[English] 日本語
Yorodumi
- PDB-4lc9: Structural Basis for Regulation of Human Glucokinase by Glucokina... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lc9
TitleStructural Basis for Regulation of Human Glucokinase by Glucokinase Regulatory Protein
Components
  • Glucokinase
  • Glucokinase regulatory protein
KeywordsTRANSFERASE/TRANSFERASE REGULATOR / Type 2 Diabetes / TRANSFERASE-TRANSFERASE REGULATOR complex
Function / homology
Function and homology information


Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / fructose-6-phosphate binding / regulation of potassium ion transport / mannokinase activity / carbohydrate derivative metabolic process / hexokinase / kinase inhibitor activity / glucose catabolic process ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / fructose-6-phosphate binding / regulation of potassium ion transport / mannokinase activity / carbohydrate derivative metabolic process / hexokinase / kinase inhibitor activity / glucose catabolic process / fructokinase activity / glucokinase activity / urate metabolic process / glucose 6-phosphate metabolic process / response to fructose / NADP+ metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / D-glucose binding / cellular response to leptin stimulus / canonical glycolysis / triglyceride homeostasis / calcium ion import / Glycolysis / regulation of glycolytic process / intracellular glucose homeostasis / Regulation of gene expression in beta cells / enzyme inhibitor activity / protein localization to nucleus / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to glucose / regulation of insulin secretion / glycolytic process / positive regulation of insulin secretion / kinase binding / cellular response to insulin stimulus / glucose metabolic process / protein import into nucleus / glucose homeostasis / carbohydrate binding / protein domain specific binding / enzyme binding / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Glucokinase regulatory protein, second SIS domain / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein N-terminal SIS domain / Glucokinase regulatory protein family signature. / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase ...: / Glucokinase regulatory protein, second SIS domain / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein N-terminal SIS domain / Glucokinase regulatory protein family signature. / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-fructofuranose / Hexokinase-4 / Glucokinase regulatory protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBeck, T. / Miller, B.G.
CitationJournal: Biochemistry / Year: 2013
Title: Structural basis for regulation of human glucokinase by glucokinase regulatory protein.
Authors: Beck, T. / Miller, B.G.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,6404
Polymers123,3572
Non-polymers2832
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.663, 105.312, 132.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glucokinase regulatory protein / Glucokinase regulator


Mass: 70152.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gckr / Production host: Escherichia coli (E. coli) / References: UniProt: Q07071
#2: Protein Glucokinase / Hexokinase type IV / HK IV / Hexokinase-4 / HK4 / Hexokinase-D


Mass: 53204.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCK / Production host: Escherichia coli (E. coli) / References: UniProt: P35557, glucokinase
#3: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / FRUCTOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-fructose / 6-O-phosphono-D-fructose / 6-O-phosphono-fructose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: Crystals were obtained at 20 C by mixing 200 nL of GCK-GKRP-F6P complex solution with 100 nL of reservoir solution containing 0.1 M HEPES, pH 7.1, and 8% w/v PEG 6000, VAPOR DIFFUSION, ...Details: Crystals were obtained at 20 C by mixing 200 nL of GCK-GKRP-F6P complex solution with 100 nL of reservoir solution containing 0.1 M HEPES, pH 7.1, and 8% w/v PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2012
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→48.93 Å / Num. all: 18995 / Num. obs: 18946 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.73 / Redundancy: 6.5 % / Rmerge(I) obs: 0.0712 / Net I/σ(I): 12.93
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 6.23 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.73 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.929 Å / SU ML: 0.57 / σ(F): 1.33 / Phase error: 34.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2922 976 5.15 %
Rwork0.2437 --
obs0.2461 18946 99.92 %
all-18995 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→48.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7682 0 17 0 7699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067817
X-RAY DIFFRACTIONf_angle_d0.95710542
X-RAY DIFFRACTIONf_dihedral_angle_d13.1862937
X-RAY DIFFRACTIONf_chiral_restr0.0381210
X-RAY DIFFRACTIONf_plane_restr0.0051353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.57920.40131470.34582475X-RAY DIFFRACTION100
3.5792-3.80340.4081390.29852533X-RAY DIFFRACTION100
3.8034-4.09690.37951360.2772518X-RAY DIFFRACTION100
4.0969-4.5090.27411550.23372536X-RAY DIFFRACTION100
4.509-5.16080.25791420.21682563X-RAY DIFFRACTION100
5.1608-6.49960.28361350.27442607X-RAY DIFFRACTION100
6.4996-48.93390.26781220.21982738X-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