0.0150.3375-0.06260.897133.449221.191216.2614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 403
2X-RAY DIFFRACTION2B7 - 403
3X-RAY DIFFRACTION3C7 - 403
4X-RAY DIFFRACTION4D7 - 403
5X-RAY DIFFRACTION5E7 - 403
6X-RAY DIFFRACTION6F7 - 403
7X-RAY DIFFRACTION7G59 - 77
8X-RAY DIFFRACTION8H59 - 77
9X-RAY DIFFRACTION9I59 - 77
10X-RAY DIFFRACTION10J59 - 77

+
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