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- PDB-3tdh: Structure of the regulatory fragment of sccharomyces cerevisiae A... -

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Basic information

Entry
Database: PDB / ID: 3tdh
TitleStructure of the regulatory fragment of sccharomyces cerevisiae AMPK in complex with AMP
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 / 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 / peroxisome organization / Macroautophagy / filamentous growth / protein kinase regulator activity / nucleotide-activated protein kinase complex / enzyme-substrate adaptor activity / vacuolar membrane / AMP-activated protein kinase activity / nuclear envelope lumen / AMP binding / establishment of mitotic spindle orientation / positive regulation of macroautophagy / response to unfolded protein / regulation of protein-containing complex assembly / cellular response to glucose starvation / positive regulation of gluconeogenesis / response to endoplasmic reticulum stress / protein serine/threonine kinase activator activity / guanyl-nucleotide exchange factor activity / molecular function activator activity / autophagy / nuclear membrane / negative regulation of translation / carbohydrate metabolic process / non-specific serine/threonine protein kinase / intracellular signal transduction / protein kinase activity / phosphorylation / 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 / cytosol / cytoplasm
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 / AMPK, C-terminal adenylate sensor domain / Adenylate sensor of SNF1-like protein kinase ...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 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / N-terminal domain of TfIIb / 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
ADENOSINE MONOPHOSPHATE / 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: 2.3 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 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)70,3504
Polymers70,0033
Non-polymers3471
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-71 kcal/mol
Surface area26190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.970, 242.378, 79.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.29 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2009
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 38885 / Num. obs: 38885 / % possible obs: 99.56 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.3→2.423 Å / % possible all: 97.33

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.025 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29013 2062 5 %RANDOM
Rwork0.24821 ---
obs0.25034 38885 99.56 %-
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: 47.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--0.29 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 23 168 4599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224520
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9561.986152
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5335553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1324.396182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3715787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2441521
X-RAY DIFFRACTIONr_chiral_restr0.060.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213291
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4741.52794
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87524556
X-RAY DIFFRACTIONr_scbond_it0.86131726
X-RAY DIFFRACTIONr_scangle_it1.5264.51596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.423 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.335 265 -
Rwork0.286 5490 -
obs--97.33 %

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