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- PDB-2nye: Crystal structure of the Bateman2 domain of yeast Snf4 -

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Basic information

Entry
Database: PDB / ID: 2nye
TitleCrystal structure of the Bateman2 domain of yeast Snf4
ComponentsNuclear protein SNF4
KeywordsPROTEIN BINDING / bateman2 domain / amp kinase / snf4
Function / homology
Function and homology information


AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / Carnitine metabolism / peroxisome organization / Macroautophagy / filamentous growth / protein kinase regulator activity / nucleotide-activated protein kinase complex ...AMPK inhibits chREBP transcriptional activation activity / Energy dependent regulation of mTOR by LKB1-AMPK / regulation of cellular response to glucose starvation / regulation of invasive growth in response to glucose limitation / Carnitine metabolism / peroxisome organization / Macroautophagy / filamentous growth / protein kinase regulator activity / nucleotide-activated protein kinase complex / nuclear envelope lumen / AMP binding / positive regulation of gluconeogenesis / protein serine/threonine kinase activator activity / autophagy / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / protein kinase binding / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CBS-domain / CBS-domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
5'-AMP-activated protein kinase subunit gamma
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRudolph, M.J. / Amodeo, G.A. / Iram, S. / Hong, S. / Pirino, G. / Carlson, M. / Tong, L.
CitationJournal: Structure / Year: 2007
Title: Structure of the Bateman2 domain of yeast Snf4: dimeric association and relevance for AMP binding.
Authors: Rudolph, M.J. / Amodeo, G.A. / Iram, S. / Hong, S.P. / Pirino, G. / Carlson, M. / Tong, L.
History
DepositionNov 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear protein SNF4
B: Nuclear protein SNF4


Theoretical massNumber of molelcules
Total (without water)32,8182
Polymers32,8182
Non-polymers00
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-26 kcal/mol
Surface area13950 Å2
MethodPISA
2
A: Nuclear protein SNF4
B: Nuclear protein SNF4
x 24


Theoretical massNumber of molelcules
Total (without water)787,64048
Polymers787,64048
Non-polymers00
Water86548
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation19_666-x+1,-z+1,-y+11
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation14_666-y+1,-x+1,-z+11
crystal symmetry operation16_655-y+1,x,z1
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation24_666-z+1,-y+1,-x+11
crystal symmetry operation23_655-z+1,y,x1
crystal symmetry operation22_565z,-y+1,x1
crystal symmetry operation21_556z,y,-x+11
Buried area130970 Å2
ΔGint-847 kcal/mol
Surface area283570 Å2
MethodPISA
3
A: Nuclear protein SNF4
B: Nuclear protein SNF4

A: Nuclear protein SNF4
B: Nuclear protein SNF4

A: Nuclear protein SNF4
B: Nuclear protein SNF4

A: Nuclear protein SNF4
B: Nuclear protein SNF4


Theoretical massNumber of molelcules
Total (without water)131,2738
Polymers131,2738
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation28_555x,-y+1/2,-z+1/21
crystal symmetry operation43_655-x+1,-z+1/2,-y+1/21
Buried area18240 Å2
ΔGint-137 kcal/mol
Surface area50850 Å2
MethodPISA
4
A: Nuclear protein SNF4
B: Nuclear protein SNF4

A: Nuclear protein SNF4
B: Nuclear protein SNF4


Theoretical massNumber of molelcules
Total (without water)65,6374
Polymers65,6374
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+1,z,y1
Buried area7870 Å2
ΔGint-64 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.618, 235.618, 235.618
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

#1: Protein Nuclear protein SNF4 / Regulatory protein CAT3


Mass: 16409.158 Da / Num. of mol.: 2 / Fragment: Bateman 2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNF4, CAT3 / Plasmid: pet26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21 de3 / References: UniProt: P12904
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4.15 Å3/Da / Density % sol: 70.37 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4.5
Details: 30% (w/v) PEG4000, 200 mM (NH4)Formate, and 3% Benzamidine, pH 4.5, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19934
Reflection shellHighest resolution: 2.5 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NYC

2nyc


Resolution: 2.5→29.45 Å
RfactorNum. reflection
Rfree0.267 -
Rwork0.238 -
obs0.239 19087
Refinement stepCycle: LAST / Resolution: 2.5→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 0 93 2151

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