[English] 日本語
Yorodumi
- PDB-3te5: structure of the regulatory fragment of sacchromyces cerevisiae a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3te5
Titlestructure of the regulatory fragment of sacchromyces cerevisiae ampk in complex with NADH
Components
  • Carbon catabolite-derepressing protein kinase
  • Nuclear protein SNF4
  • SNF1 protein kinase subunit beta-2
KeywordsTRANSFERASE / CBS domain / Nucleotide binding / cytosol
Function / homology
Function and homology information


fungal-type cell wall assembly / positive regulation of pseudohyphal growth / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cellular response to glucose starvation / single-species surface biofilm formation / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine shuttle ...fungal-type cell wall assembly / positive regulation of pseudohyphal growth / AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cellular response to glucose starvation / single-species surface biofilm formation / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / regulation of invasive growth in response to glucose limitation / cellular bud neck septin ring / Carnitine shuttle / negative regulation of inositol phosphate biosynthetic process / invasive growth in response to glucose limitation / Macroautophagy / AMP-activated protein kinase activity / peroxisome organization / regulation of carbon utilization / nucleotide-activated protein kinase complex / filamentous growth / protein kinase regulator activity / vacuolar membrane / regulation of glycolytic process / AMP binding / cellular response to stress / nuclear envelope lumen / establishment of mitotic spindle orientation / positive regulation of macroautophagy / response to unfolded protein / enzyme-substrate adaptor activity / regulation of protein-containing complex assembly / cellular response to glucose starvation / positive regulation of gluconeogenesis / response to endoplasmic reticulum stress / molecular function activator activity / guanyl-nucleotide exchange factor activity / protein serine/threonine kinase activator activity / autophagy / nuclear membrane / non-specific serine/threonine protein kinase / protein kinase activity / negative regulation of translation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / mitochondrion / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
N-terminal domain of TfIIb - #290 / Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / Kinase associated domain 1, KA1 / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain ...N-terminal domain of TfIIb - #290 / Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain / Ubiquitin associated domain (UBA) / Kinase associated domain 1, KA1 / : / Association with the SNF1 complex (ASC) domain / ASC domain superfamily / : / 5'-AMP-activated protein kinase beta subunit, interaction domain / 5'-AMP-activated protein kinase beta subunit, interation domain / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase / AMP-activated protein kinase, glycogen-binding domain / Glycogen recognition site of AMP-activated protein kinase / CBS-domain / CBS-domain / KA1 domain/Ssp2, C-terminal / TATA-Binding Protein / N-terminal domain of TfIIb / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Single Sheet / Immunoglobulin E-set / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Carbon catabolite-derepressing protein kinase / 5'-AMP-activated protein kinase subunit gamma / SNF1 protein kinase subunit beta-2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMayer, F.V. / Heath, R. / Underwood, E. / Sanders, M.J. / Carmena, D. / McCartney, R. / Leiper, F.C. / Xiao, B. / Jing, C. / Walker, P.A. ...Mayer, F.V. / Heath, R. / Underwood, E. / Sanders, M.J. / Carmena, D. / McCartney, R. / Leiper, F.C. / Xiao, B. / Jing, C. / Walker, P.A. / Haire, L.F. / Ogrodowicz, R. / Martin, S.R. / Schmidt, M.C. / Gamblin, S.J. / Carling, D.
CitationJournal: Cell Metab / Year: 2011
Title: ADP Regulates SNF1, the Saccharomyces cerevisiae Homolog of AMP-Activated Protein Kinase.
Authors: Mayer, F.V. / Heath, R. / Underwood, E. / Sanders, M.J. / Carmena, D. / McCartney, R.R. / Leiper, F.C. / Xiao, B. / Jing, C. / Walker, P.A. / Haire, L.F. / Ogrodowicz, R. / Martin, S.R. / ...Authors: Mayer, F.V. / Heath, R. / Underwood, E. / Sanders, M.J. / Carmena, D. / McCartney, R.R. / Leiper, F.C. / Xiao, B. / Jing, C. / Walker, P.A. / Haire, L.F. / Ogrodowicz, R. / Martin, S.R. / Schmidt, M.C. / Gamblin, S.J. / Carling, D.
History
DepositionAug 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbon catabolite-derepressing protein kinase
B: SNF1 protein kinase subunit beta-2
C: Nuclear protein SNF4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6684
Polymers70,0033
Non-polymers6651
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-66 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.732, 240.236, 79.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Carbon catabolite-derepressing protein kinase


Mass: 20454.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SNF1, CAT1, CCR1, GLC2, PAS14, YDR477W, D8035.20 / Production host: Escherichia coli (E. coli)
References: UniProt: P06782, non-specific serine/threonine protein kinase
#2: Protein SNF1 protein kinase subunit beta-2 / Protein SPM2 / SNF1-interacting protein 2


Mass: 13036.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SIP2, SPM2, YGL208W, G1155 / Production host: Escherichia coli (E. coli) / References: UniProt: P34164
#3: Protein Nuclear protein SNF4 / Regulatory protein CAT3


Mass: 36512.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SNF4, CAT3, YGL115W / Production host: Escherichia coli (E. coli) / References: UniProt: P12904
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M Succinic Acid, 0.1M Hepes, 1% w/v Polyethylene glycol monomethyl ether 2000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 30340 / Num. obs: 30327 / % possible obs: 99.84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.901 / SU B: 9.088 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28087 1618 5.1 %RANDOM
Rwork0.24064 ---
obs0.24277 30327 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.014 Å2
Baniso -1Baniso -2Baniso -3
1-1.37 Å20 Å20 Å2
2---0.18 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4365 0 44 214 4623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224499
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.9856126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7855547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58123.966179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02315774
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9261524
X-RAY DIFFRACTIONr_chiral_restr0.0620.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213271
X-RAY DIFFRACTIONr_mcbond_it0.4671.52768
X-RAY DIFFRACTIONr_mcangle_it0.85924509
X-RAY DIFFRACTIONr_scbond_it0.86231731
X-RAY DIFFRACTIONr_scangle_it1.544.51617
LS refinement shellResolution: 2.5→2.635 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.344 219 -
Rwork0.273 4313 -
obs--99.04 %

+
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