[English] 日本語
Yorodumi
- PDB-3dae: Crystal structure of phosphorylated SNF1 kinase domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dae
TitleCrystal structure of phosphorylated SNF1 kinase domain
ComponentsCarbon catabolite-derepressing protein kinase
KeywordsTRANSFERASE / kinase / AMPK / snf1 / ATP-binding / Carbohydrate metabolism / Membrane / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase
Function / homology
Function and homology information


fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism ...fungal-type cell wall assembly / positive regulation of pseudohyphal growth / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / single-species surface biofilm formation / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine metabolism / invasive growth in response to glucose limitation / Macroautophagy / filamentous growth / nucleotide-activated protein kinase complex / vacuolar membrane / AMP-activated protein kinase activity / nuclear envelope lumen / establishment of mitotic spindle orientation / positive regulation of macroautophagy / response to unfolded protein / positive regulation of gluconeogenesis / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / molecular function activator activity / nuclear membrane / negative regulation of translation / non-specific serine/threonine protein kinase / carbohydrate metabolic process / protein kinase activity / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site ...Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / KA1 domain/Ssp2, C-terminal / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Carbon catabolite-derepressing protein kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.899 Å
AuthorsZheng, L.-S. / Chen, L. / Jiao, Z.-H. / Wu, J.-W.
CitationJournal: Nature / Year: 2009
Title: Structural insight into the autoinhibition mechanism of AMP-activated protein kinase
Authors: Chen, L. / Jiao, Z.-H. / Zheng, L.-S. / Zhang, Y.-Y. / Xie, S.-T. / Wang, Z.-X. / Wu, J.-W.
History
DepositionMay 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbon catabolite-derepressing protein kinase
B: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)64,8732
Polymers64,8732
Non-polymers00
Water3,369187
1
A: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)32,4371
Polymers32,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbon catabolite-derepressing protein kinase


Theoretical massNumber of molelcules
Total (without water)32,4371
Polymers32,4371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-8 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.607, 72.370, 112.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE DEPOSITORS THINK THE SOFTWARE PREDICTED QUATERNARY STRUCTURE IS NOT CONSISTENT WITH BIOCHEMICAL DATA AND MONOMER IS THE BIOLOGICAL UNIT. THE DIMER FORMATION MAY BE DUE TO CRYSTAL PACKING.

-
Components

#1: Protein Carbon catabolite-derepressing protein kinase / SNF1


Mass: 32436.666 Da / Num. of mol.: 2 / Fragment: Kinase Domain, UNP residue 41-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNF1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P06782, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris pH 8.5, 3.2-3.6M NH4Ac, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.00001 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 24, 2007
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.899→47.2 Å / Num. all: 14122 / Num. obs: 14122 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 50.35 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.7 / Num. measured all: 102012
Reflection shellResolution: 2.899→3 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 4.29 / Num. unique all: 1369 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EUE

2eue
PDB Unreleased entry


Resolution: 2.899→47.192 Å / FOM work R set: 0.792 / σ(F): 1.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.265 706 5.01 %random
Rwork0.227 ---
obs0.229 14082 99.9 %-
all-14122 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.136 Å2 / ksol: 0.317 e/Å3
Displacement parametersBiso max: 8.63 Å2 / Biso mean: 53.73 Å2 / Biso min: 205.13 Å2
Baniso -1Baniso -2Baniso -3
1-9.182 Å20 Å2-0 Å2
2--6.52 Å20 Å2
3----1.483 Å2
Refinement stepCycle: LAST / Resolution: 2.899→47.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3994 0 0 187 4181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134080
X-RAY DIFFRACTIONf_angle_d1.4195512
X-RAY DIFFRACTIONf_chiral_restr0.092619
X-RAY DIFFRACTIONf_plane_restr0.008697
X-RAY DIFFRACTIONf_dihedral_angle_d18.7771516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.898-3.1220.3461490.28525882737
3.122-3.4360.2751390.25326392778
3.436-3.9340.2641420.20426542796
3.934-4.9550.1881320.18226932825
4.955-47.1980.2881440.23828022946

+
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