[English] 日本語
Yorodumi
- PDB-7qf7: Orthorhombic crystal structure of PTG CBM21 in complex with beta-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7qf7
TitleOrthorhombic crystal structure of PTG CBM21 in complex with beta-cyclodextrin
ComponentsProtein phosphatase 1 regulatory subunit 3C
KeywordsSUGAR BINDING PROTEIN / carbohydrate binding / immunoglobulin-like fold
Function / homology
Function and homology information


glycogen binding / regulation of glycogen biosynthetic process / protein phosphatase type 1 complex / protein phosphatase 1 binding / glycogen biosynthetic process / glycogen metabolic process / protein serine/threonine phosphatase activity / Myoclonic epilepsy of Lafora / Glycogen synthesis / protein phosphatase binding ...glycogen binding / regulation of glycogen biosynthetic process / protein phosphatase type 1 complex / protein phosphatase 1 binding / glycogen biosynthetic process / glycogen metabolic process / protein serine/threonine phosphatase activity / Myoclonic epilepsy of Lafora / Glycogen synthesis / protein phosphatase binding / molecular adaptor activity / cytosol
Similarity search - Function
Protein phosphatase 1 regulatory subunit 3C / Protein phosphatase 1 regulatory subunit 3B/C/D, metazoa / : / Carbohydrate binding type-21 domain / CBM21 (carbohydrate binding type-21) domain / CBM21 domain superfamily / Carbohydrate/starch-binding module (family 21) / CBM21 (carbohydrate binding type-21) domain profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-cyclodextrin / Protein phosphatase 1 regulatory subunit 3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsSemrau, M.S. / Storici, P. / Lolli, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Molecular architecture of the glycogen- committed PP1/PTG holoenzyme.
Authors: Semrau, M.S. / Giachin, G. / Covaceuszach, S. / Cassetta, A. / Demitri, N. / Storici, P. / Lolli, G.
History
DepositionDec 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein phosphatase 1 regulatory subunit 3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8243
Polymers15,6481
Non-polymers1,1762
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint6 kcal/mol
Surface area7580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.593, 56.443, 70.553
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Protein phosphatase 1 regulatory subunit 3C / Protein phosphatase 1 regulatory subunit 5 / PP1 subunit R5 / Protein targeting to glycogen / PTG


Mass: 15647.529 Da / Num. of mol.: 1 / Fragment: CBM21 domain (residues 132-264) / Mutation: First residue S derives from the expression tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1R3C, PPP1R5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UQK1
#2: Polysaccharide Cycloheptakis-(1-4)-(alpha-D-glucopyranose)


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.91 % / Mosaicity: 0.16 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 3 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.47→44.074 Å / Num. obs: 26941 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.47-1.57.10.981932813140.8370.3911.0582.1100
8.05-44.075.20.03810652040.9980.0180.04242.799.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.11.1refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EEF

2eef


Resolution: 1.47→44.074 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 1320 4.91 %
Rwork0.1755 25563 -
obs0.1765 26883 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.34 Å2 / Biso mean: 33.8912 Å2 / Biso min: 17.14 Å2
Refinement stepCycle: final / Resolution: 1.47→44.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 78 134 1268
Biso mean--24.66 40 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051179
X-RAY DIFFRACTIONf_angle_d0.9351613
X-RAY DIFFRACTIONf_chiral_restr0.09196
X-RAY DIFFRACTIONf_plane_restr0.004193
X-RAY DIFFRACTIONf_dihedral_angle_d21.169399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.47-1.52890.28031510.23952785
1.5289-1.59850.26891400.21192779
1.5985-1.68270.23051410.18752821
1.6827-1.78820.20921340.1672813
1.7882-1.92620.20651650.15792803
1.9262-2.12010.19051480.15362816
2.1201-2.42680.19141630.16582833
2.4268-3.05750.21881280.19382891
3.0575-44.0740.17361500.17163022

+
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