[English] 日本語
Yorodumi
- PDB-3w0l: The crystal structure of Xenopus Glucokinase and Glucokinase Regu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w0l
TitleThe crystal structure of Xenopus Glucokinase and Glucokinase Regulatory Protein complex
Components
  • Glucokinase regulatory protein
  • Glucokinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / aba sandwich / typical hexokanse fold / kinase / sugar binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


hexose metabolic process / detection of glucose / negative regulation of glucokinase activity / fructose-6-phosphate binding / carbohydrate derivative metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / glucokinase activity / glucose binding / cellular glucose homeostasis / positive regulation of insulin secretion ...hexose metabolic process / detection of glucose / negative regulation of glucokinase activity / fructose-6-phosphate binding / carbohydrate derivative metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / glucokinase activity / glucose binding / cellular glucose homeostasis / positive regulation of insulin secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / glycolytic process / glucose homeostasis / carbohydrate metabolic process / mitochondrion / nucleoplasm / ATP binding / cytoplasm
Similarity search - Function
Rossmann fold - #12620 / Helicase, Ruva Protein; domain 3 - #1080 / Glucokinase regulatory protein family signature. / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Hexokinase-4, chordate / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase, C-terminal / Hexokinase domain profile. ...Rossmann fold - #12620 / Helicase, Ruva Protein; domain 3 - #1080 / Glucokinase regulatory protein family signature. / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Hexokinase-4, chordate / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase, C-terminal / Hexokinase domain profile. / Hexokinase, N-terminal / Hexokinase, binding site / Hexokinase / Hexokinase / Hexokinase / Hexokinase domain signature. / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / ATPase, nucleotide binding domain / Helicase, Ruva Protein; domain 3 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FRUCTOSE -6-PHOSPHATE / Phosphotransferase / Glucokinase regulatory protein
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsChoi, J.M. / Seo, M.H. / Kyeong, H.H. / Kim, E. / Kim, H.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Molecular basis for the role of glucokinase regulatory protein as the allosteric switch for glucokinase
Authors: Choi, J.M. / Seo, M.H. / Kyeong, H.H. / Kim, E. / Kim, H.S.
History
DepositionOct 31, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucokinase
B: Glucokinase regulatory protein
C: Glucokinase
D: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,86612
Polymers239,9154
Non-polymers9518
Water1,53185
1
A: Glucokinase
B: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5297
Polymers119,9582
Non-polymers5715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-73 kcal/mol
Surface area40440 Å2
MethodPISA
2
C: Glucokinase
D: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,3375
Polymers119,9582
Non-polymers3793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-37 kcal/mol
Surface area39190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.318, 130.030, 175.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Glucokinase / / Hexokinase IV


Mass: 51144.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: gck / Production host: Escherichia coli (E. coli) / References: UniProt: Q91753, glucokinase
#2: Protein Glucokinase regulatory protein / / Hexokinase IV inhibitor / Glucokinase regulator


Mass: 68813.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: gckr / Production host: Escherichia coli (E. coli) / References: UniProt: Q91754

-
Non-polymers , 4 types, 93 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-F6R / FRUCTOSE -6-PHOSPHATE / Fructose 6-phosphate


Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHIS SEUQENCE IS ACCORDING TO REFERENCE SEQUENCE NM_001089807.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.005M MgSO4, 0.05M MES, 5% PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Oct 22, 2011 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 54529 / Num. obs: 54157 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 50.23 Å2
Reflection shellResolution: 2.9→2.95 Å / % possible all: 99.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V4T, 1NRI
Resolution: 2.92→28.478 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.5 / σ(F): 1.33 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 2662 4.99 %random
Rwork0.242 ---
all0.247 53375 --
obs0.2438 53354 97.32 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.667 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso max: 139.34 Å2 / Biso mean: 54.8746 Å2 / Biso min: 15.78 Å2
Baniso -1Baniso -2Baniso -3
1--20.2106 Å20 Å20 Å2
2--18.1073 Å20 Å2
3---2.1033 Å2
Refinement stepCycle: LAST / Resolution: 2.92→28.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15661 0 54 85 15800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315963
X-RAY DIFFRACTIONf_angle_d0.53121537
X-RAY DIFFRACTIONf_chiral_restr0.0372466
X-RAY DIFFRACTIONf_plane_restr0.0022755
X-RAY DIFFRACTIONf_dihedral_angle_d13.4595947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9203-2.97330.54361110.48852207231881
2.9733-3.03040.57911370.45112599273696
3.0304-3.09220.46471360.39032590272696
3.0922-3.15940.44291390.33812629276898
3.1594-3.23280.34511420.27562690283299
3.2328-3.31350.31631430.260627122855100
3.3135-3.40290.2851420.273327042846100
3.4029-3.50290.29451430.272227162859100
3.5029-3.61580.28211440.272327202864100
3.6158-3.74470.31761420.260727072849100
3.7447-3.89430.25841430.21222705284899
3.8943-4.0710.2451410.21682645278696
4.071-4.2850.25181340.21292601273595
4.285-4.55250.22771420.19062715285799
4.5525-4.90230.26361370.19882669280697
4.9023-5.39270.22821460.21442722286899
5.3927-6.16610.27591460.245827672913100
6.1661-7.74270.22921480.207128172965100
7.7427-28.4790.18191460.18382777292395

+
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