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- PDB-2ooy: Crystal structure of the adenylate sensor from AMP-activated prot... -

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Basic information

Entry
Database: PDB / ID: 2ooy
TitleCrystal structure of the adenylate sensor from AMP-activated protein kinase complexed with ATP
Components
  • Hypothetical protein C1556.08c in chromosome I
  • SNF1-like protein kinase ssp2
  • SPCC1919.03c protein
KeywordsTRANSFERASE / AMPK / kinase / AMP
Function / homology
Function and homology information


positive regulation of flocculation / positive regulation of ascus development / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / mitotic spindle pole body ...positive regulation of flocculation / positive regulation of ascus development / positive regulation of cell cycle switching, mitotic to meiotic cell cycle / AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / induction of conjugation with cellular fusion / Energy dependent regulation of mTOR by LKB1-AMPK / TP53 Regulates Metabolic Genes / Macroautophagy / mitotic spindle pole body / SREBP signaling pathway / CAMKK-AMPK signaling cascade / nucleotide-activated protein kinase complex / protein kinase regulator activity / protein kinase activator activity / AMP binding / negative regulation of cytoplasmic translation / negative regulation of TORC1 signaling / ADP binding / non-specific serine/threonine protein kinase / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein kinase binding / signal transduction / positive regulation of transcription by RNA polymerase II / ATP 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 / 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 / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / 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-5'-TRIPHOSPHATE / CITRATE ANION / SNF1-like protein kinase ssp2 / 5'-AMP-activated protein kinase subunit beta / 5'-AMP-activated protein kinase subunit gamma
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsTownley, R. / Shapiro, L.
CitationJournal: Science / Year: 2007
Title: Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase.
Authors: Townley, R. / Shapiro, L.
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). AUTHORS STATE THAT THE DEFINITIVE BIOLOGICAL UNIT IS A HETEROTRIMER (THERE ARE TWO SUCH TRIMERS: A+B+G AND C+D+E IN THE ASYMMETRIC UNIT), AND THAT THE DIMER OF THESE HETEROTRIMERS (SEE REMARK 350) IS ALSO PHYSIOLOGICALLY RELEVANT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SNF1-like protein kinase ssp2
B: SPCC1919.03c protein
G: Hypothetical protein C1556.08c in chromosome I
C: SNF1-like protein kinase ssp2
D: SPCC1919.03c protein
E: Hypothetical protein C1556.08c in chromosome I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4719
Polymers128,2686
Non-polymers1,2033
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22120 Å2
ΔGint-132 kcal/mol
Surface area44980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.902, 77.666, 107.576
Angle α, β, γ (deg.)90.00, 123.99, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

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Protein , 3 types, 6 molecules ACBDGE

#1: Protein SNF1-like protein kinase ssp2


Mass: 15903.413 Da / Num. of mol.: 2 / Fragment: C-terminal domain: Residues 440-576
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: ssp2, SPCC74.03c / Plasmid: pSMT3, pET-Duet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O74536, non-specific serine/threonine protein kinase
#2: Protein SPCC1919.03c protein


Mass: 10865.345 Da / Num. of mol.: 2 / Fragment: C-terminal domain: Residues 203-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: SPCC1919.03c / Plasmid: pSMT3, pET-Duet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P78789
#3: Protein Hypothetical protein C1556.08c in chromosome I


Mass: 37364.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / Gene: SPAC1556.08c, SPAC1F12.01c / Plasmid: pSMT3, pET-Duet-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q10343

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Non-polymers , 3 types, 431 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7.3-8.1% PEG3350, 0.1M HEPES, pH 7.5, 5mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2006
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. all: 25963 / Num. obs: 24969 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.3
Reflection shellResolution: 2.88→3 Å / Rmerge(I) obs: 0.417 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OOX

2oox


Resolution: 2.88→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.879 / SU B: 20.894 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.546 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29784 1265 5.1 %RANDOM
Rwork0.18902 ---
obs0.1946 23704 96.28 %-
all-24969 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20.36 Å2
2--1.21 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8507 0 75 428 9010
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0228781
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.371.9811942
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.96351080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.18124.016371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.74151501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4441549
X-RAY DIFFRACTIONr_chiral_restr0.1540.21382
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026525
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3330.25839
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.350.26089
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3040.2752
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3810.2150
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0751.55552
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.90928804
X-RAY DIFFRACTIONr_scbond_it2.31333638
X-RAY DIFFRACTIONr_scangle_it3.8024.53136
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.88→2.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.513 83 -
Rwork0.399 1499 -
obs--83.79 %

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